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Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
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2
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Hansen T, Lee J, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies PL. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. eLife 2023; 12:RP91976. [PMID: 38109272 PMCID: PMC10727499 DOI: 10.7554/elife.91976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins (INPs) of common environmental bacteria like Pseudomonas syringae and Pseudomonas borealis. However, individually, these 100 kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an INP gene into Escherichia coli led to efficient ice nucleation. Here, we demonstrate that a positively charged subdomain at the C-terminal end of the central β-solenoid of the INP is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the INP multimers form fibres that are ~5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.
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Affiliation(s)
- Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Jocelyn Lee
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Naama Reicher
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Gil Ovadia
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Shuaiqi Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
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3
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Summers JA, Yarbrough M, Liu M, McDonald WH, Hudson BG, Pastor-Pareja JC, Boudko SP. Collagen IV of basement membranes: IV. Adaptive mechanism of collagen IV scaffold assembly in Drosophila. J Biol Chem 2023; 299:105394. [PMID: 37890775 PMCID: PMC10694668 DOI: 10.1016/j.jbc.2023.105394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Collagen IV is an essential structural protein in all metazoans. It provides a scaffold for the assembly of basement membranes, a specialized form of extracellular matrix, which anchors and signals cells and provides microscale tensile strength. Defective scaffolds cause basement membrane destabilization and tissue dysfunction. Scaffolds are composed of α-chains that coassemble into triple-helical protomers of distinct chain compositions, which in turn oligomerize into supramolecular scaffolds. Chloride ions mediate the oligomerization via NC1 trimeric domains, forming an NC1 hexamer at the protomer-protomer interface. The chloride concentration-"chloride pressure"-on the outside of cells is a primordial innovation that drives the assembly and dynamic stabilization of collagen IV scaffolds. However, a Cl-independent mechanism is operative in Ctenophora, Ecdysozoa, and Rotifera, which suggests evolutionary adaptations to environmental or tissue conditions. An understanding of these exceptions, such as the example of Drosophila, could shed light on the fundamentals of how NC1 trimers direct the oligomerization of protomers into scaffolds. Here, we investigated the NC1 assembly of Drosophila. We solved the crystal structure of the NC1 hexamer, determined the chain composition of protomers, and found that Drosophila adapted an evolutionarily unique mechanism of scaffold assembly that requires divalent cations. By studying the Drosophila case we highlighted the mechanistic role of chloride pressure for maintaining functionality of the NC1 domain in humans. Moreover, we discovered that the NC1 trimers encode information for homing protomers to distant tissue locations, providing clues for the development of protein replacement therapy for collagen IV genetic diseases.
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Affiliation(s)
- Jacob A Summers
- Aspirnaut Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Madison Yarbrough
- Aspirnaut Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Min Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - W Hayes McDonald
- Proteomics Laboratory, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Billy G Hudson
- Aspirnaut Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - José C Pastor-Pareja
- School of Life Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; Institute of Neurosciences, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Sergei P Boudko
- Aspirnaut Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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Boudko SP, Pedchenko VK, Pokidysheva EN, Budko AM, Baugh R, Coates PT, Fidler AL, Hudson HM, Ivanov SV, Luer C, Pedchenko T, Preston RL, Rafi M, Vanacore R, Bhave G, Hudson JK, Hudson BG. Collagen IV of basement membranes: III. Chloride pressure is a primordial innovation that drives and maintains the assembly of scaffolds. J Biol Chem 2023; 299:105318. [PMID: 37797699 PMCID: PMC10656227 DOI: 10.1016/j.jbc.2023.105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
Collagen IV scaffold is a primordial innovation enabling the assembly of a fundamental architectural unit of epithelial tissues-a basement membrane attached to polarized cells. A family of six α-chains (α1 to α6) coassemble into three distinct protomers that form supramolecular scaffolds, noted as collagen IVα121, collagen IVα345, and collagen IVα121-α556. Chloride ions play a pivotal role in scaffold assembly, based on studies of NC1 hexamers from mammalian tissues. First, Cl- activates a molecular switch within trimeric NC1 domains that initiates protomer oligomerization, forming an NC1 hexamer between adjoining protomers. Second, Cl- stabilizes the hexamer structure. Whether this Cl--dependent mechanism is of fundamental importance in animal evolution is unknown. Here, we developed a simple in vitro method of SDS-PAGE to determine the role of solution Cl- in hexamer stability. Hexamers were characterized from 34 animal species across 15 major phyla, including the basal Cnidarian and Ctenophora phyla. We found that solution Cl- stabilized the quaternary hexamer structure across all phyla except Ctenophora, Ecdysozoa, and Rotifera. Further analysis of hexamers from peroxidasin knockout mice, a model for decreasing hexamer crosslinks, showed that solution Cl- also stabilized the hexamer surface conformation. The presence of sufficient chloride concentration in solution or "chloride pressure" dynamically maintains the native form of the hexamer. Collectively, our findings revealed that chloride pressure on the outside of cells is a primordial innovation that drives and maintains the quaternary and conformational structure of NC1 hexamers of collagen IV scaffolds.
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Affiliation(s)
- Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
| | - Vadim K Pedchenko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elena N Pokidysheva
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Rachel Baugh
- Department of Medical Education and Administration, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Patrick Toby Coates
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, Australia
| | - Aaron L Fidler
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Heather M Hudson
- Department of Rehabilitation Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Sergey V Ivanov
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Carl Luer
- Mote Marine Laboratory, Sarasota, Florida, USA
| | - Tetyana Pedchenko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robert L Preston
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Mohamed Rafi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Roberto Vanacore
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gautam Bhave
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Julie K Hudson
- Department of Medical Education and Administration, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Billy G Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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5
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He M, Cheng Z, Wang Z, Li M, Liang H, Liu H, Yu L, Zhao L, Yu F. Controllable Regulation of Ag 2 S Quantum-Dot-Mediated Protein Nanoassemblies for Imaging-Guided Synergistic PDT/PTT/Chemotherapy against Hypoxic Tumor. Adv Healthc Mater 2023; 12:e2300752. [PMID: 37306666 DOI: 10.1002/adhm.202300752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/24/2023] [Indexed: 06/13/2023]
Abstract
The combination of phototherapy and chemotherapy holds great potential for cancer treatment, while hypoxia in tumor as well as unexpected drug release largely restricts anticancer therapy. Inspired by the natural intelligence, herein, for the first time, a "bottom-up" protein self-assembly strategy mediated by near-infrared (NIR) quantum dots (QDs) with multicharged electrostatic interactions is presented to develop a tumor microenvironment (TME)-responsive theranostic nanoplatform for imaging-guided synergistic photodynamic therapy (PDT)/photothermal therapy (PTT)/chemotherapy. Catalase (CAT) possesses diverse surface charge distribution under different pH conditions. After modification by chlorin e6 (Ce6), the formulated CAT-Ce6 with patchy negative charges can be assembled with NIR Ag2 S QDs by regulating their electrostatic interactions, allowing for effective incorporation of specific anticancer drug oxaliplatin (Oxa). Such Ag2 S@CAT-Ce6@Oxa nanosystems are able to visualize nanoparticle (NP) accumulation to guide subsequent phototherapy, together with significant alleviation of tumor hypoxia to further enhance PDT. Moreover, the acidic TME triggers controllable disassembly through weakening the CAT surface charge to disrupt electrostatic interactions, allowing for sustained drug release. Both in vitro and in vivo results demonstrate remarkable inhibition of colorectal tumor growth with a synergistic effect. Overall, this multicharged electrostatic protein self-assembly strategy provides a versatile platform for realizing TME-specific theranostics with high efficiency and safety, promising for clinical translation.
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Affiliation(s)
- Mengjie He
- Medical Imaging Department, Affiliated Cancer Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570312, China
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Ziyi Cheng
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Zhenkai Wang
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Min Li
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Huixian Liang
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Heng Liu
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Lijuan Yu
- Medical Imaging Department, Affiliated Cancer Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570312, China
| | - Linlu Zhao
- Medical Imaging Department, Affiliated Cancer Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570312, China
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
| | - Fabiao Yu
- Medical Imaging Department, Affiliated Cancer Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570312, China
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, College of Emergency and Trauma, Hainan Medical University, Haikou, 571199, China
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Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023; 32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase-separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain-level organization and compute a sequence-based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase-separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
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Affiliation(s)
- Colorado Wilson
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
- Present address:
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Karen A. Lewis
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
| | - Nicholas C. Fitzkee
- Department of ChemistryMississippi State UniversityMississippi StateMississippiUSA
| | - Loren E. Hough
- Department of PhysicsUniversity of Colorado BoulderBoulderColoradoUSA
- BioFrontiers InstituteUniversity of Colorado BoulderBoulderColoradoUSA
| | - Steven T. Whitten
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
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Boudko SP, Konopka EH, Kim W, Taga Y, Mizuno K, Springer TA, Hudson BG, Moy TI, Lin FY. A recombinant technique for mapping functional sites of heterotrimeric collagen helices: Collagen IV CB3 fragment as a prototype for integrin binding. J Biol Chem 2023; 299:104901. [PMID: 37302550 PMCID: PMC10404678 DOI: 10.1016/j.jbc.2023.104901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Collagen superfamily of proteins is a major component of the extracellular matrix. Defects in collagens underlie the cause of nearly 40 human genetic diseases in millions of people worldwide. Pathogenesis typically involves genetic alterations of the triple helix, a hallmark structural feature that bestows exceptional mechanical resistance to tensile forces and a capacity to bind a plethora of macromolecules. Yet, there is a paramount knowledge gap in understanding the functionality of distinct sites along the triple helix. Here, we present a recombinant technique to produce triple helical fragments for functional studies. The experimental strategy utilizes the unique capacity of the NC2 heterotrimerization domain of collagen IX to drive three α-chain selection and registering the triple helix stagger. For proof of principle, we produced and characterized long triple helical fragments of collagen IV that were expressed in a mammalian system. The heterotrimeric fragments encompassed the CB3 trimeric peptide of collagen IV, which harbors the binding motifs for α1β1 and α2β1 integrins. Fragments were characterized and shown to have a stable triple helix, post-translational modifications, and high affinity and specific binding of integrins. The NC2 technique is a universal tool for the high-yield production of heterotrimeric fragments of collagens. Fragments are suitable for mapping functional sites, determining coding sequences of binding sites, elucidating pathogenicity and pathogenic mechanisms of genetic mutations, and production of fragments for protein replacement therapy.
