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Sun X, Yu Y, Saleh ASM, Akhtar KH, Li W, Zhang D, Wang Z. Conformational changes induced by selected flavor compounds from spices regulate the binding ability of myofibrillar proteins to aldehyde compounds. Food Chem 2024; 451:139455. [PMID: 38678659 DOI: 10.1016/j.foodchem.2024.139455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/08/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
Interactions among flavor compounds from spices (FCS) and myofibrillar proteins (MP) were investigated. Fluorescence and Fourier transform infrared spectroscopy showed that hydrogen bonding and hydrophobic interactions were the main binding forces between FCS and MP. The FCS increased the particle size and SH content of MP and caused a reduction of zeta potential from -5.23 to -6.50 mV. Furthermore, FCS could modify the binding ability of MP and aldehydes. Eugenol reduced the ability of MP to bond with aldehydes by 22.70-47.87 %. Molecular dynamics simulations demonstrated that eugenol may combat nonanal to attain binding site of amino acid residue (PHE165) and induce protein conformational changes. Electrostatic interactions and van der Waals forces within myosin-nonanal may be disrupted by these alterations, which could reduce stability of complex and cause release of nonanal. This study could provide new insights into regulating the ability of proteins to release and hold flavors.
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Affiliation(s)
- Xiangxiang Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Yumei Yu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ahmed S M Saleh
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Kumayl Hassan Akhtar
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Wenhao Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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2
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Lorenz CD, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nat Commun 2024; 15:4912. [PMID: 38851738 PMCID: PMC11162425 DOI: 10.1038/s41467-024-49255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Anna Katarina Antonovic
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Maria Baczynska
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Carlton O Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Giulia Mastroianni
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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3
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.01.543259. [PMID: 37333393 PMCID: PMC10274692 DOI: 10.1101/2023.06.01.543259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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4
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Zühlke MK, Ficko-Blean E, Bartosik D, Terrapon N, Jeudy A, Jam M, Wang F, Welsch N, Dürwald A, Martin LT, Larocque R, Jouanneau D, Eisenack T, Thomas F, Trautwein-Schult A, Teeling H, Becher D, Schweder T, Czjzek M. Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms. Environ Microbiol 2024; 26:e16624. [PMID: 38757353 DOI: 10.1111/1462-2920.16624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Laminarin, a β(1,3)-glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate-binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin-binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin-binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan-binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin-binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102- and CBM103-containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization.
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Affiliation(s)
- Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Elizabeth Ficko-Blean
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU, UMR7257), CNRS, Marseille, France
| | - Alexandra Jeudy
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Murielle Jam
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Fengqing Wang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Laura Torres Martin
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Robert Larocque
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Diane Jouanneau
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Tom Eisenack
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - François Thomas
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Mirjam Czjzek
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
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5
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Ravala SK, Adame-Garcia SR, Li S, Chen CL, Cianfrocco MA, Gutkind JS, Cash JN, Tesmer JJG. Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557836. [PMID: 37745379 PMCID: PMC10515948 DOI: 10.1101/2023.09.15.557836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3 and the heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4 (IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH-DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH-DEP1 and PH-4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
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Affiliation(s)
- Sandeep K. Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sendi Rafael Adame-Garcia
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chun-Liang Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael A. Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - J. Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer N. Cash
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, CA, 95616, USA
| | - John J. G. Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
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Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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7
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Tamburrini KC, Kodama S, Grisel S, Haon M, Nishiuchi T, Bissaro B, Kubo Y, Longhi S, Berrin JG. The disordered C-terminal tail of fungal LPMOs from phytopathogens mediates protein dimerization and impacts plant penetration. Proc Natl Acad Sci U S A 2024; 121:e2319998121. [PMID: 38513096 PMCID: PMC10990093 DOI: 10.1073/pnas.2319998121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes that oxidatively degrade various polysaccharides, such as cellulose. Despite extensive research on this class of enzymes, the role played by their C-terminal regions predicted to be intrinsically disordered (dCTR) has been overlooked. Here, we investigated the function of the dCTR of an LPMO, called CoAA9A, up-regulated during plant infection by Colletotrichum orbiculare, the causative agent of anthracnose. After recombinant production of the full-length protein, we found that the dCTR mediates CoAA9A dimerization in vitro, via a disulfide bridge, a hitherto-never-reported property that positively affects both binding and activity on cellulose. Using SAXS experiments, we show that the homodimer is in an extended conformation. In vivo, we demonstrate that gene deletion impairs formation of the infection-specialized cell called appressorium and delays penetration of the plant. Using immunochemistry, we show that the protein is a dimer not only in vitro but also in vivo when secreted by the appressorium. As these peculiar LPMOs are also found in other plant pathogens, our findings open up broad avenues for crop protection.
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Affiliation(s)
- Ketty C. Tamburrini
- CNRS Aix Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
| | - Sayo Kodama
- Faculty of Agriculture, Setsunan University, Osaka573-0101, Japan
| | - Sacha Grisel
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Aix Marseille Université, 3PE Platform, Marseille13009, France
| | - Mireille Haon
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Aix Marseille Université, 3PE Platform, Marseille13009, France
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa920-1164, Japan
| | - Bastien Bissaro
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
| | - Yasuyuki Kubo
- Faculty of Agriculture, Setsunan University, Osaka573-0101, Japan
| | - Sonia Longhi
- CNRS Aix Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille13009, France
| | - Jean-Guy Berrin
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
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8
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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9
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Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024; 32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAsAsp,Asn,His,Tyr for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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10
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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11
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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12
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Kravikass M, Koren G, Saleh OA, Beck R. From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:13. [PMID: 38358563 PMCID: PMC10869404 DOI: 10.1140/epje/s10189-024-00409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
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Affiliation(s)
- Mathar Kravikass
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Gil Koren
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, USA
- Physics Department, University of California, Santa Barbara, USA
| | - Roy Beck
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.