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Affiliation(s)
- Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
| | | | - Woojin Kim
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Yuki Taga
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Billy G Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Terence I Moy
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Fu-Yang Lin
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA.
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8
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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9
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Bana J, Warwar J, Bayer EA, Livnah O. Self-assembly of a dimeric avidin into unique higher-order oligomers. FEBS J 2023. [PMID: 36853192 DOI: 10.1111/febs.16764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
The dimeric avidin family has been expanded in recent years to include many new members. All of them lack the intermonomeric Trp that plays a critical role in biotin-binding. Nevertheless, these new members of the avidins maintain the high affinity towards biotin. Additionally, all of the dimeric avidins share a very unique property: namely, the cylindrical oligomerization in the crystal structure. The newest member described here, agroavidin from the agrobacterium, Rhizobium sp. AAP43, shares their important structural features. However, the affinity of agroavidin towards biotin is lower than all other members of the avidin family, due to the presence of phenylalanine instead of a conserved tyrosine in the biotin-binding site. Mutating this phenylalanine into tyrosine regenerated the high affinity, which emphasizes the importance of this particular tyrosine residue. Another unique feature that distinguishes agroavidin from the other dimeric avidins is that it does not produce oligomers in its crystal structure. In order to understand the factors that promote oligomerization in dimeric avidins, we exchanged the C-terminal region of agroavidin with that of hoefavidin that produced octamers. This exchange resulted in a decamer rather than an octamer. This unusual outcome demonstrates the impact of the C-terminal region on the ability to produce oligomers. The decameric assembly of agroavidin expands the avidin-biotin toolbox even further and could well pave the path into new biotin-based technologies. Moreover, uncovering the factors that induce dimeric avidins into oligomeric assemblies may aid in better understanding the general molecular determinants that promote oligomerization.
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Affiliation(s)
- Juana Bana
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Jessica Warwar
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
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10
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Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022; 299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein phase separation is thought to be a primary driving force for the formation of membrane-less organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. Among phase-separating (PS) proteins, many have intrinsically disordered regions (IDRs) that are needed for phase separation to occur. Accurate identification of IDRs that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and PS ID sequences. We then used these sequence sets to examine how broadly existing amino acid property scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving protein phase separation. Collectively, our findings provide further insight into the classification of IDRs and the elements involved in protein phase separation.
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Affiliation(s)
- Ayyam Y. Ibrahim
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | | | - John J. Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Loren E. Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA,For correspondence: Steven T. Whitten; Loren E. Hough
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA,For correspondence: Steven T. Whitten; Loren E. Hough
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11
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Krzek M, Stroobants S, Gelin P, De Malsche W, Maes D. Influence of Centrifugation and Shaking on the Self-Assembly of Lysozyme Fibrils. Biomolecules 2022; 12:biom12121746. [PMID: 36551175 PMCID: PMC9775142 DOI: 10.3390/biom12121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Protein self-assembly into fibrils and oligomers plays a key role in the etiology of degenerative diseases. Several pathways for this self-assembly process have been described and shown to result in different types and ratios of final assemblies, therewith defining the effective physiological response. Known factors that influence assembly pathways are chemical conditions and the presence or lack of agitation. However, in natural and industrial systems, proteins are exposed to a sequence of different and often complex mass transfers. In this paper, we compare the effect of two fundamentally different mass transfer processes on the fibrilization process. Aggregation-prone solutions of hen egg white lysozyme were subjected to predominantly non-advective mass transfer by employing centrifugation and to advective mass transport represented by orbital shaking. In both cases, fibrilization was triggered, while in quiescent only oligomers were formed. The fibrils obtained by shaking compared to fibrils obtained through centrifugation were shorter, thicker, and more rigid. They had rod-like protofibrils as building blocks and a significantly higher β-sheet content was observed. In contrast, fibrils from centrifugation were more flexible and braided. They consisted of intertwined filaments and had low β-sheet content at the expense of random coil. To the best of our knowledge, this is the first evidence of a fibrilization pathway selectivity, with the fibrilization route determined by the mass transfer and mixing configuration (shaking versus centrifugation). This selectivity can be potentially employed for directed protein fibrilization.
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Affiliation(s)
- Marzena Krzek
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sander Stroobants
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Pierre Gelin
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Wim De Malsche
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Correspondence:
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12
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Diaz-Parga P, Gould A, de Alba E. Natural and engineered inflammasome adapter proteins reveal optimum linker length for self-assembly. J Biol Chem 2022; 298:102501. [PMID: 36116550 PMCID: PMC9640978 DOI: 10.1016/j.jbc.2022.102501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The inflammasome is a multiprotein complex that triggers the activation of proinflammatory cytokines. The adapter ASC and its isoform ASCb mediate inflammasome assembly via self-association and oligomerization with other inflammasome proteins by homotypic interactions of their two identical Death Domains, PYD and CARD, connected by a linker of different length: 23 (ASC) and 4 (ASCb) amino acids long. However, ASC is a more potent inflammasome activator compared to ASCb. Thus, adapter isoforms might be involved in the regulation of the inflammatory response. As previously reported, ASC's faster and less polydisperse self-association compared to ASCb points to interdomain flexibility resulting from the linker length as a key factor in inflammasome regulation. To test the influence of linker length in self-association, we have engineered the isoform ASC3X with identical PYD and CARD connected by a 69 amino acid-long linker (i.e., three-times longer than ASC's linker). Real-time NMR and dynamic light scattering data indicate that ASC3X polymerization is less effective and more polydisperse compared to ASC or ASCb. However, transmission electron micrographs show that ASC3X can polymerize into filaments. Comparative interdomain dynamics of the three isoforms obtained from NMR relaxation data reveal that ASCb tumbles as a rod, whereas the PYD and CARD of ASC and ASC3X tumble independently with marginally higher interdomain flexibility in ASC3X. Altogether, our data suggest that ASC's linker length is optimized for self-association by allowing enough flexibility to favor intermolecular homotypic interactions but simultaneously keeping both domains sufficiently close for essential participation in filament formation.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA; Quantitative Systems Biology PhD Program, University of California Merced, California, USA
| | - Andrea Gould
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA.
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13
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Turbant F, Waeytens J, Campidelli C, Bombled M, Martinez D, Grélard A, Habenstein B, Raussens V, Velez M, Wien F, Arluison V. Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq. Int J Mol Sci 2022; 23:ijms23158739. [PMID: 35955871 PMCID: PMC9369112 DOI: 10.3390/ijms23158739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Camille Campidelli
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Marianne Bombled
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie, 2, Cantoblanco, E-28049 Madrid, Spain
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR SDV, Université Paris Cité, 75006 Paris, France
- Correspondence: (F.W.); (V.A.)
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14
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Zwierzchowski-Zarate AN, Mendoza-Oliva A, Kashmer OM, Collazo-Lopez JE, White CL, Diamond MI. RNA induces unique tau strains and stabilizes Alzheimer's disease seeds. J Biol Chem 2022; 298:102132. [PMID: 35700826 PMCID: PMC9364032 DOI: 10.1016/j.jbc.2022.102132] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Tau aggregation underlies neurodegenerative tauopathies, and trans-cellular propagation of tau assemblies of unique structure, i.e. strains, may underlie the diversity of these disorders. Polyanions have been reported to induce tau aggregation in vitro, but the precise trigger to convert tau from an inert to a seed-competent form in disease states is unknown. RNA triggers tau fibril formation in vitro and has been observed to associate with neurofibrillary tangles in human brain. Here we have tested whether RNA exerts sequence-specific effects on tau assembly and strain formation. We found that three RNA homopolymers, polyA, polyU, and polyC, all bound tau, but only polyA RNA triggered seed and fibril formation. In addition, polyA:tau seeds and fibrils were sensitive to RNase. We also observed that the origin of the RNA influenced the ability of tau to adopt a structure that would form stable strains. Human RNA potently induced tau seed formation and created tau conformations that preferentially formed stable strains in a HEK293T cell model, whereas RNA from other sources, or heparin, produced strains that were not stably maintained in cultured cells. Finally, we found that soluble, but not insoluble seeds from Alzheimer's disease (AD) brain were also sensitive to RNase. We conclude that human RNA specifically induces formation of stable tau strains, and may trigger the formation of dominant pathological assemblies that propagate in AD, and possibly other tauopathies.
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Affiliation(s)
- Amy N Zwierzchowski-Zarate
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Aydé Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Josue E Collazo-Lopez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Charles L White
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA.
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15
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Mondino S, San Martin F, Buschiazzo A. 3D cryo-electron microscopic imaging of bacterial flagella: novel structural and mechanistic insights into cell motility. J Biol Chem 2022; 298:102105. [PMID: 35671822 PMCID: PMC9254593 DOI: 10.1016/j.jbc.2022.102105] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022] Open
Abstract
Bacterial flagella are nanomachines that enable cells to move at high speeds. Comprising ≳25 different types of proteins, the flagellum is a large supramolecular assembly organized into three widely conserved substructures: a basal body including the rotary motor, a connecting hook, and a long filament. The whole flagellum from Escherichia coli weighs ∼20 MDa, without considering its filament portion, which is by itself a ∼1.6 GDa structure arranged as a multimer of ∼30,000 flagellin protomers. Breakthroughs regarding flagellar structure and function have been achieved in the last few years, mainly due to the revolutionary improvements in 3D cryo-electron microscopy methods. This review discusses novel structures and mechanistic insights derived from such high-resolution studies, advancing our understanding of each one of the three major flagellar segments. The rotation mechanism of the motor has been unveiled with unprecedented detail, showing a two-cogwheel machine propelled by a Brownian ratchet device. Additionally, by imaging the flagellin-like protomers that make up the hook in its native bent configuration, their unexpected conformational plasticity challenges the paradigm of a two-state conformational rearrangement mechanism for flagellin-fold proteins. Finally, imaging of the filaments of periplasmic flagella, which endow Spirochete bacteria with their singular motility style, uncovered a strikingly asymmetric protein sheath that coats the flagellin core, challenging the view of filaments as simple homopolymeric structures that work as freely whirling whips. Further research will shed more light on the functional details of this amazing nanomachine, but our current understanding has definitely come a long way.
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Affiliation(s)
- Sonia Mondino
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay
| | - Fabiana San Martin
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay; Microbiology Department, Institut Pasteur, Paris, France.
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16
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Javitt G, Fass D. Helical self-assembly of a mucin segment suggests an evolutionary origin for von Willebrand factor tubules. Proc Natl Acad Sci U S A 2022; 119:e2116790119. [PMID: 35377815 DOI: 10.1073/pnas.2116790119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Extracellular proteins with mechanical functions often require specialized assembly processes to form covalent oligomers. Progress in tissue bioengineering and repair will benefit from an understanding of how to harness and manipulate these processes. Here, we show that a particular supramolecular assembly mode was pre-encoded in the ancient domain organization common to gel-forming mucins and von Willebrand factor, glycoproteins that are deceptively different due to their divergence for distinct mechanical tasks. This finding highlights symmetry principles and building blocks retooled in nature to construct polymers with wide-ranging properties. These building blocks and knowledge of their self-assembly can be used to design new polymeric structures. The glycoprotein von Willebrand factor (VWF) contributes to hemostasis by stanching injuries in blood vessel walls. A distinctive feature of VWF is its assembly into long, helical tubules in endothelial cells prior to secretion. When VWF is released into the bloodstream, these tubules unfurl to release linear polymers that bind subendothelial collagen at wound sites, recruit platelets, and initiate the clotting cascade. VWF evolved from gel-forming mucins, the polymeric glycoproteins that coat and protect exposed epithelia. Despite the divergent function of VWF in blood vessel repair, sequence conservation and shared domain organization imply that VWF retained key aspects of the mucin bioassembly mechanism. Here, we show using cryo-electron microscopy that the ability to form tubules, a property hitherto thought to have arisen as a VWF adaptation to the vasculature, is a feature of the amino-terminal region of mucin. This segment of the human intestinal gel-forming mucin (MUC2) was found to self-assemble into tubules with a striking resemblance to those of VWF itself. To facilitate a comparison, we determined the residue-resolution structure of tubules formed by the homologous segment of VWF. The structures of the MUC2 and VWF tubules revealed the flexible joints and the intermolecular interactions required for tubule formation. Steric constraints in full-length MUC2 suggest that linear filaments, a previously observed supramolecular assembly form, are more likely than tubules to be the physiological mucin storage intermediate. Nevertheless, MUC2 tubules indicate a possible evolutionary origin for VWF tubules and elucidate design principles present in mucins and VWF.
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17
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Côté-Cyr M, Zottig X, Gauthier L, Archambault D, Bourgault S. Self-Assembly of Flagellin into Immunostimulatory Ring-like Nanostructures as an Antigen Delivery System. ACS Biomater Sci Eng 2022; 8:694-707. [PMID: 35080372 DOI: 10.1021/acsbiomaterials.1c01332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteinaceous nanoparticles represent attractive antigen carriers for vaccination as their size and repetitive antigen displays that mimic most viral particles enable efficient immune processing. However, these nanocarriers are often unable to stimulate efficiently the innate immune system, requiring coadministration with adjuvants to promote long-lasting protective immunity. The protein flagellin, which constitutes the primary constituent of the bacterial flagellum, has been widely evaluated as an antigen carrier due to its intrinsic adjuvant properties involving activation of the innate immune receptor Toll-like receptor 5 (TLR5). Although flagellin is known for its ability to self-assemble into micron-scale length nanotubes, few studies have evaluated the potential usage of flagellin-based nanostructures as immunostimulatory antigen carriers. In this study, we reported for the first time a strategy to guide the self-assembly of a flagellin protein from Bacillus subtilis, Hag, into lower aspect ratio nanoparticles by hindering non-covalent interactions responsible for its elongation into nanotubes. We observed that addition of an antigenic sequence derived from the influenza A virus (3M2e) at the C-terminus of this flagellin, as opposed to positioning the epitope into mid-sequence, precluded filament elongation and resulted in low aspect ratio ring-like nanostructures upon salting-out-induced self-assembly. These nanostructures displayed the antigen at their surface and shared morphological and structural characteristics with flagellin nanotubes, with a diameter of approximately 12 nm, and an α-helix-rich secondary structure. Flagellin ring-like nanostructures were efficiently internalized by antigen-presenting cells, and avidly activated the TLR5 in vitro as well as the innate and adaptive immune responses. Intranasal immunization of mice with these nanostructures resulted in the potentiation of the antigen-specific antibody response and protection against a lethal infection with the influenza A virus, illustrating the potential of these intrinsically immunostimulatory nanostructures as antigen carriers.
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Affiliation(s)
- Mélanie Côté-Cyr
- Chemistry Department, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec G1V 0A6, Canada.,Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Saint-Hyacinthe J2S 2M2, Canada
| | - Ximena Zottig
- Chemistry Department, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec G1V 0A6, Canada.,Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Saint-Hyacinthe J2S 2M2, Canada
| | - Laurie Gauthier
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec G1V 0A6, Canada.,Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Saint-Hyacinthe J2S 2M2, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Saint-Hyacinthe J2S 2M2, Canada
| | - Steve Bourgault
- Chemistry Department, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec G1V 0A6, Canada.,The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Saint-Hyacinthe J2S 2M2, Canada
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18
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Rashidinejad A, Jameson GB, Singh H. The Effect of pH and Sodium Caseinate on the Aqueous Solubility, Stability, and Crystallinity of Rutin towards Concentrated Colloidally Stable Particles for the Incorporation into Functional Foods. Molecules 2022; 27:534. [PMID: 35056844 DOI: 10.3390/molecules27020534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
Poor water solubility and low bioavailability of hydrophobic flavonoids such as rutin remain as substantial challenges to their oral delivery via functional foods. In this study, the effect of pH and the addition of a protein (sodium caseinate; NaCas) on the aqueous solubility and stability of rutin was studied, from which an efficient delivery system for the incorporation of rutin into functional food products was developed. The aqueous solubility, chemical stability, crystallinity, and morphology of rutin (0.1–5% w/v) under various pH (1–11) and protein concentrations (0.2–8% w/v) were studied. To manufacture the concentrated colloidally stable rutin–NaCas particles, rutin was dissolved and deprotonated in a NaCas solution at alkaline pH before its subsequent neutralisation at pH 7. The excess water was removed using ultrafiltration to improve the loading capacity. Rutin showed the highest solubility at pH 11, while the addition of NaCas resulted in the improvement of both solubility and chemical stability. Critically, to achieve particles with colloidal stability, the NaCas:rutin ratio (w/w) had to be greater than 2.5 and 40 respectively for the lowest (0.2% w/v) and highest (4 to 8% w/v) concentrations of NaCas. The rutin–NaCas particles in the concentrated formulations were physically stable, with a size in the range of 185 to 230 nm and zeta potential of −36.8 to −38.1 mV, depending on the NaCas:rutin ratio. Encapsulation efficiency and loading capacity of rutin in different systems were 76% to 83% and 2% to 22%, respectively. The concentrated formulation containing 5% w/v NaCas and 2% w/v rutin was chosen as the most efficient delivery system due to the ideal protein:flavonoid ratio (2.5:1), which resulted in the highest loading capacity (22%). Taken together, the findings show that the delivery system developed in this study can be a promising method for the incorporation of a high concentration of hydrophobic flavonoids such as rutin into functional foods.
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19
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Paiz EA, Allen JH, Correia JJ, Fitzkee NC, Hough LE, Whitten ST. Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. J Biol Chem 2021; 297:101343. [PMID: 34710373 PMCID: PMC8592878 DOI: 10.1016/j.jbc.2021.101343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
The complex cellular milieu can spontaneously demix, or phase separate, in a process controlled in part by intrinsically disordered (ID) proteins. A protein's propensity to phase separate is thought to be driven by a preference for protein-protein over protein-solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesized that mean v, as predicted by protein sequence, would be smaller for proteins with a strong propensity to phase separate. To test this hypothesis, we analyzed protein databases containing subsets of proteins that are folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase-separating disordered proteins, on average, had lower calculated values of v compared with their non-phase-separating counterparts. Moreover, these proteins had a higher sequence-predicted propensity for β-turns. Using a simple, surface area-based model, we propose a physical mechanism for this difference: transient β-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in π/sp2 valence electron interactions. By this mechanism, β-turns could act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) utilized biologically for phase separation. Phase-separating IDRs, non-phase-separating IDRs, and folded regions could be distinguished by combining v and β-turn propensity. Finally, we propose a new algorithm, ParSe (partition sequence), for predicting phase-separating protein regions, and which is able to accurately identify folded, disordered, and phase-separating protein regions based on the primary sequence.