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13
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Li L, Wang J, Zhong X, Jiang Y, Pei G, Yang X, Zhang K, Shen S, Jin X, Sun G, Su C, Chen S, Yin H. ADP-Hep-Induced Liquid Phase Condensation of TIFA-TRAF6 Activates ALPK1/TIFA-Dependent Innate Immune Responses. RESEARCH (WASHINGTON, D.C.) 2024; 7:0315. [PMID: 38357697 PMCID: PMC10865109 DOI: 10.34133/research.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
The ALPK1 (alpha-kinase 1)-TIFA (TRAF-interacting protein with fork head-associated domain)-TRAF6 signaling pathway plays a pivotal role in regulating inflammatory processes, with TIFA and TRAF6 serving as key molecules in this cascade. Despite its significance, the functional mechanism of TIFA-TRAF6 remains incompletely understood. In this study, we unveil that TIFA undergoes liquid-liquid phase separation (LLPS) induced by ALPK1 in response to adenosine diphosphate (ADP)-β-D-manno-heptose (ADP-Hep) recognition. The phase separation of TIFA is primarily driven by ALPK1, the pT9-FHA domain, and the intrinsically disordered region segment. Simultaneously, TRAF6 exhibits phase separation during ADP-Hep-induced inflammation, a phenomenon observed consistently across various inflammatory signal pathways. Moreover, TRAF6 is recruited within the TIFA condensates, facilitating lysine (K) 63-linked polyubiquitin chain synthesis. The subsequent recruitment, enrichment, and activation of downstream effectors within these condensates contribute to robust inflammatory signal transduction. Utilizing a novel chemical probe (compound 22), our analysis demonstrates that the activation of the ALPK1-TIFA-TRAF6 signaling pathway in response to small molecules necessitates the phase separation of TIFA. In summary, our findings reveal TIFA as a sensor for upstream signals, initiating the LLPS of itself and downstream proteins. This process results in the formation of membraneless condensates within the ALPK1-TIFA-TRAF6 pathway, suggesting potential applications in therapeutic biotechnology development.
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Affiliation(s)
- Liping Li
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology,
Peking University, Beijing, China
| | - Xincheng Zhong
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yaoyao Jiang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- School of Life Sciences,
Tsinghua University, Beijing, 100084, China
| | - Xikang Yang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Siqi Shen
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xue Jin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaoge Sun
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Chaofei Su
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shuzhen Chen
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hang Yin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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14
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Yang K, Chen G, Yu F, Fang X, Zhang J, Zhang Z, Shi Y, Zhang L. Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape. Commun Biol 2024; 7:158. [PMID: 38326406 PMCID: PMC10850505 DOI: 10.1038/s42003-024-05845-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
Immunotherapy, including immune checkpoint inhibitors and adoptive cell transfer, has obtained great progress, but their efficiencies vary among patients due to the genetic and epigenetic differences. Human MEX3B (hMEX3B) protein is an RNA-binding protein that contains two KH domains at the N-terminus and a RING domain at its C-terminus, which has the activity of E3 ubiquitin ligase and is essential for RNA degradation. Current evidence suggests that hMEX3B is involved in many important biological processes, including tumor immune evasion and HLA-A regulation, but the sequence of substrate RNA recognized by hMEX3B and the functional molecular mechanisms are unclear. Here, we first screened the optimized hMEX3B binding sequence on the HLA-A mRNA and reported that the two tandem KH domains can bind with their substrate one hundred times more than the individual KH domains. We systematically investigated the binding characteristics between the two KH domains and their RNA substrates by nuclear magnetic resonance (NMR). Based on this information and the small-angle X-ray scattering (SAXS) data, we used molecular dynamics simulations to obtain structural models of KH domains in complex with their corresponding RNAs. By analyzing the models, we noticed that on the KH domains' variable loops, there were two pairs of threonines and arginines that can disrupt the recognition of the RNA completely, and this influence had also been verified both in vitro and in vivo. Finally, we presented a functional model of the hMEX3B protein, which indicated that hMEX3B regulated the degradation of its substrate mRNAs in many biological processes. Taken together, our research illustrated how the hMEX3B protein played a key role in translation inhibition during the immune response to tumor cells and provided an idea and a lead for the study of the molecular mechanism and function of other MEX3 family proteins.
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Affiliation(s)
- Kanglong Yang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Guanglin Chen
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Fan Yu
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, PR China
| | - Jiahai Zhang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Zhiyong Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, PR China.
| | - Yunyu Shi
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China.
| | - Liang Zhang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China.
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15
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Mukhopadhyay S, Subedi S, Hopkins JB, Ugrinov A, Chakravarthy S, Colbert CL, Sinha SC. Invariant BECN1 CXXC motifs bind Zn 2+ and regulate structure and function of the BECN1 intrinsically disordered region. Autophagy 2024; 20:380-396. [PMID: 37791766 PMCID: PMC10813572 DOI: 10.1080/15548627.2023.2259707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
ABBREVIATIONS AFM: aromatic finger mutant; BH3D: BCL2 homology 3 domain; CCD: coiled-coil domain; CD: circular dichroism spectroscopy; [CysDM1]: C18S and C21S double mutant; [CysDM2]: C137S, and C140S double mutant; [CysTM], C18S, C21S, C137S, and C140S tetrad mutant; Dmax: maximum particle diameter; dRI, differential refractive index; EFA: evolving factor analysis; FHD: flexible helical domain; FL: full length; GFP: green fluorescent protein; HDX-MS: hydrogen/deuterium exchange mass spectrometry; ICP-MS: inductively coupled plasma mass spectrometry; IDR: intrinsically disordered region; ITC, isothermal titration calorimetry; MALS, multi angle light scattering; MBP: maltose-binding protein; MoRFs: molecular recognition features; P(r): pairwise-distance distribution; PtdIns3K: class III phosphatidylinositol 3-kinase; Rg: radius of gyration; SASBDB: small angle scattering biological data bank; SEC: size-exclusion chromatography; SEC-SAXS: size-exclusion chromatography in tandem with small angle X-ray scattering; TEV: tobacco-etch virus; TFE: 2,2,2-trifluoroethanol; TPEN: N,N,N,N-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine; Vc: volume of correlation; WT: wild-type.
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Affiliation(s)
- Shreya Mukhopadhyay
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Subeksha Subedi
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | | | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
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16
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Sun X, Alfermann J, Li H, Watkins MB, Chen YT, Morrell TE, Mayerthaler F, Wang CY, Komatsuzaki T, Chu JW, Ando N, Mootz HD, Yang H. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nat Chem 2024; 16:259-268. [PMID: 38049653 DOI: 10.1038/s41557-023-01361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A-PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed.
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Affiliation(s)
- Xun Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonas Alfermann
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Hao Li
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Thomas E Morrell
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Chia-Ying Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tamiki Komatsuzaki
- Research Centre of Mathematics for Social Creativity, Research Institute for Electronic Science; The Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany.
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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17
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Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B. Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 2024; 7:e202302051. [PMID: 37949474 PMCID: PMC10638095 DOI: 10.26508/lsa.202302051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
GRP94, an ER paralog of the heat-shock protein 90 family, binds and hydrolyses ATP to chaperone the folding and maturation of its selected clients. Compared with other hsp90 proteins, the in-solution conformational dynamics of GRP94 along the ATP hydrolysis cycle are less understood, hindering our understanding of its chaperoning mechanism. Leveraging small-angle X-ray scattering, negative-staining EM, and hydrogen-deuterium exchange coupled mass-spec, here we show that in its apo form, ∼60% of mouse GRP94 (mGRP94) populates an "extended" conformation, whereas the rest exist in either "close V" or "twist V" like "compact" conformations. Different from other hsp90 proteins, the presence of AMPPNP only impacts the relative abundance of the two compact conformations, rather than shifting the equilibrium between the "extended" and "compact" conformations of mGRP94. HDX-MS study of apo, AMPPNP-bound, and ADP-bound mGRP94 suggests a conformational transition from "twist V" to "close V" upon ATP binding and a back transition from "close V" to "twist V" upon ATP hydrolysis. These results illustrate the dissimilarities of GRP94 in conformation transition during ATP hydrolysis from other hsp90 paralogs.
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Affiliation(s)
- Shangwu Sun
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Rui Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mengyao Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Wang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai, China
| | - Bei Yang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- https://ror.org/030bhh786 Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
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18
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Theisen FF, Prestel A, Elkjær S, Leurs YHA, Morffy N, Strader LC, O'Shea C, Teilum K, Kragelund BB, Skriver K. Molecular switching in transcription through splicing and proline-isomerization regulates stress responses in plants. Nat Commun 2024; 15:592. [PMID: 38238333 PMCID: PMC10796322 DOI: 10.1038/s41467-024-44859-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
The Arabidopsis thaliana DREB2A transcription factor interacts with the negative regulator RCD1 and the ACID domain of subunit 25 of the transcriptional co-regulator mediator (Med25) to integrate stress signals for gene expression, with elusive molecular interplay. Using biophysical and structural analyses together with high-throughput screening, we reveal a bivalent binding switch in DREB2A containing an ACID-binding motif (ABS) and the known RCD1-binding motif (RIM). The RIM is lacking in a stress-induced DREB2A splice variant with retained transcriptional activity. ABS and RIM bind to separate sites on Med25-ACID, and NMR analyses show a structurally heterogeneous complex deriving from a DREB2A-ABS proline residue populating cis- and trans-isomers with remote impact on the RIM. The cis-isomer stabilizes an α-helix, while the trans-isomer may introduce energetic frustration facilitating rapid exchange between activators and repressors. Thus, DREB2A uses a post-transcriptionally and post-translationally modulated switch for transcriptional regulation.
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Affiliation(s)
- Frederik Friis Theisen
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Steffie Elkjær
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yannick H A Leurs
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Charlotte O'Shea
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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19
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Taneja I, Lasker K. Machine-learning-based methods to generate conformational ensembles of disordered proteins. Biophys J 2024; 123:101-113. [PMID: 38053335 PMCID: PMC10808026 DOI: 10.1016/j.bpj.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/24/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023] Open
Abstract
Intrinsically disordered proteins are characterized by a conformational ensemble. While computational approaches such as molecular dynamics simulations have been used to generate such ensembles, their computational costs can be prohibitive. An alternative approach is to learn from data and train machine-learning models to generate conformational ensembles of disordered proteins. This has been a relatively unexplored approach, and in this work we demonstrate a proof-of-principle approach to do so. Specifically, we devised a two-stage computational pipeline: in the first stage, we employed supervised machine-learning models to predict ensemble-derived two-dimensional (2D) properties of a sequence, given the conformational ensemble of a closely related sequence. In the second stage, we used denoising diffusion models to generate three-dimensional (3D) coarse-grained conformational ensembles, given the two-dimensional predictions outputted by the first stage. We trained our models on a data set of coarse-grained molecular dynamics simulations of thousands of rationally designed synthetic sequences. The accuracy of our 2D and 3D predictions was validated across multiple metrics, and our work demonstrates the applicability of machine-learning techniques to predicting higher-dimensional properties of disordered proteins.
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Affiliation(s)
- Ishan Taneja
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California
| | - Keren Lasker
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California.
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20
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Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG. Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie 2024; 216:56-70. [PMID: 37806617 DOI: 10.1016/j.biochi.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.
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Affiliation(s)
- Cátia Bárria
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Diogo Athayde
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Guillem Hernandez
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Leonor Fonseca
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Jorge Casinhas
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tiago N Cordeiro
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Margarida Archer
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Cecília M Arraiano
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José A Brito
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Rute G Matos
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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21
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Sun X, Saleh ASM, Wang Z, Yu Y, Li W, Zhang D. Insights into the interactions between etheric compounds and myofibrillar proteins using multi-spectroscopy, molecular docking, and molecular dynamics simulation. Food Res Int 2024; 175:113787. [PMID: 38129009 DOI: 10.1016/j.foodres.2023.113787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/26/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This study aimed to examine how the addition of etheric compounds (EC) affects the characteristics of myofibrillar proteins (MP) and to understand underlying interaction mechanisms. Fourier transform infrared spectroscopy confirmed that the EC-MP complex was formed through hydrogen bonding. The addition of EC resulted in an increase in the α-helix content and a decrease in the β-sheet content of MP, which would promote the protein unfolding. The unfolding of MP led to aggregation and formation of larger and non-uniform particles. As a result, the exposure of negative charge on the MP surface was enhanced, and zeta potential was decreased from -5.33 mV to -7.45 mV. Moreover, the EC-induced modification of MP conformation resulted in a less rigid three-dimensional network structure of MP gel and enhanced the discharge of aldehyde compounds (C > 6). Moreover, the rheological characteristics of MP were enhanced by the suppression of protein-protein interactions due to the MP unfolding. Molecular dynamics simulations revealed that anethole reduced the binding capacity of myosin to decanal by raising its binding energy from -22.22 kcal/mol to -19.38 kcal/mol. In the meantime, anethole competed for the amino acid residue (PHE165) where myosin connects to decanal. This caused the hydrogen bonds and hydrophobic contacts between the two molecules to dissolve, altering myosin's conformation and releasing decanal. The results might be useful in predicting and controlling the ability of proteins to release and hold onto flavors.
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Affiliation(s)
- Xiangxiang Sun
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ahmed S M Saleh
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yumei Yu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Wenhao Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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22
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Hutin S, Tully MD, Brennich M. Small-Angle X-Ray Scattering for Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:163-172. [PMID: 38507206 DOI: 10.1007/978-3-031-52193-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.