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Affiliation(s)
- Elisia A Paiz
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Jeffre H Allen
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA.
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20
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Dannenmaier S, Desroches Altamirano C, Schüler L, Zhang Y, Hummel J, Milanov M, Oeljeklaus S, Koch HG, Rospert S, Alberti S, Warscheid B. Quantitative proteomics identifies the universally conserved ATPase Ola1p as a positive regulator of heat shock response in Saccharomyces cerevisiae. J Biol Chem 2021; 297:101050. [PMID: 34571008 PMCID: PMC8531669 DOI: 10.1016/j.jbc.2021.101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/24/2021] [Accepted: 08/04/2021] [Indexed: 12/02/2022] Open
Abstract
The universally conserved P-loop ATPase Ola1 is implicated in various cellular stress response pathways, as well as in cancer and tumor progression. However, Ola1p functions are divergent between species, and the involved mechanisms are only poorly understood. Here, we studied the role of Ola1p in the heat shock response of the yeast Saccharomyces cerevisiae using a combination of quantitative and pulse labeling-based proteomics approaches, in vitro studies, and cell-based assays. Our data show that when heat stress is applied to cells lacking Ola1p, the expression of stress-protective proteins is enhanced. During heat stress Ola1p associates with detergent-resistant protein aggregates and rapidly forms assemblies that localize to stress granules. The assembly of Ola1p was also observed in vitro using purified protein and conditions, which resembled those in living cells. We show that loss of Ola1p results in increased protein ubiquitination of detergent-insoluble aggregates recovered from heat-shocked cells. When cells lacking Ola1p were subsequently relieved from heat stress, reinitiation of translation was delayed, whereas, at the same time, de novo synthesis of central factors required for protein refolding and the clearance of aggregates was enhanced when compared with wild-type cells. The combined data suggest that upon acute heat stress, Ola1p is involved in the stabilization of misfolded proteins, which become sequestered in cytoplasmic stress granules. This function of Ola1p enables cells to resume translation in a timely manner as soon as heat stress is relieved.
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Affiliation(s)
- Stefan Dannenmaier
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Lisa Schüler
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ying Zhang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Hummel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Simon Alberti
- BIOTEC and CMCB, Technische Universität Dresden, Dresden, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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21
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Harkness RW, Toyama Y, Ripstein ZA, Zhao H, Sever AIM, Luan Q, Brady JP, Clark PL, Schuck P, Kay LE. Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP. Proc Natl Acad Sci U S A 2021. [PMID: 34362850 DOI: proc/self/fd/32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.
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Affiliation(s)
- Robert W Harkness
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Yuki Toyama
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Zev A Ripstein
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Huaying Zhao
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
| | - Alexander I M Sever
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Qing Luan
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jacob P Brady
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Patricia L Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Peter Schuck
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
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22
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Harkness RW, Toyama Y, Ripstein ZA, Zhao H, Sever AIM, Luan Q, Brady JP, Clark PL, Schuck P, Kay LE. Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP. Proc Natl Acad Sci U S A 2021; 118:e2109732118. [PMID: 34362850 DOI: 10.1073/pnas.2109732118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.
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23
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Kamps J, Lin YH, Oliva R, Bader V, Winter R, Winklhofer KF, Tatzelt J. The N-terminal domain of the prion protein is required and sufficient for liquid-liquid phase separation: A crucial role of the Aβ-binding domain. J Biol Chem 2021; 297:100860. [PMID: 34102212 PMCID: PMC8254114 DOI: 10.1016/j.jbc.2021.100860] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/26/2022] Open
Abstract
Formation of biomolecular condensates through liquid–liquid phase separation (LLPS) has been described for several pathogenic proteins linked to neurodegenerative diseases and is discussed as an early step in the formation of protein aggregates with neurotoxic properties. In prion diseases, neurodegeneration and formation of infectious prions is caused by aberrant folding of the cellular prion protein (PrPC). PrPC is characterized by a large intrinsically disordered N-terminal domain and a structured C-terminal globular domain. A significant fraction of mature PrPC is proteolytically processed in vivo into an entirely unstructured fragment, designated N1, and the corresponding C-terminal fragment C1 harboring the globular domain. Notably, N1 contains a polybasic motif that serves as a binding site for neurotoxic Aβ oligomers. PrP can undergo LLPS; however, nothing is known how phase separation of PrP is triggered on a molecular scale. Here, we show that the intrinsically disordered N1 domain is necessary and sufficient for LLPS of PrP. Similar to full-length PrP, the N1 fragment formed highly dynamic liquid-like droplets. Remarkably, a slightly shorter unstructured fragment, designated N2, which lacks the Aβ-binding domain and is generated under stress conditions, failed to form liquid-like droplets and instead formed amorphous assemblies of irregular structures. Through a mutational analysis, we identified three positively charged lysines in the postoctarepeat region as essential drivers of condensate formation, presumably largely via cation–π interactions. These findings provide insights into the molecular basis of LLPS of the mammalian prion protein and reveal a crucial role of the Aβ-binding domain in this process.
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Affiliation(s)
- Janine Kamps
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany; Cluster of Excellence RESOLV, Ruhr University Bochum, Bochum, Germany
| | - Yu-Hsuan Lin
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Division of Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Verian Bader
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Roland Winter
- Cluster of Excellence RESOLV, Ruhr University Bochum, Bochum, Germany; Division of Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Konstanze F Winklhofer
- Cluster of Excellence RESOLV, Ruhr University Bochum, Bochum, Germany; Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany; Cluster of Excellence RESOLV, Ruhr University Bochum, Bochum, Germany.
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24
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Tang J, Liu Y, Qi D, Yang L, Chen H, Wang C, Feng X. Nucleus-Targeted Delivery of Multi- Protein Self-Assembly for Combined Anticancer Therapy. Small 2021; 17:e2101219. [PMID: 34028978 DOI: 10.1002/smll.202101219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Protein therapy has the potential to revolutionize medicine, but the delivery of multiple proteins is challenging because it requires the development of a strategy that enables different proteins to be combined together and transported not only into cells, but also to the desired cell compartments, such as the nucleus. Here, an efficient intranuclear protein delivery nanoplatform based on modified ribonuclease A (RNase A) tuned self-assembly is presented. RNase A bioreversibly modified with adamantane is functionalized with wind chime-like lysine modified cyclodextrin (WLC) to generate RNase A-WLC (R-WLC). R-WLC can not only enhance the cellular uptake of RNase A and accumulate it into the nucleus, but also works as nanovehicles to efficiently transport deoxyribonuclease I (DNase I) into the nucleus, resulting in greatly improved antitumor efficacy in vitro and in vivo. This protein co-assembly strategy can be applied to other functional proteins and has great prospects in the treatment of many diseases.
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Affiliation(s)
- Jiakun Tang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Ye Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Dongmei Qi
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Lan Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Hui Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Chenhui Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Xuli Feng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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25
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Li R, Xu J, Wang T, Wang L, Li F, Liu S, Jiang X, Luo Q, Liu J. Dynamically Tunable Ultrathin Protein Membranes for Controlled Molecular Separation. ACS Appl Mater Interfaces 2021; 13:12359-12365. [PMID: 33666409 DOI: 10.1021/acsami.0c21817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developing the ultrathin membranes for high-performance separation still faces the challenge of both high permeance and selectivity. Herein, a large-area protein membrane was fabricated by the interfacial self-assembly of bovine serum albumin (BSA) and surfactants at the oil/water interface of emulsions. Benefiting from the ultrathin thickness and unique protein-surrounded tortuous channels, the membrane displays ultrahigh permeation flux and selective sieving capability for various molecules ranging from small dye molecules to proteins based on a dual filtration mechanism. More importantly, the rejection precision can also be reversibly regulated by the folding/unfolding transition of proteins to control the effective pore size of transport channels, even under a pressure-driven condition. This dynamically tunable ultrathin protein membrane combines the advantages of high permeance, selectivity, controllability, recyclability, and mechanical stability, which may create new opportunities for advanced applications in extended fields.
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Affiliation(s)
- Ruyu Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 310000, China
| | - Tingting Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Liang Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shengda Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xiaojia Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 310000, China
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26
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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27
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Chakraborty R, Fan JS, Lai CC, Raghuvamsi PV, Chee PX, Anand GS, Yang D. Structural Basis of Oligomerization of N-Terminal Domain of Spider Aciniform Silk Protein. Int J Mol Sci 2020; 21:ijms21124466. [PMID: 32586030 PMCID: PMC7352312 DOI: 10.3390/ijms21124466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/28/2023] Open
Abstract
Spider silk is self-assembled from water-soluble silk proteins through changes in the environment, including pH, salt concentrations, and shear force. The N-terminal domains of major and minor ampullate silk proteins have been found to play an important role in the assembly process through salt- and pH-dependent dimerization. Here, we identified the sequences of the N-terminal domains of aciniform silk protein (AcSpN) and major ampullate silk protein (MaSpN) from Nephila antipodiana (NA). Different from MaSpN, our biophysical characterization indicated that AcSpN assembles to form large oligomers, instead of a dimer, upon condition changes from neutral to acidic pH and/or from a high to low salt concentration. Our structural studies, by nuclear magnetic resonance spectroscopy and homology modelling, revealed that AcSpN and MaSpN monomers adopt similar overall structures, but have very different charge distributions contributing to the differential self-association features. The intermolecular interaction interfaces for AcSp oligomers were identified using hydrogen–deuterium exchange mass spectrometry and mutagenesis. On the basis of the monomeric structure and identified interfaces, the oligomeric structures of AcSpN were modelled. The structural information obtained will facilitate an understanding of silk fiber formation mechanisms for aciniform silk protein.
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Chen YX, Ing NL, Wang F, Xu D, Sloan NB, Lam NT, Winter DL, Egelman EH, Hochbaum AI, Clark DS, Glover DJ. Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires. ACS Nano 2020; 14:6559-6569. [PMID: 32347705 PMCID: PMC8034818 DOI: 10.1021/acsnano.9b09405] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The transfer of electrons through protein complexes is central to cellular respiration. Exploiting proteins for charge transfer in a controllable fashion has the potential to revolutionize the integration of biological systems and electronic devices. Here we characterize the structure of an ultrastable protein filament and engineer the filament subunits to create electronically conductive nanowires under aqueous conditions. Cryoelectron microscopy was used to resolve the helical structure of gamma-prefoldin, a filamentous protein from a hyperthermophilic archaeon. Conjugation of tetra-heme c3-type cytochromes along the longitudinal axis of the filament created nanowires capable of long-range electron transfer. Electrochemical transport measurements indicated networks of the nanowires capable of conducting current between electrodes at the redox potential of the cytochromes. Functionalization of these highly engineerable nanowires with other molecules, such as redox enzymes, may be useful for bioelectronic applications.
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Affiliation(s)
- Yun X. Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicole L. Ing
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Nancy B. Sloan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Nga T. Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Allon I. Hochbaum
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominic J. Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Sun H, Li Y, Yu S, Liu J. Hierarchical Self-Assembly of Proteins Through Rationally Designed Supramolecular Interfaces. Front Bioeng Biotechnol 2020; 8:295. [PMID: 32426335 PMCID: PMC7212437 DOI: 10.3389/fbioe.2020.00295] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022] Open
Abstract
With the increasing advances in the basic understanding of pathogenesis mechanism and fabrication of advanced biological materials, protein nanomaterials are being developed for their potential bioengineering research and biomedical applications. Among different fabrication strategies, supramolecular self-assembly provides a versatile approach to construct hierarchical nanostructures from polyhedral cages, filaments, tubules, monolayer sheets to even cubic crystals through rationally designed supramolecular interfaces. In this mini review, we will briefly recall recent progress in reconstituting protein interfaces for hierarchical self-assembly and classify by the types of designed protein-protein interactions into receptor-ligand recognition, electrostatic interaction, metal coordination, and non-specific interaction networks. Moreover, some attempts on functionalization of protein superstructures for bioengineering and/or biomedical applications are also shortly discussed. We believe this mini review will outline the stream of hierarchical self-assembly of proteins through rationally designed supramolecular interfaces, which would open minds in visualizing protein-protein recognition and assembly in living cells and organisms, and even constructing multifarious functional bionanomaterials.
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Affiliation(s)
- Hongcheng Sun
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Yan Li
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, China
| | - Shuangjiang Yu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Junqiu Liu
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
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30
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Kepiro IE, Nardone B, Page A, Ryadnov MG. Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy. Micromachines (Basel) 2020; 11:E251. [PMID: 32120860 DOI: 10.3390/mi11030251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.
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31
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Li Y, Ramachandran S, Nguyen TTT, Stalnecker CA, Cerione RA, Erickson JW. The activation loop and substrate-binding cleft of glutaminase C are allosterically coupled. J Biol Chem 2020; 295:1328-1337. [PMID: 31871054 DOI: 10.1074/jbc.ra119.010314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/12/2019] [Indexed: 11/06/2022] Open
Abstract
The glutaminase C (GAC) isoform of mitochondrial glutaminase is overexpressed in many cancer cells and therefore represents a potential therapeutic target. Understanding the regulation of GAC activity has been guided by the development of spectroscopic approaches that measure glutaminase activity in real time. Previously, we engineered a GAC protein (GAC(F327W)) in which a tryptophan residue is substituted for phenylalanine in an activation loop to explore the role of this loop in enzyme activity. We showed that the fluorescence emission of Trp-327 is enhanced in response to activator binding, but quenched by inhibitors of the BPTES class that bind to the GAC tetramer and contact the activation loop, thereby constraining it in an inactive conformation. In the present work, we took advantage of a tryptophan substitution at position 471, proximal to the GAC catalytic site, to examine the conformational coupling between the activation loop and the substrate-binding cleft, separated by ∼16 Å. Comparison of glutamine binding in the presence or absence of the BPTES analog CB-839 revealed a reciprocal relationship between the constraints imposed on the activation loop position and the affinity of GAC for substrate. Binding of the inhibitor weakened the affinity of GAC for glutamine, whereas activating anions such as Pi increased this affinity. These results indicate that the conformations of the activation loop and the substrate-binding cleft in GAC are allosterically coupled and that this coupling determines substrate affinity and enzymatic activity and explains the activities of CB-839, which is currently in clinical trials.
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Affiliation(s)
- Yunxing Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Sekar Ramachandran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853.,Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Thuy-Tien T Nguyen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Clint A Stalnecker
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 .,Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Jon W Erickson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853.,Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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Herrmann J, Li PN, Jabbarpour F, Chan ACK, Rajkovic I, Matsui T, Shapiro L, Smit J, Weiss TM, Murphy MEP, Wakatsuki S. A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly. Proc Natl Acad Sci U S A 2020; 117:388-94. [PMID: 31848245 DOI: 10.1073/pnas.1909798116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Many microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell, and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multistep pathway involving a crystalline intermediate. Upon calcium binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle X-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization. Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the Caulobacter crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multistep assembly pathway. This pathway involves 2 domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2-dimensional (2D) crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using a time course of electron cryo-microscopy (Cryo-EM) imaging reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the 2 domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.
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Levenson R, Bracken C, Sharma C, Santos J, Arata C, Malady B, Morse DE. Calibration between trigger and color: Neutralization of a genetically encoded coulombic switch and dynamic arrest precisely tune reflectin assembly. J Biol Chem 2019; 294:16804-16815. [PMID: 31558609 DOI: 10.1074/jbc.ra119.010339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Indexed: 12/28/2022] Open
Abstract
Reflectin proteins are widely distributed in reflective structures in cephalopods. However, only in loliginid squids are they and the subwavelength photonic structures they control dynamically tunable, driving changes in skin color for camouflage and communication. The reflectins are block copolymers with repeated canonical domains interspersed with cationic linkers. Neurotransmitter-activated signal transduction culminates in catalytic phosphorylation of the tunable reflectins' cationic linkers; the resulting charge neutralization overcomes coulombic repulsion to progressively allow condensation, folding, and assembly into multimeric spheres of tunable well-defined size and low polydispersity. Here, we used dynamic light scattering, transmission EM, CD, atomic force microscopy, and fluorimetry to analyze the structural transitions of reflectins A1 and A2. We also analyzed the assembly behavior of phosphomimetic, deletion, and other mutants in conjunction with pH titration as an in vitro surrogate of phosphorylation. Our experiments uncovered a previously unsuspected, precisely predictive relationship between the extent of neutralization of a reflectin's net charge density and the size of resulting multimeric protein assemblies of narrow polydispersity. Comparisons of mutants revealed that this sensitivity to neutralization resides in the linkers and is spatially distributed along the protein. Imaging of large particles and analysis of sequence composition suggested that assembly may proceed through a dynamically arrested liquid-liquid phase-separated intermediate. Intriguingly, it is this dynamic arrest that enables the observed fine-tuning by charge and the resulting calibration between neuronal trigger and color in the squid. These results offer insights into the basis of reflectin-based biophotonics, opening paths for the design of new materials with tunable properties.
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Affiliation(s)
- Robert Levenson
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Colton Bracken
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Cristian Sharma
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Jerome Santos
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Claire Arata
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Brandon Malady
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
| | - Daniel E Morse
- Department of Molecular, Cellular and Developmental Biology and the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100
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Nesterenko Y, Hill CJ, Fleming JR, Murray P, Mayans O. The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications. Int J Mol Sci 2019; 20:E4299. [PMID: 31484291 PMCID: PMC6747707 DOI: 10.3390/ijms20174299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
The development of cell culture systems for the naturalistic propagation, self-renewal and differentiation of cells ex vivo is a high goal of molecular engineering. Despite significant success in recent years, the high cost of up-scaling cultures, the need for xeno-free culture conditions, and the degree of mimicry of the natural extracellular matrix attainable in vitro using designer substrates continue to pose obstacles to the translation of cell-based technologies. In this regard, the ZT biopolymer is a protein-based, stable, scalable, and economical cell substrate of high promise. ZT is based on the naturally occurring assembly of two human proteins: titin-Z1Z2 and telethonin. These protein building blocks are robust scaffolds that can be conveniently functionalized with full-length proteins and bioactive peptidic motifs by genetic manipulation, prior to self-assembly. The polymer is, thereby, fully encodable. Functionalized versions of the ZT polymer have been shown to successfully sustain the long-term culturing of human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs), and murine mesenchymal stromal cells (mMSCs). Pluripotency of hESCs and hiPSCs was retained for the longest period assayed (4 months). Results point to the large potential of the ZT system for the creation of a modular, pluri-functional biomaterial for cell-based applications.