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Affiliation(s)
- Stephanie Hutin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Mark D Tully
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble, Grenoble, France.
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23
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Rinaldi F, Schipani F, Balboni B, Catalano F, Marotta R, Myers SH, Previtali V, Veronesi M, Scietti L, Cecatiello V, Pasqualato S, Ortega JA, Girotto S, Cavalli A. Isolation and Characterization of Monomeric Human RAD51: A Novel Tool for Investigating Homologous Recombination in Cancer. Angew Chem Int Ed Engl 2023; 62:e202312517. [PMID: 37924230 DOI: 10.1002/anie.202312517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
DNA repair protein RAD51 is a key player in the homologous recombination pathway. Upon DNA damage, RAD51 is transported into the nucleus by BRCA2, where it can repair DNA double-strand breaks. Due to the structural complexity and dynamics, researchers have not yet clarified the mechanistic details of every step of RAD51 recruitment and DNA repair. RAD51 possesses an intrinsic tendency to form oligomeric structures, which make it challenging to conduct biochemical and biophysical investigations. Here, for the first time, we report on the isolation and characterization of a human monomeric RAD51 recombinant form, obtained through a double mutation, which preserves the protein's integrity and functionality. We investigated different buffers to identify the most suitable condition needed to definitively stabilize the monomer. The monomer of human RAD51 provides the community with a unique biological tool for investigating RAD51-mediated homologous recombination, and paves the way for more reliable structural, mechanistic, and drug discovery studies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Samuel H Myers
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marina Veronesi
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luigi Scietti
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina Cecatiello
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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24
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Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
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Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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25
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570962. [PMID: 38106198 PMCID: PMC10723406 DOI: 10.1101/2023.12.10.570962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Anna K. Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E. McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Carlton O. Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giulia Mastroianni
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M. Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
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26
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EswarKumar N, Yang CH, Tewary S, Peng WH, Chen GC, Yeh YQ, Yang HC, Ho MC. An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation. Structure 2023; 31:1567-1577.e5. [PMID: 37794594 DOI: 10.1016/j.str.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.
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Affiliation(s)
- Nadendla EswarKumar
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Sunilkumar Tewary
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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27
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Kieslich B, Weiße RH, Brendler J, Ricken A, Schöneberg T, Sträter N. The dimerized pentraxin-like domain of the adhesion G protein-coupled receptor 112 (ADGRG4) suggests function in sensing mechanical forces. J Biol Chem 2023; 299:105356. [PMID: 37863265 PMCID: PMC10687090 DOI: 10.1016/j.jbc.2023.105356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) feature large extracellular regions with modular domains that often resemble protein classes of various function. The pentraxin (PTX) domain, which is predicted by sequence homology within the extracellular region of four different aGPCR members, is well known to form pentamers and other oligomers. Oligomerization of GPCRs is frequently reported and mainly driven by interactions of the seven-transmembrane region and N or C termini. While the functional importance of dimers is well-established for some class C GPCRs, relatively little is known about aGPCR multimerization. Here, we showcase the example of ADGRG4, an orphan aGPCR that possesses a PTX-like domain at its very N-terminal tip, followed by an extremely long stalk containing serine-threonine repeats. Using X-ray crystallography and biophysical methods, we determined the structure of this unusual PTX-like domain and provide experimental evidence for a homodimer equilibrium of this domain which is Ca2+-independent and driven by intermolecular contacts that differ vastly from the known soluble PTXs. The formation of this dimer seems to be conserved in mammalian ADGRG4 indicating functional relevance. Our data alongside of theoretical considerations lead to the hypothesis that ADGRG4 acts as an in vivo sensor for shear forces in enterochromaffin and Paneth cells of the small intestine.
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Affiliation(s)
- Björn Kieslich
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany; Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Jana Brendler
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert Ricken
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany.
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28
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Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernadó P, Banères JL, Sibille N. Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction. Structure 2023; 31:1394-1406.e7. [PMID: 37669668 DOI: 10.1016/j.str.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
Arrestin-dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR's C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three rhodopsin-like GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR), and the β2-adernergic receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motifs (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transitions appear to favor arrestin-2 binding. Hence, our results suggest a model in which the phosphorylation-dependent structuration of the GPCR C-terminal regions would modulate arrestin binding and therefore signaling outcomes in arrestin-dependent pathways.
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Affiliation(s)
- Myriam Guillien
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Glaécia A N Pereira
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélien Thureau
- HélioBio Section, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91190 Gif-sur-Yvette, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France.
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29
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Gonzalez JP, Frandsen KEH, Kesten C. The role of intrinsic disorder in binding of plant microtubule-associated proteins to the cytoskeleton. Cytoskeleton (Hoboken) 2023; 80:404-436. [PMID: 37578201 DOI: 10.1002/cm.21773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/15/2023]
Abstract
Microtubules (MTs) represent one of the main components of the eukaryotic cytoskeleton and support numerous critical cellular functions. MTs are in principle tube-like structures that can grow and shrink in a highly dynamic manner; a process largely controlled by microtubule-associated proteins (MAPs). Plant MAPs are a phylogenetically diverse group of proteins that nonetheless share many common biophysical characteristics and often contain large stretches of intrinsic protein disorder. These intrinsically disordered regions are determinants of many MAP-MT interactions, in which structural flexibility enables low-affinity protein-protein interactions that enable a fine-tuned regulation of MT cytoskeleton dynamics. Notably, intrinsic disorder is one of the major obstacles in functional and structural studies of MAPs and represents the principal present-day challenge to decipher how MAPs interact with MTs. Here, we review plant MAPs from an intrinsic protein disorder perspective, by providing a complete and up-to-date summary of all currently known members, and address the current and future challenges in functional and structural characterization of MAPs.