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Affiliation(s)
| | - Christopher J Hill
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | | | - Patricia Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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35
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Muñoz-Juan A, Carreño A, Mendoza R, Corchero JL. Latest Advances in the Development of Eukaryotic Vaults as Targeted Drug Delivery Systems. Pharmaceutics 2019; 11:E300. [PMID: 31261673 PMCID: PMC6680493 DOI: 10.3390/pharmaceutics11070300] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 12/04/2022] Open
Abstract
The use of smart drug delivery systems (DDSs) is one of the most promising approaches to overcome some of the drawbacks of drug-based therapies, such as improper biodistribution and lack of specific targeting. Some of the most attractive candidates as DDSs are naturally occurring, self-assembling protein nanoparticles, such as viruses, virus-like particles, ferritin cages, bacterial microcompartments, or eukaryotic vaults. Vaults are large ribonucleoprotein nanoparticles present in almost all eukaryotic cells. Expression in different cell factories of recombinant versions of the "major vault protein" (MVP) results in the production of recombinant vaults indistinguishable from native counterparts. Such recombinant vaults can encapsulate virtually any cargo protein, and they can be specifically targeted by engineering the C-terminus of MVP monomer. These properties, together with nanometric size, a lumen large enough to accommodate cargo molecules, biodegradability, biocompatibility and no immunogenicity, has raised the interest in vaults as smart DDSs. In this work we provide an overview of eukaryotic vaults as a new, self-assembling protein-based DDS, focusing in the latest advances in the production and purification of this platform, its application in nanomedicine, and the current preclinical and clinical assays going on based on this nanovehicle.
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Affiliation(s)
- Amanda Muñoz-Juan
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aida Carreño
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rosa Mendoza
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - José L Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain.
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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36
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Abstract
The synaptonemal complex (SC) is a supramolecular protein assembly that mediates homologous chromosome synapsis during meiosis. This zipper-like structure assembles in a continuous manner between homologous chromosome axes, enforcing a 100-nm separation along their entire length and providing the necessary three-dimensional framework for cross-over formation. The mammalian SC comprises eight components-synaptonemal complex protein 1-3 (SYCP1-3), synaptonemal complex central element protein 1-3 (SYCE1-3), testis-expressed 12 (TEX12), and six6 opposite strand transcript 1 (SIX6OS1)-arranged in transverse and longitudinal structures. These largely α-helical, coiled-coil proteins undergo heterotypic interactions, coupled with recursive self-assembly of SYCP1, SYCE2-TEX12, and SYCP2-SYCP3, to achieve the vast supramolecular SC structure. Here, we report a novel self-assembly mechanism of the SC central element component SYCE3, identified through multi-angle light scattering and small-angle X-ray scattering (SAXS) experiments. These analyses revealed that SYCE3 adopts a dimeric four-helical bundle structure that acts as the building block for concentration-dependent self-assembly into a series of discrete higher-order oligomers. We observed that this is achieved through staggered lateral interactions between self-assembly surfaces of SYCE3 dimers and through end-on interactions that likely occur through intermolecular domain swapping between dimer folds. These mechanisms are combined to achieve potentially limitless SYCE3 assembly, particularly favoring formation of dodecamers of three laterally associated end-on tetramers. Our findings extend the family of self-assembling proteins within the SC and reveal additional means for structural stabilization of the SC central element.
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Affiliation(s)
- Orla M Dunne
- From the Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Owen R Davies
- From the Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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37
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Bulutoglu B, Macazo FC, Bale J, King N, Baker D, Minteer SD, Banta S. Multimerization of an Alcohol Dehydrogenase by Fusion to a Designed Self-Assembling Protein Results in Enhanced Bioelectrocatalytic Operational Stability. ACS Appl Mater Interfaces 2019; 11:20022-20028. [PMID: 31066271 DOI: 10.1021/acsami.9b04256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteins designed for supramolecular assembly provide a simple means to immobilize and organize enzymes for biotechnology applications. We have genetically fused the thermostable alcohol dehydrogenase D (AdhD) from Pyrococcus furiosus to a computationally designed cage-forming protein (O3-33). The trimeric form of the O3-33-AdhD fusion protein was most active in solution. The immobilization of the fusion protein on bioelectrodes leads to a doubling of the electrochemical operational stability as compared to the unfused control proteins. Thus, the fusion of enzymes to the designed self-assembling domains offers a simple strategy to increase the stability in biocatalytic systems.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering , Columbia University , New York , New York 10027 , United States
| | - Florika C Macazo
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112 , United States
| | | | | | | | - Shelley D Minteer
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112 , United States
| | - Scott Banta
- Department of Chemical Engineering , Columbia University , New York , New York 10027 , United States
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38
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Hill CJ, Fleming JR, Mousavinejad M, Nicholson R, Tzokov SB, Bullough PA, Bogomolovas J, Morgan MR, Mayans O, Murray P. Self-Assembling Proteins as High-Performance Substrates for Embryonic Stem Cell Self-Renewal. Adv Mater 2019; 31:e1807521. [PMID: 30866118 DOI: 10.1002/adma.201807521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/28/2019] [Indexed: 06/09/2023]
Abstract
The development of extracellular matrix mimetics that imitate niche stem cell microenvironments and support cell growth for technological applications is intensely pursued. Specifically, mimetics are sought that can enact control over the self-renewal and directed differentiation of human pluripotent stem cells (hPSCs) for clinical use. Despite considerable progress in the field, a major impediment to the clinical translation of hPSCs is the difficulty and high cost of large-scale cell production under xeno-free culture conditions using current matrices. Here, a bioactive, recombinant, protein-based polymer, termed ZTFn , is presented that closely mimics human plasma fibronectin and serves as an economical, xeno-free, biodegradable, and functionally adaptable cell substrate. The ZTFn substrate supports with high performance the propagation and long-term self-renewal of human embryonic stem cells while preserving their pluripotency. The ZTFn polymer can, therefore, be proposed as an efficient and affordable replacement for fibronectin in clinical grade cell culturing. Further, it can be postulated that the ZT polymer has significant engineering potential for further orthogonal functionalization in complex cell applications.
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Affiliation(s)
- Christopher J Hill
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Nuffield Building, Crown Street, Liverpool, L69 3BX, UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | | | - Masoumeh Mousavinejad
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Nuffield Building, Crown Street, Liverpool, L69 3BX, UK
| | - Rachael Nicholson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Nuffield Building, Crown Street, Liverpool, L69 3BX, UK
| | - Svetomir B Tzokov
- Department of Molecular Biology and Biotechnology, The Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Per A Bullough
- Department of Molecular Biology and Biotechnology, The Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Julius Bogomolovas
- Department of Medicine, UCSD, La Jolla, CA, 92093, USA
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Mark R Morgan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Nuffield Building, Crown Street, Liverpool, L69 3BX, UK
| | - Olga Mayans
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Patricia Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Nuffield Building, Crown Street, Liverpool, L69 3BX, UK
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Pedchenko V, Bauer R, Pokidysheva EN, Al-Shaer A, Forde NR, Fidler AL, Hudson BG, Boudko SP. A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes. J Biol Chem 2019; 294:7968-7981. [PMID: 30923125 PMCID: PMC6527180 DOI: 10.1074/jbc.ra119.007426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
Collagen IV scaffold is a principal component of the basement membrane (BM), a specialized extracellular matrix that is essential for animal multicellularity and tissue evolution. Scaffold assembly begins with the trimerization of α-chains into protomers inside the cell, which then are secreted and undergo oligomerization outside the cell. For the ubiquitous scaffold composed of α1- and α2-chains, both intracellular and extracellular stages are mediated by the noncollagenous domain (NC1). The association of protomers is chloride-dependent, whereby chloride ions induce interactions of the protomers' trimeric NC1 domains leading to NC1 hexamer formation. Here, we investigated the mechanisms, kinetics, and functionality of the chloride ion-mediated protomer assembly by using a single-chain technology to produce a stable NC1 trimer comprising α1, α2, and α1 NC1 monomers. We observed that in the presence of chloride, the single-chain NC1-trimer self-assembles into a hexamer, for which the crystal structure was determined. We discovered that a chloride ring, comprising 12 ions, induces the assembly of and stabilizes the NC1 hexamer. Furthermore, we found that the chloride ring is evolutionarily conserved across all animals, first appearing in cnidarians. These findings reveal a fundamental role for the chloride ring in the assembly of collagen IV scaffolds of BMs, a critical event enabling tissue evolution and development. Moreover, the single-chain technology is foundational for generating trimeric NC1 domains of other α-chain compositions to investigate the α121, α345, and α565 collagen IV scaffolds and to develop therapies for managing Alport syndrome, Goodpasture's disease, and cancerous tumor growth.
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Affiliation(s)
- Vadim Pedchenko
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Ryan Bauer
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Elena N Pokidysheva
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Alaa Al-Shaer
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Nancy R Forde
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Aaron L Fidler
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of AspirnautTM Program, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of AspirnautTM Program, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232; Department of Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232; Department of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
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40
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Lyon YA, Collier MP, Riggs DL, Degiacomi MT, Benesch JLP, Julian RR. Structural and functional consequences of age-related isomerization in α-crystallins. J Biol Chem 2019; 294:7546-7555. [PMID: 30804217 PMCID: PMC6514633 DOI: 10.1074/jbc.ra118.007052] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
Long-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as side-chain isomerization. Recently, tandem MS has enabled identification and characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here, we examined the impact of isomerization of aspartic acid or epimerization of serine at four sites mapping to crucial oligomeric interfaces in human αA- and αB-crystallin, the most abundant chaperone proteins in the eye lens. To characterize the effect of isomerization on quaternary assembly, we utilized synthetic peptide mimics, enzyme assays, molecular dynamics calculations, and native MS experiments. The oligomerization of recombinant forms of αA- and αB-crystallin that mimic isomerized residues deviated from native behavior in all cases. Isomerization also perturbs recognition of peptide substrates, either enhancing or inhibiting kinase activity. Specifically, epimerization of serine (αASer-162) dramatically weakened inter-subunit binding. Furthermore, phosphorylation of αBSer-59, known to play an important regulatory role in oligomerization, was severely inhibited by serine epimerization and altered by isomerization of nearby αBAsp-62. Similarly, isomerization of αBAsp-109 disrupted a vital salt bridge with αBArg-120, a contact that when broken has previously been shown to yield aberrant oligomerization and aggregation in several disease-associated variants. Our results illustrate how isomerization of amino acid residues, which may seem to be only a minor structural perturbation, can disrupt native structural interactions with profound consequences for protein assembly and activity.
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Affiliation(s)
- Yana A Lyon
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Miranda P Collier
- the Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom, and
| | - Dylan L Riggs
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Matteo T Degiacomi
- the Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Justin L P Benesch
- the Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom, and
| | - Ryan R Julian
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521,
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41
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Fitzgerald BW. The physiology of impenetrable skin: Colossus of the X-Men. Adv Physiol Educ 2018; 42:529-540. [PMID: 30192188 DOI: 10.1152/advan.00107.2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The X-Men are an ensemble of superheroes whose powers are associated with the X-Gene, a mutant genetic factor. The powers exhibited by each character differ and are dependent on how the X-Gene has modified their individual genomes. For instance, Wolverine possesses regenerative healing, Storm can control local weather systems, and Colossus can create an impenetrable "organic steel" layer around his body. Thanks to the establishment of the superhero genre in modern cinema, audiences are familiar with Colossus from films such as X-Men: Days of Future Past and Deadpool. While attaining this power might be attractive to many people, there are innumerate scientific obstacles to be overcome to replicate this "organic steel" layer. Due to its unique combination of high strength and flexibility, a graphene-based layer might be a more realistic material for Colossus' impenetrable skin and would also address a number of physiological issues associated with an "organic steel" layer. The actualization of this layer would depend on complex processes associated with protein folding, protein self-assembly, and changing the structure of his skin. In the classroom, Colossus can foster a multidisciplinary learning environment where concepts in physiology can overlap with topics in physics, engineering, and materials science. Just like other superheroes, Colossus can also be used to promote scientific content in outreach for the general public.
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Affiliation(s)
- Barry W Fitzgerald
- Intensified Reaction and Separation Systems, Department of Process and Energy, Delft University of Technology , Delft , The Netherlands
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42
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Pakharukova N, McKenna S, Tuittila M, Paavilainen S, Malmi H, Xu Y, Parilova O, Matthews S, Zavialov AV. Archaic and alternative chaperones preserve pilin folding energy by providing incomplete structural information. J Biol Chem 2018; 293:17070-17080. [PMID: 30228191 DOI: 10.1074/jbc.ra118.004170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/14/2018] [Indexed: 11/06/2022] Open
Abstract
Adhesive pili are external component of fibrous adhesive organelles and help bacteria attach to biotic or abiotic surfaces. The biogenesis of adhesive pili via the chaperone-usher pathway (CUP) is independent of external energy sources. In the classical CUP, chaperones transport assembly-competent pilins in a folded but expanded conformation. During donor-strand exchange, pilins subsequently collapse, producing a tightly packed hydrophobic core and releasing the necessary free energy to drive fiber formation. Here, we show that pilus biogenesis in non-classical, archaic, and alternative CUPs uses a different source of conformational energy. High-resolution structures of the archaic Csu-pili system from Acinetobacter baumannii revealed that non-classical chaperones employ a short donor strand motif that is insufficient to fully complement the pilin fold. This results in chaperone-bound pilins being trapped in a substantially unfolded intermediate. The exchange of this short motif with the longer donor strand from adjacent pilin provides the full steric information essential for folding, and thereby induces a large unfolded-to-folded conformational transition to drive assembly. Our findings may inform the development of anti-adhesion drugs (pilicides) to combat bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sophie McKenna
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Minna Tuittila
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sari Paavilainen
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Henri Malmi
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Yingqi Xu
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Olena Parilova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Steve Matthews
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Anton V Zavialov
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
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43
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Faltova L, Küffner AM, Hondele M, Weis K, Arosio P. Multifunctional Protein Materials and Microreactors using Low Complexity Domains as Molecular Adhesives. ACS Nano 2018; 12:9991-9999. [PMID: 30216718 DOI: 10.1021/acsnano.8b04304] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recent findings indicate that a class of disordered amino acid sequences promotes functional phase transition of biomolecules in nature. Such sequences consist of low complexity domains (LCDs) that are rich in specific amino acids. In this work, we exploit these sequences by conjugating them to soluble globular domains to develop molecular adhesives that enable sensitive, controlled self-assembly of these proteins into supramolecular architectures. In particular, we used the enzyme adenylate kinase and the green fluorescent protein as soluble domains, and we show that the addition of low complexity regions induces the formation of protein particles via a multistep process. This multistep pathway involves an initial liquid-liquid phase transition, which creates protein-rich droplets that mature into protein aggregates over time. These protein aggregates consist of permeable structures that maintain activity and release active soluble proteins. We show that the LCDs dictate specific noncovalent intermolecular interactions and phase properties that are largely independent of the given globular domain. We further demonstrate that this feature, together with the dynamic state of the initial dense liquid phase, allows one to directly assemble different globular domains within the same architecture, thereby enabling the generation of both static multifunctional biomaterials and dynamic microscale bioreactors.
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44
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Hong CS, Park JH, Lee S, Rhoo KY, Lee JT, Paik SR. Fabrication of Protease-Sensitive and Light-Responsive Microcapsules Encompassed with Single Layer of Gold Nanoparticles by Using Self-Assembly Protein of α-Synuclein. ACS Appl Mater Interfaces 2018; 10:26628-26640. [PMID: 30052414 DOI: 10.1021/acsami.8b07661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A bioapplicable cargo delivery system requires the following characteristics of biocompatibility, in vivo stability, and selective cargo release at target sites. We introduce herein the microcapsules enclosed with a single-layered shell of gold nanoparticles (AuNPs) mutually connected by an amyloidogenic protein of α-synuclein (αS). The microcapsules were fabricated by producing oil(chloroform)-in-water Pickering emulsions of the αS-encapsulated AuNPs and subsequent molecular engagement of the outlying αS molecules, leading to formidable β-sheet formation in the presence of chloroform. The wrinkled skin of microcapsules obtained after evaporation of the internal chloroform also reflects robustness of the protein-protein interaction, which was experimentally confirmed by their rheological stability. For the emulsions loaded with rhodamine 6G, their dye release was demonstrated to be controlled by proteases. Along with their photothermal activity, the AuNP-containing microcapsules and their proteolyzed fragments were therefore suggested to be capable of eliminating aberrant cells in the protease-activated pathologically affected areas. Orthogonal cargo loading was also achieved by encapsulating both hydrophobic and hydrophilic substances either directly dissolved in chloroform or prepackaged in inverted micelles, respectively. Microcapsule's functionality was further expanded by localizing quantum dots, magnetic nanoparticles, and antibodies inside or on the surface of the microcapsules. Taken together, these multimodal AuNP microcapsules are suggested to be an ideal cargo carrier system, which could be employed in not only biomedical theranostic applications as they exhibit structural robustness, specific targeting, triggered release, and photothermal activity but also sensor development in general.
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Affiliation(s)
- Chul-Suk Hong
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
| | - Jae Hyung Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
| | - Soonkoo Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
| | - Kun Yil Rhoo
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
| | - Jong Tak Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
| | - Seung R Paik
- School of Chemical and Biological Engineering, Institute of Chemical Processes, College of Engineering , Seoul National University , Seoul 08826 , Korea
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45
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Rege NK, Wickramasinghe NP, Tustan AN, Phillips NFB, Yee VC, Ismail-Beigi F, Weiss MA. Structure-based stabilization of insulin as a therapeutic protein assembly via enhanced aromatic-aromatic interactions. J Biol Chem 2018; 293:10895-10910. [PMID: 29880646 PMCID: PMC6052209 DOI: 10.1074/jbc.ra118.003650] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
Key contributions to protein structure and stability are provided by weakly polar interactions, which arise from asymmetric electronic distributions within amino acids and peptide bonds. Of particular interest are aromatic side chains whose directional π-systems commonly stabilize protein interiors and interfaces. Here, we consider aromatic-aromatic interactions within a model protein assembly: the dimer interface of insulin. Semi-classical simulations of aromatic-aromatic interactions at this interface suggested that substitution of residue TyrB26 by Trp would preserve native structure while enhancing dimerization (and hence hexamer stability). The crystal structure of a [TrpB26]insulin analog (determined as a T3Rf3 zinc hexamer at a resolution of 2.25 Å) was observed to be essentially identical to that of WT insulin. Remarkably and yet in general accordance with theoretical expectations, spectroscopic studies demonstrated a 150-fold increase in the in vitro lifetime of the variant hexamer, a critical pharmacokinetic parameter influencing design of long-acting formulations. Functional studies in diabetic rats indeed revealed prolonged action following subcutaneous injection. The potency of the TrpB26-modified analog was equal to or greater than an unmodified control. Thus, exploiting a general quantum-chemical feature of protein structure and stability, our results exemplify a mechanism-based approach to the optimization of a therapeutic protein assembly.