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Affiliation(s)
- Jordy Perez Gonzalez
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristian E H Frandsen
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christopher Kesten
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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30
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Chen R, Song Y, Wang Z, Ji H, Du Z, Ma Q, Yang Y, Liu X, Li N, Sun Y. Developments in small-angle X-ray scattering (SAXS) for characterizing the structure of surfactant-macromolecule interactions and their complex. Int J Biol Macromol 2023; 251:126288. [PMID: 37582436 DOI: 10.1016/j.ijbiomac.2023.126288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
The surfactant-macromolecule interactions (SMI) are one of the most critical topics for scientific research and industrial application. Small-angle X-ray scattering (SAXS) is a powerful tool for comprehensively studying the structural and conformational features of macromolecules at a size ranging from Angstroms to hundreds of nanometers with a time-resolve in milliseconds scale. The SAXS integrative techniques have emerged for comprehensively analyzing the SMI and the structure of their complex in solution. Here, the various types of emerging interactions of surfactant with macromolecules, such as protein, lipid, nuclear acid, polysaccharide and virus, etc. have been systematically reviewed. Additionally, the principle of SAXS and theoretical models of SAXS for describing the structure of SMI as well as their complex has been summarized. Moreover, the recent developments in the applications of SAXS for charactering the structure of SMI have been also highlighted. Prospectively, the capacity to complement artificial intelligence (AI) in the structure prediction of biological macromolecules and the high-throughput bioinformatics sequencing data make SAXS integrative structural techniques expected to be the primary methodology for illuminating the self-assembling dynamics and nanoscale structure of SMI. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Yang Song
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhichun Wang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Hang Ji
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhongyao Du
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Qingwen Ma
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Ying Yang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Xingxun Liu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China.
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31
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Ogbu CP, Kapoor S, Vecchio AJ. Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin. Toxins (Basel) 2023; 15:637. [PMID: 37999500 PMCID: PMC10674488 DOI: 10.3390/toxins15110637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin's role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.
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Affiliation(s)
| | | | - Alex J. Vecchio
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY 14203, USA; (C.P.O.); (S.K.)
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32
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Wang T, Coshic K, Badiee M, Aksimentiev A, Pollack L, Leung AKL. Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564012. [PMID: 37961637 PMCID: PMC10634823 DOI: 10.1101/2023.10.25.564012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Poly(ADP-ribose) (PAR), as part of a post-translational modification, serves as a flexible scaffold for noncovalent protein binding. Such binding is influenced by PAR chain length through a mechanism yet to be elucidated. Structural insights have been elusive, partly due to the difficulties associated with synthesizing PAR chains of defined lengths. Here, we employ an integrated approach combining molecular dynamics (MD) simulations with small-angle X-ray scattering (SAXS) experiments, enabling us to identify highly heterogeneous ensembles of PAR conformers at two different, physiologically relevant lengths: PAR 15 and PAR 22 . Our findings reveal that numerous factors including backbone conformation, base stacking, and chain length contribute to determining the structural ensembles. We also observe length-dependent compaction of PAR upon the addition of small amounts of Mg 2+ ions, with the 22-mer exhibiting ADP-ribose bundles formed through local intramolecular coil-to-globule transitions. This study illuminates how such bundling could be instrumental in deciphering the length-dependent action of PAR. GRAPHICAL ABSTRACT
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33
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Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
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34
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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35
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Voigt B, Bhatia T, Hesselbarth J, Baumann M, Schmidt C, Ott M, Balbach J. The Prenucleation Equilibrium of the Parathyroid Hormone Determines the Critical Aggregation Concentration and Amyloid Fibril Nucleation. Chemphyschem 2023; 24:e202300439. [PMID: 37477386 DOI: 10.1002/cphc.202300439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Nucleation and growth of amyloid fibrils were found to only occur in supersaturated solutions above a critical concentration (ccrit ). The biophysical meaning of ccrit remained mostly obscure, since typical low values of ccrit in the sub-μM range hamper investigations of potential oligomeric states and their structure. Here, we investigate the parathyroid hormone PTH84 as an example of a functional amyloid fibril forming peptide with a comparably high ccrit of 67±21 μM. We describe a complex concentration dependent prenucleation ensemble of oligomers of different sizes and secondary structure compositions and highlight the occurrence of a trimer and tetramer at ccrit as possible precursors for primary fibril nucleation. Furthermore, the soluble state found in equilibrium with fibrils adopts to the prenucleation state present at ccrit . Our study sheds light onto early events of amyloid formation directly related to the critical concentration and underlines oligomer formation as a key feature of fibril nucleation. Our results contribute to a deeper understanding of the determinants of supersaturated peptide solutions. In the current study we present a biophysical approach to investigate ccrit of amyloid fibril formation of PTH84 in terms of secondary structure, cluster size and residue resolved intermolecular interactions during oligomer formation. Throughout the investigated range of concentrations (1 μM to 500 μM) we found different states of oligomerization with varying ability to contribute to primary fibril nucleation and with a concentration dependent equilibrium. In this context, we identified the previously described ccrit of PTH84 to mark a minimum concentration for the formation of homo-trimers/tetramers. These investigations allowed us to characterize molecular interactions of various oligomeric states that are further converted into elongation competent fibril nuclei during the lag phase of a functional amyloid forming peptide.
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Affiliation(s)
- Bruno Voigt
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
| | - Twinkle Bhatia
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Julia Hesselbarth
- present address: Johannes Gutenberg University Mainz, Institute of Chemistry - Biochemistry, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Martin Luther University Halle-Wittenberg, Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3a, 06120, Halle, Germany
| | - Monika Baumann
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
| | - Carla Schmidt
- present address: Johannes Gutenberg University Mainz, Institute of Chemistry - Biochemistry, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Martin Luther University Halle-Wittenberg, Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3a, 06120, Halle, Germany
| | - Maria Ott
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Jochen Balbach
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
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36
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Rusbjerg-Weberskov C, Johansen ML, Nowak JS, Otzen DE, Pedersen JS, Enghild JJ, Nielsen NS. Periostin C-Terminal Is Intrinsically Disordered and Interacts with 143 Proteins in an In Vitro Epidermal Model of Atopic Dermatitis. Biochemistry 2023; 62:2803-2815. [PMID: 37704583 PMCID: PMC10552548 DOI: 10.1021/acs.biochem.3c00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/18/2023] [Indexed: 09/15/2023]
Abstract
Human periostin is a 78-91 kDa matricellular protein implicated in extracellular matrix remodeling, tumor development, metastasis, and inflammatory diseases like atopic dermatitis, psoriasis, and asthma. The protein consists of six domains, including an N-terminal Cys-rich CROPT domain, four fasciclin-1 domains, and a C-terminal domain. The exons encoding the C-terminal domain may be alternatively spliced by shuffling four exons, generating ten variants of unknown function. Here, we investigate the structure and interactome of the full-length variant of the C-terminal domain with no exons spliced out. The structural analysis showed that the C-terminal domain lacked a tertiary structure and was intrinsically disordered. In addition, we show that the motif responsible for heparin-binding is in the conserved very C-terminal part of periostin. Pull-down confirmed three known interaction partners and identified an additional 140 proteins, among which nine previously have been implicated in atopic dermatitis. Based on our findings, we suggest that the C-terminal domain of periostin facilitates interactions between connective tissue components in concert with the four fasciclin domains.
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Affiliation(s)
| | - Mette Liere Johansen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Jan S. Nowak
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Daniel E. Otzen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan Skov Pedersen
- Department
of Chemistry, Aarhus University, Aarhus C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan J. Enghild
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Nadia Sukusu Nielsen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
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37
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Le LTHL, Lee J, Im D, Park S, Hwang K, Lee JH, Jiang Y, Lee Y, Suh YH, Kim HI, Lee MJ. Self-Aggregating Tau Fragments Recapitulate Pathologic Phenotypes and Neurotoxicity of Alzheimer's Disease in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302035. [PMID: 37594721 PMCID: PMC10582461 DOI: 10.1002/advs.202302035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/10/2023] [Indexed: 08/19/2023]
Abstract
In tauopathy conditions, such as Alzheimer's disease (AD), highly soluble and natively unfolded tau polymerizes into an insoluble filament; however, the mechanistic details of this process remain unclear. In the brains of AD patients, only a minor segment of tau forms β-helix-stacked protofilaments, while its flanking regions form disordered fuzzy coats. Here, it is demonstrated that the tau AD nucleation core (tau-AC) sufficiently induced self-aggregation and recruited full-length tau to filaments. Unexpectedly, phospho-mimetic forms of tau-AC (at Ser324 or Ser356) show markedly reduced oligomerization and seeding propensities. Biophysical analysis reveal that the N-terminus of tau-AC facilitates the fibrillization kinetics as a nucleation motif, which becomes sterically shielded through phosphorylation-induced conformational changes in tau-AC. Tau-AC oligomers are efficiently internalized into cells via endocytosis and induced endogenous tau aggregation. In primary hippocampal neurons, tau-AC impaired axon initial segment plasticity upon chronic depolarization and is mislocalized to the somatodendritic compartments. Furthermore, it is observed significantly impaired memory retrieval in mice intrahippocampally injected with tau-AC fibrils, which corresponds to the neuropathological staining and neuronal loss in the brain. These findings identify tau-AC species as a key neuropathological driver in AD, suggesting novel strategies for therapeutic intervention.
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Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
| | - Jeeyoung Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Brain Science InstituteKorea Institute of Science and TechnologySeoul02792South Korea
| | - Dongjoon Im
- Department of ChemistryKorea UniversitySeoul02841South Korea
| | - Sunha Park
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
| | - Kyoung‐Doo Hwang
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Department of PhysiologySeoul National University College of MedicineSeoul03080South Korea
| | - Jung Hoon Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
| | - Yanxialei Jiang
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- School of MedicineLinyi UniversityLinyi276000China
| | - Yong‐Seok Lee
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Department of PhysiologySeoul National University College of MedicineSeoul03080South Korea
- Neuroscience Research InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Young Ho Suh
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Neuroscience Research InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoul02841South Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Ischemic/Hypoxic Disease Institute, Convergence Research Center for DementiaSeoul National University College of MedicineSeoul03080South Korea
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38
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Quek AJ, Cowieson NP, Caradoc-Davies TT, Conroy PJ, Whisstock JC, Law RHP. A High-Throughput Small-Angle X-ray Scattering Assay to Determine the Conformational Change of Plasminogen. Int J Mol Sci 2023; 24:14258. [PMID: 37762561 PMCID: PMC10531915 DOI: 10.3390/ijms241814258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Plasminogen (Plg) is the inactive form of plasmin (Plm) that exists in two major glycoforms, referred to as glycoforms I and II (GI and GII). In the circulation, Plg assumes an activation-resistant "closed" conformation via interdomain interactions and is mediated by the lysine binding site (LBS) on the kringle (KR) domains. These inter-domain interactions can be readily disrupted when Plg binds to lysine/arginine residues on protein targets or free L-lysine and analogues. This causes Plg to convert into an "open" form, which is crucial for activation by host activators. In this study, we investigated how various ligands affect the kinetics of Plg conformational change using small-angle X-ray scattering (SAXS). We began by examining the open and closed conformations of Plg using size-exclusion chromatography (SEC) coupled with SAXS. Next, we developed a high-throughput (HTP) 96-well SAXS assay to study the conformational change of Plg. This method enables us to determine the Kopen value, which is used to directly compare the effect of different ligands on Plg conformation. Based on our analysis using Plg GII, we have found that the Kopen of ε-aminocaproic acid (EACA) is approximately three times greater than that of tranexamic acid (TXA), which is widely recognized as a highly effective ligand. We demonstrated further that Plg undergoes a conformational change when it binds to the C-terminal peptides of the inhibitor α2-antiplasmin (α2AP) and receptor Plg-RKT. Our findings suggest that in addition to the C-terminal lysine, internal lysine(s) are also necessary for the formation of open Plg. Finally, we compared the conformational changes of Plg GI and GII directly and found that the closed form of GI, which has an N-linked glycosylation, is less stable. To summarize, we have successfully determined the response of Plg to various ligand/receptor peptides by directly measuring the kinetics of its conformational changes.
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Affiliation(s)
- Adam J. Quek
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Nathan P. Cowieson
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Tom T. Caradoc-Davies
- Australian Synchrotron, ANSTO_Melbourne, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - Paul J. Conroy
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - James C. Whisstock
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ruby H. P. Law
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
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39
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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40
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Mistry H, Kumari S, Aswal VK, Gupta GD. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein. Int J Biol Macromol 2023; 247:125792. [PMID: 37442507 DOI: 10.1016/j.ijbiomac.2023.125792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.