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Affiliation(s)
| | | | - Alisar N Tustan
- Medicine, Case Western Reserve University, Cleveland, Ohio 44106 and
| | | | | | | | - Michael A Weiss
- From the Departments of Biochemistry and
- the Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202
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46
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Grignaschi E, Cereghetti G, Grigolato F, Kopp MRG, Caimi S, Faltova L, Saad S, Peter M, Arosio P. A hydrophobic low-complexity region regulates aggregation of the yeast pyruvate kinase Cdc19 into amyloid-like aggregates in vitro. J Biol Chem 2018; 293:11424-11432. [PMID: 29853641 DOI: 10.1074/jbc.ra117.001628] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/15/2018] [Indexed: 11/06/2022] Open
Abstract
Cells form stress granules (SGs) upon stress stimuli to protect sensitive proteins and RNA from degradation. In the yeast Saccharomyces cerevisiae, specific stresses such as nutrient starvation and heat-shock trigger recruitment of the yeast pyruvate kinase Cdc19 into SGs. This RNA-binding protein was shown to form amyloid-like aggregates that are physiologically reversible and essential for cell cycle restart after stress. Cellular Cdc19 exists in an equilibrium between a homotetramer and monomer state. Here, we show that Cdc19 aggregation in vitro is governed by protein quaternary structure, and we investigate the physical-chemical basis of Cdc19's assembly properties. Equilibrium shift toward the monomer state exposes a hydrophobic low-complexity region (LCR), which is prone to induce intermolecular interactions with surrounding proteins. We further demonstrate that hydrophobic/hydrophilic interfaces can trigger Cdc19 aggregation in vitro Moreover, we performed in vitro biophysical analyses to compare Cdc19 aggregates with fibrils produced by two known dysfunctional amyloidogenic peptides. We show that the Cdc19 aggregates share several structural features with pathological amyloids formed by human insulin and the Alzheimer's disease-associated Aβ42 peptide, particularly secondary β-sheet structure, thermodynamic stability, and staining by the thioflavin T dye. However, Cdc19 aggregates could not seed aggregation. These results indicate that Cdc19 adopts an amyloid-like structure in vitro that is regulated by the exposure of a hydrophobic LCR in its monomeric form. Together, our results highlight striking structural similarities between functional and dysfunctional amyloids and reveal the crucial role of hydrophobic/hydrophilic interfaces in regulating Cdc19 aggregation.
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Affiliation(s)
- Erica Grignaschi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Gea Cereghetti
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Stefano Caimi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Shady Saad
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland.
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47
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Rose F, Roovers S, Fano M, Harloff-Helleberg S, Kirkensgaard JJK, Hejnaes K, Fischer P, Foged C. Temperature-Induced Self-Assembly of the Group B Streptococcus (GBS) Fusion Antigen GBS-NN. Mol Pharm 2018; 15:2584-2593. [PMID: 29745668 DOI: 10.1021/acs.molpharmaceut.8b00101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Group B Streptococcus (GBS) is a leading cause of serious bacterial neonatal infections worldwide, which provides an unmet medical need for a globally effective vaccine. The recombinant GBS fusion antigen GBS-NN contains the N-terminal regions of the GBS Rib and Alpha C proteins. It shows promising immunogenicity eliciting protective immunity in mice and encouraging results in early human clinical trials. Understanding the physical stability of GBS-NN containing conformational B-cell epitopes is crucial to ensure optimal vaccine stability, efficacy, and safety. We initially discovered that GBS-NN is prone to form higher-order structures at elevated temperatures. We therefore investigated the self-assembly behavior of GBS-NN and characterized the higher-order conformational structures as a function of temperature. In the native state, GBS-NN exists as a monomer and has a secondary structure containing α-helix and β-sheet. Langmuir studies demonstrated that the native protein is highly surface-active and forms a monolayer film at the air-water interface because of its amphipathic properties. The conformational stability of GBS-NN was measured as a function of temperature. GBS-NN has an unusual thermal behavior with a phase transition of approximately 61 °C, which is not accompanied by any major changes in the secondary structure. However, the antigen showed irreversible self-assembly as a function of temperature into higher-order structures with a hydrodynamic diameter of approximately 100 nm. Cryo-transmission electron microscopy analyses demonstrated that these self-assemblies consist of vesicular, ring-like structures with a hollow aqueous interior. Therefore, GBS-NN is a physically stable monomeric protein but is prone to temperature-induced self-assembly above 61 °C.
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Affiliation(s)
| | - Silke Roovers
- Laboratory of General Biochemistry and Physical Pharmacy , Ghent University , Ottergemsesteenweg 460 , 9000 Ghent , Belgium
| | | | | | - Jacob J K Kirkensgaard
- Niels Bohr Institute, Faculty of Science , University of Copenhagen , Universitetsparken 5 , DK-2100 Copenhagen Ø , Denmark
| | - Kim Hejnaes
- MinervaX ApS , Ole Maaløes Vej 3 , DK-2200 Copenhagen N , Denmark
| | - Per Fischer
- MinervaX ApS , Ole Maaløes Vej 3 , DK-2200 Copenhagen N , Denmark
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48
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Del Poggetto E, Toto A, Aloise C, Di Piro F, Gori L, Malatesta F, Gianni S, Chiti F, Bemporad F. Stability of an aggregation-prone partially folded state of human profilin-1 correlates with aggregation propensity. J Biol Chem 2018; 293:10303-10313. [PMID: 29760185 DOI: 10.1074/jbc.ra118.002087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/02/2018] [Indexed: 12/11/2022] Open
Abstract
A set of missense mutations in the gene encoding profilin-1 has been linked to the onset of familial forms of ALS (fALS), also known as Lou Gehrig's disease. The pathogenic potential of these mutations is linked to the formation of intracellular inclusions of the mutant proteins and correlates with the mutation-induced destabilization of its native, fully folded state. However, the mechanism by which these mutations promote misfolding and self-assembly is yet unclear. Here, using temperature-jump and stopped-flow kinetic measurements, we show that, during refolding, WT profilin-1 transiently populates a partially folded (PF) state endowed with hydrophobic clusters exposed to the solvent and with no detectable secondary structure. We observed that this conformational state is marginally stable at neutral pH but becomes significantly populated at mildly acidic pH. Interestingly, the fALS-associated mutations did not cause a change in the refolding mechanism of profilin-1, but induced a stabilization of the PF state. In the presence of preformed profilin-1 aggregates, the PF state, unlike the unfolded and folded states, could interact with these aggregates via nonspecific hydrophobic interactions and also increase thioflavin-T fluorescence, revealing its amyloidogenic potential. Moreover, in the variants tested, we found a correlation between conformational stability of PF and aggregation propensity, defining this conformational state as an aggregation-prone folding intermediate. In conclusion, our findings indicate that mutation-induced stabilization of a partially folded state can enhance profilin-1 aggregation and thereby contribute to the pathogenicity of the mutations.
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Affiliation(s)
- Edoardo Del Poggetto
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy
| | - Angelo Toto
- the Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza University of Rome, 00185 Rome, Italy, and
| | - Chiara Aloise
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy
| | - Francesco Di Piro
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy
| | - Ludovica Gori
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy
| | - Francesco Malatesta
- the Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza University of Rome, 00185 Rome, Italy, and
| | - Stefano Gianni
- the Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza University of Rome, 00185 Rome, Italy, and.,the Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, 00185 Rome, Italy
| | - Fabrizio Chiti
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy
| | - Francesco Bemporad
- From the Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Viale G. B. Morgagni 50, 50134, Firenze, Italy,
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49
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Mao CP, Peng S, Yang A, He L, Tsai YC, Hung CF, Wu TC. Programmed self-assembly of peptide-major histocompatibility complex for antigen-specific immune modulation. Proc Natl Acad Sci U S A 2018; 115:E4032-40. [PMID: 29632186 DOI: 10.1073/pnas.1718434115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A technology to prime desired populations of T cells in the body-particularly those that possess low avidity against target antigen-would pave the way for the design of new types of vaccination for intractable infectious diseases or cancer. Here, we report such a technology based on positive feedback-driven, programmed self-assembly of peptide-major histocompatibility complex (pMHC) directly on the membrane of cognate T cells. Our design capitalizes on the unique features of the protein annexin V (ANXA5), which-in a concerted and synergistic manner-couples the early onset of TCR signaling by cognate pMHC with a surge in pMHC-TCR affinity, with repeated pMHC encounters, and with widespread TCR cross-linking. In our system, ANXA5 is linked to pMHC and firmly engages the plasma membrane of cognate T cells upon (and only upon) the early onset of TCR signaling. ANXA5, in turn, exerts a mechanical force that stabilizes interactions at the TCR-pMHC interface and facilitates repeated, serial pMHC encounters. Furthermore, ANXA5 quickly arranges into uniform 2D matrices, thereby prompting TCR cross-linking. Fusion of ANXA5 to pMHC augments lymphocyte activation by several orders of magnitude (>1,000-fold), bypasses the need for costimulation, and breaks tolerance against a model self-antigen in vivo. Our study opens the door to the application of synthetic, feedback-driven self-assembly platforms in immune modulation.
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50
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Roschger C, Schubert M, Regl C, Andosch A, Marquez A, Berger T, Huber CG, Lütz-Meindl U, Cabrele C. The Recombinant Inhibitor of DNA Binding Id2 Forms Multimeric Structures via the Helix-Loop-Helix Domain and the Nuclear Export Signal. Int J Mol Sci 2018; 19:E1105. [PMID: 29642431 DOI: 10.3390/ijms19041105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 12/24/2022] Open
Abstract
The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E. coli, solubilized from inclusion bodies with urea, purified and dissolved in water at pH~4. Under these conditions, Id2 was obtained with both cysteine residues disulfide-bonded to β-mercaptoethanol that was present during the solubilization process. Moreover, it existed in a self-assembled state, in which the N-terminus remained highly flexible, while the HLH domain and, surprisingly, part of the C-terminus, which corresponds to the nuclear export signal (NES), both were involved in slowly tumbling, rigid structures. The protein oligomers also formed twisted fibrils that were several micrometers long and up to 80 nm thick. These results show that self-assembly decreases the backbone flexibility of those two protein regions (HLH and NES) that are important for interaction with basic-HLH transcription factors or for nucleocytoplasmic shuttling.
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