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Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Shweta Kumari
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
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Wieczorek P, Jarmołowski A, Szweykowska-Kulińska Z, Kozak M, Taube M. Solution structure and behaviour of the Arabidopsis thaliana HYL1 protein. Biochim Biophys Acta Gen Subj 2023; 1867:130376. [PMID: 37150226 DOI: 10.1016/j.bbagen.2023.130376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
In plants, microRNA biogenesis involves the complex assembly of molecular processes that are mostly governed by three proteins: RNase III protein DCL1 and two RNA binding proteins, SERRATE and HYL1. HYL1 protein is a double stranded RNA binding protein that is needed for the precise excision of miRNA/miRNA* duplex from the stem-loop containing primary miRNA gene transcripts. Moreover, HYL1 protein partners with HSP90 and CARP9 proteins to load the miRNA molecules onto the AGO1 endonuclease. HYL1 protein as a crucial player in the biogenesis pathway is regulated by its phosphorylation status to fine tune the levels of miRNA in various physiological conditions. HYL1 protein consists of two dsRNA binding domains (dsRBD) that are involved in RNA binding and dimerization and a C-terminal disordered tail of unknown function. Although the spatial structures of the individual dsRBDs have been determined there is a lack of information about the behaviour and structure of the full length protein. Using small the angle X-ray scattering (SAXS) technique we investigated the structure and dynamic of the HYL1 protein from Arabidopsis thaliana in solution. We show that the C-terminal domain is disordered and dynamic in solution and that HYL1 protein dimerization is dependent on the concentration. HYL1 protein lacking a C-terminal tail and a nuclear localisation signal (NLS) fragment is almost exclusively monomeric and similarly to full-length protein has a dynamic nature in solution. Our results point for the first time to the role of the C-terminal fragment in stabilisation of HYL1 dimer formation.
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Affiliation(s)
- Przemysław Wieczorek
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland.
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42
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Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R. Intramolecular structural heterogeneity altered by long-range contacts in an intrinsically disordered protein. Proc Natl Acad Sci U S A 2023; 120:e2220180120. [PMID: 37459524 PMCID: PMC10372579 DOI: 10.1073/pnas.2220180120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function.
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Affiliation(s)
- Gil Koren
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Sagi Meir
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Lennard Holschuh
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | | | - Tamara Ehm
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany
| | - Nadav Yahalom
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adina Golombek
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tal Schwartz
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg22607, Germany
| | - Omar A. Saleh
- BMSE Program, University of California, Santa Barbara, CA93110
- Materials Department, University of California, Santa Barbara, CA93110
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | - Roy Beck
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
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43
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Goretzki B, Wiedemann C, McCray BA, Schäfer SL, Jansen J, Tebbe F, Mitrovic SA, Nöth J, Cabezudo AC, Donohue JK, Jeffries CM, Steinchen W, Stengel F, Sumner CJ, Hummer G, Hellmich UA. Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nat Commun 2023; 14:4165. [PMID: 37443299 PMCID: PMC10344929 DOI: 10.1038/s41467-023-39808-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Intrinsically disordered regions (IDRs) are essential for membrane receptor regulation but often remain unresolved in structural studies. TRPV4, a member of the TRP vanilloid channel family involved in thermo- and osmosensation, has a large N-terminal IDR of approximately 150 amino acids. With an integrated structural biology approach, we analyze the structural ensemble of the TRPV4 IDR and the network of antagonistic regulatory elements it encodes. These modulate channel activity in a hierarchical lipid-dependent manner through transient long-range interactions. A highly conserved autoinhibitory patch acts as a master regulator by competing with PIP2 binding to attenuate channel activity. Molecular dynamics simulations show that loss of the interaction between the PIP2-binding site and the membrane reduces the force exerted by the IDR on the structured core of TRPV4. This work demonstrates that IDR structural dynamics are coupled to TRPV4 activity and highlights the importance of IDRs for TRP channel function and regulation.
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Affiliation(s)
- Benedikt Goretzki
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany
| | - Christoph Wiedemann
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stefan L Schäfer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jasmin Jansen
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Frederike Tebbe
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Sarah-Ana Mitrovic
- Department of Chemistry, Section Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Julia Nöth
- Department of Chemistry, Section Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ainara Claveras Cabezudo
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Frankfurt am Main, Germany
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cy M Jeffries
- European Molecular Biology Laboratory, EMBL Hamburg Unit, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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44
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Sun X, Yu Y, Saleh ASM, Yang X, Ma J, Gao Z, Li W, Wang Z, Zhang D. Structural changes induced by ultrasound improve the ability of the myofibrillar protein to bind flavor compounds from spices. ULTRASONICS SONOCHEMISTRY 2023; 98:106510. [PMID: 37418951 PMCID: PMC10359944 DOI: 10.1016/j.ultsonch.2023.106510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Effects of ultrasound (UT) treatments on the structural, physicochemical, and functional properties of myofibrillar proteins (MPs), as well as their ability to bind to flavor compounds from spices, were investigated. The results demonstrated that UT treatment enhanced surface hydrophobicity, SH content, and absolute ζ-potential value of the MPs. Atomic force microscopy analysis displayed formation of MPs aggregates with small particle size in the UT-treated MPs samples. Meanwhile, UT treatment could improve the emulsifying properties and physical stability of MPs' emulsion. Additionally, the MPs gel network structure and stability significantly improved following UT treatment. Changes in the structural, physicochemical, and functional properties enhanced the ability of MPs to bind to flavor substances from spices depending on the duration of UT treatment. Furthermore, correlation analysis showed that the ability of myristicin, anethole, and estragole to bind to MPs was highly correlated with surface hydrophobicity, ζ-potential value, and α-helix content of MPs. The results of this study may help in understanding the relationship between the changes in MPs properties during the processing of meat products and their ability to bind to flavors from spices, thereby improving flavors retention and taste of processed meat products.
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Affiliation(s)
- Xiangxiang Sun
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Yumei Yu
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ahmed S M Saleh
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Xinyu Yang
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Jiale Ma
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ziwu Gao
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Wenhao Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Zhenyu Wang
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
| | - Dequan Zhang
- Key Laboratory of Agro-Products Processing, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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45
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Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023; 34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Oulu, Finland
- Corresponding author. Department of Biomedicine, University of Bergen, Norway.
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Wang J, Koduru T, Harish B, McCallum SA, Larsen KP, Patel KS, Peters EV, Gillilan RE, Puglisi EV, Puglisi JD, Makhatadze G, Royer CA. Pressure pushes tRNA Lys3 into excited conformational states. Proc Natl Acad Sci U S A 2023; 120:e2215556120. [PMID: 37339210 PMCID: PMC10293818 DOI: 10.1073/pnas.2215556120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 05/16/2023] [Indexed: 06/22/2023] Open
Abstract
Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNALys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U-A and G-C base pairs of tRNALys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.
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Affiliation(s)
- Jinqiu Wang
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Tejaswi Koduru
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Scott A. McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Kevin P. Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Karishma S. Patel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Edgar V. Peters
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
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47
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Watkins M, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy. Proc Natl Acad Sci U S A 2023; 120:e2302531120. [PMID: 37339208 PMCID: PMC10293825 DOI: 10.1073/pnas.2302531120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH3-H4folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S-adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multidomain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryoelectron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present a structural description of the full-length MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH3-H4folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
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Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY14853
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Field of Biophysics, Cornell University, Ithaca, NY14853
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48
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Shi B, Matsui T, Qian S, Weiss TM, Nicholl ID, Callaway DJE, Bu Z. An ensemble of cadherin-catenin-vinculin complex employs vinculin as the major F-actin binding mode. Biophys J 2023; 122:2456-2474. [PMID: 37147801 PMCID: PMC10323030 DOI: 10.1016/j.bpj.2023.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/14/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023] Open
Abstract
The cell-cell adhesion cadherin-catenin complexes recruit vinculin to the adherens junction (AJ) to modulate the mechanical couplings between neighboring cells. However, it is unclear how vinculin influences the AJ structure and function. Here, we identified two patches of salt bridges that lock vinculin in the head-tail autoinhibited conformation and reconstituted the full-length vinculin activation mimetics bound to the cadherin-catenin complex. The cadherin-catenin-vinculin complex contains multiple disordered linkers and is highly dynamic, which poses a challenge for structural studies. We determined the ensemble conformation of this complex using small-angle x-ray and selective deuteration/contrast variation small-angle neutron scattering. In the complex, both α-catenin and vinculin adopt an ensemble of flexible conformations, but vinculin has fully open conformations with the vinculin head and actin-binding tail domains well separated from each other. F-actin binding experiments show that the cadherin-catenin-vinculin complex binds and bundles F-actin. However, when the vinculin actin-binding domain is removed from the complex, only a minor fraction of the complex binds to F-actin. The results show that the dynamic cadherin-catenin-vinculin complex employs vinculin as the primary F-actin binding mode to strengthen AJ-cytoskeleton interactions.
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Affiliation(s)
- Bright Shi
- Department of Chemistry and Biochemistry, City College of New York, City University of New York (CUNY), New York; PhD Programs in Chemistry and Biochemistry, CUNY Graduate Center, New York
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, Menlo Park, California
| | - Shuo Qian
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Light Source, Menlo Park, California
| | - Iain D Nicholl
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - David J E Callaway
- Department of Chemistry and Biochemistry, City College of New York, City University of New York (CUNY), New York.
| | - Zimei Bu
- Department of Chemistry and Biochemistry, City College of New York, City University of New York (CUNY), New York; PhD Programs in Chemistry and Biochemistry, CUNY Graduate Center, New York.
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49
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Sacerdoti M, Gross LZF, Riley AM, Zehnder K, Ghode A, Klinke S, Anand GS, Paris K, Winkel A, Herbrand AK, Godage HY, Cozier GE, Süß E, Schulze JO, Pastor-Flores D, Bollini M, Cappellari MV, Svergun D, Gräwert MA, Aramendia PF, Leroux AE, Potter BVL, Camacho CJ, Biondi RM. Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein. Sci Signal 2023; 16:eadd3184. [PMID: 37311034 DOI: 10.1126/scisignal.add3184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/19/2023] [Indexed: 06/15/2023]
Abstract
The activation of at least 23 different mammalian kinases requires the phosphorylation of their hydrophobic motifs by the kinase PDK1. A linker connects the phosphoinositide-binding PH domain to the catalytic domain, which contains a docking site for substrates called the PIF pocket. Here, we used a chemical biology approach to show that PDK1 existed in equilibrium between at least three distinct conformations with differing substrate specificities. The inositol polyphosphate derivative HYG8 bound to the PH domain and disrupted PDK1 dimerization by stabilizing a monomeric conformation in which the PH domain associated with the catalytic domain and the PIF pocket was accessible. In the absence of lipids, HYG8 potently inhibited the phosphorylation of Akt (also termed PKB) but did not affect the intrinsic activity of PDK1 or the phosphorylation of SGK, which requires docking to the PIF pocket. In contrast, the small-molecule valsartan bound to the PIF pocket and stabilized a second distinct monomeric conformation. Our study reveals dynamic conformations of full-length PDK1 in which the location of the linker and the PH domain relative to the catalytic domain determines the selective phosphorylation of PDK1 substrates. The study further suggests new approaches for the design of drugs to selectively modulate signaling downstream of PDK1.
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Affiliation(s)
- Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Andrew M Riley
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Karin Zehnder
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Abhijeet Ghode
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires C1405BWE, Argentina
| | - Ganesh Srinivasan Anand
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
- Department of Chemistry, Huck Institutes of the Life Sciences, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
| | - Kristina Paris
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Statistics, University of Pittsburgh, WWPH 1821, Pittsburgh, PA 15213, USA
| | - Angelika Winkel
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Amanda K Herbrand
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - H Yasmin Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Gyles E Cozier
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Evelyn Süß
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jörg O Schulze
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Daniel Pastor-Flores
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- KBI Biopharma, Technologielaan 8, B-3001 Leuven, Belgium
| | - Mariela Bollini
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - María Victoria Cappellari
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Melissa A Gräwert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Pedro F Aramendia
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, FCEN, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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50
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Del Giudice A, Gurrieri L, Galantini L, Fanti S, Trost P, Sparla F, Fermani S. Conformational Disorder Analysis of the Conditionally Disordered Protein CP12 from Arabidopsis thaliana in Its Different Redox States. Int J Mol Sci 2023; 24:ijms24119308. [PMID: 37298260 DOI: 10.3390/ijms24119308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
CP12 is a redox-dependent conditionally disordered protein universally distributed in oxygenic photosynthetic organisms. It is primarily known as a light-dependent redox switch regulating the reductive step of the metabolic phase of photosynthesis. In the present study, a small angle X-ray scattering (SAXS) analysis of recombinant Arabidopsis CP12 (AtCP12) in a reduced and oxidized form confirmed the highly disordered nature of this regulatory protein. However, it clearly pointed out a decrease in the average size and a lower level of conformational disorder upon oxidation. We compared the experimental data with the theoretical profiles of pools of conformers generated with different assumptions and show that the reduced form is fully disordered, whereas the oxidized form is better described by conformers comprising both the circular motif around the C-terminal disulfide bond detected in previous structural analysis and the N-terminal disulfide bond. Despite the fact that disulfide bridges are usually thought to confer rigidity to protein structures, in the oxidized AtCP12, their presence coexists with a disordered nature. Our results rule out the existence of significant amounts of structured and compact conformations of free AtCP12 in a solution, even in its oxidized form, thereby highlighting the importance of recruiting partner proteins to complete its structured final folding.
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Affiliation(s)
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Luciano Galantini
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064 Bologna, Italy
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