1
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Konuma T, Takai T, Tsuchiya C, Nishida M, Hashiba M, Yamada Y, Shirai H, Motoda Y, Nagadoi A, Chikaishi E, Akagi K, Akashi S, Yamazaki T, Akutsu H, Ikegami T. Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria. Protein Sci 2024; 33:e5002. [PMID: 38723146 PMCID: PMC11081423 DOI: 10.1002/pro.5002] [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: 12/06/2023] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
Bacteria that have acquired resistance to most antibiotics, particularly those causing nosocomial infections, create serious problems. Among these, the emergence of vancomycin-resistant enterococci was a tremendous shock, considering that vancomycin is the last resort for controlling methicillin-resistant Staphylococcus aureus. Therefore, there is an urgent need to develop an inhibitor of VanX, a protein involved in vancomycin resistance. Although the crystal structure of VanX has been resolved, its asymmetric unit contains six molecules aligned in a row. We have developed a structural model of VanX as a stable dimer in solution, primarily utilizing nuclear magnetic resonance (NMR) residual dipolar coupling. Despite the 46 kDa molecular mass of the dimer, the analyses, which are typically not as straightforward as those of small proteins around 10 kDa, were successfully conducted. We assigned the main chain using an amino acid-selective unlabeling method. Because we found that the zinc ion-coordinating active sites in the dimer structure were situated in the opposite direction to the dimer interface, we generated an active monomer by replacing an amino acid at the dimer interface. The monomer consists of only 202 amino acids and is expected to be used in future studies to screen and improve inhibitors using NMR.
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Tomoyo Takai
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Chieko Tsuchiya
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Masayuki Nishida
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Miyu Hashiba
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Yudai Yamada
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Haruka Shirai
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Yoko Motoda
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Aritaka Nagadoi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | | | - Ken‐ichi Akagi
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Satoko Akashi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | | | - Hideo Akutsu
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Takahisa Ikegami
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
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2
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Erba EB, Pastore A. The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions. Adv Exp Med Biol 2024; 3234:109-123. [PMID: 38507203 DOI: 10.1007/978-3-031-52193-5_8] [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: 03/22/2024]
Abstract
Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.
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3
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Ye Y, Tyndall ER, Bui V, Bewley MC, Wang G, Hong X, Shen Y, Flanagan JM, Wang HG, Tian F. Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy. Nat Commun 2023; 14:5503. [PMID: 37679347 PMCID: PMC10485044 DOI: 10.1038/s41467-023-41243-4] [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: 01/26/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Autophagosome formation, a crucial step in macroautophagy (autophagy), requires the covalent conjugation of LC3 proteins to the amino headgroup of phosphatidylethanolamine (PE) lipids. Atg3, an E2-like enzyme, catalyzes the transfer of LC3 from LC3-Atg3 to PEs in targeted membranes. Here we show that the catalytically important C-terminal regions of human Atg3 (hAtg3) are conformationally dynamic and directly interact with the membrane, in collaboration with its N-terminal membrane curvature-sensitive helix. The functional relevance of these interactions was confirmed by in vitro conjugation and in vivo cellular assays. Therefore, highly curved phagophoric rims not only serve as a geometric cue for hAtg3 recruitment, but also their interaction with hAtg3 promotes LC3-PE conjugation by targeting its catalytic center to the membrane surface and bringing substrates into proximity. Our studies advance the notion that autophagosome biogenesis is directly guided by the spatial interactions of Atg3 with highly curved phagophoric rims.
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Affiliation(s)
- Yansheng Ye
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Erin R Tyndall
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Van Bui
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maria C Bewley
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Guifang Wang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Xupeng Hong
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA
| | - John M Flanagan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Hong-Gang Wang
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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4
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Grassmann G, Di Rienzo L, Gosti G, Leonetti M, Ruocco G, Miotto M, Milanetti E. Electrostatic complementarity at the interface drives transient protein-protein interactions. Sci Rep 2023; 13:10207. [PMID: 37353566 PMCID: PMC10290103 DOI: 10.1038/s41598-023-37130-z] [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: 02/14/2023] [Accepted: 06/16/2023] [Indexed: 06/25/2023] Open
Abstract
Understanding the mechanisms driving bio-molecules binding and determining the resulting complexes' stability is fundamental for the prediction of binding regions, which is the starting point for drug-ability and design. Characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions, and the consequent shape complementarity between the interacting molecular surfaces are well established. However, no consensus has yet been reached on the role of electrostatic. Here, we perform extensive analyses on a large dataset of protein complexes for which both experimental binding affinity and pH data were available. Probing the amino acid composition, the disposition of the charges, and the electrostatic potential they generated on the protein molecular surfaces, we found that (i) although different classes of dimers do not present marked differences in the amino acid composition and charges disposition in the binding region, (ii) homodimers with identical binding region show higher electrostatic compatibility with respect to both homodimers with non-identical binding region and heterodimers. Interestingly, (iii) shape and electrostatic complementarity, for patches defined on short-range interactions, behave oppositely when one stratifies the complexes by their binding affinity: complexes with higher binding affinity present high values of shape complementarity (the role of the Lennard-Jones potential predominates) while electrostatic tends to be randomly distributed. Conversely, complexes with low values of binding affinity exploit Coulombic complementarity to acquire specificity, suggesting that electrostatic complementarity may play a greater role in transient (or less stable) complexes. In light of these results, (iv) we provide a novel, fast, and efficient method, based on the 2D Zernike polynomial formalism, to measure electrostatic complementarity without the need of knowing the complex structure. Expanding the electrostatic potential on a basis of 2D orthogonal polynomials, we can discriminate between transient and permanent protein complexes with an AUC of the ROC of [Formula: see text] 0.8. Ultimately, our work helps shedding light on the non-trivial relationship between the hydrophobic and electrostatic contributions in the binding interfaces, thus favoring the development of new predictive methods for binding affinity characterization.
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Affiliation(s)
- Greta Grassmann
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Giorgio Gosti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, 00185, Rome, Italy
| | - Marco Leonetti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, 00185, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Mattia Miotto
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Edoardo Milanetti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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5
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Haubrich K, Spiteri VA, Farnaby W, Sobott F, Ciulli A. Breaking free from the crystal lattice: Structural biology in solution to study protein degraders. Curr Opin Struct Biol 2023; 79:102534. [PMID: 36804675 DOI: 10.1016/j.sbi.2023.102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 02/17/2023]
Abstract
Structural biology offers a versatile arsenal of techniques and methods to investigate the structure and conformational dynamics of proteins and their assemblies. The growing field of targeted protein degradation centres on the premise of developing small molecules, termed degraders, to induce proximity between an E3 ligase and a protein of interest to be signalled for degradation. This new drug modality brings with it new opportunities and challenges to structural biologists. Here we discuss how several structural biology techniques, including nuclear magnetic resonance, cryo-electron microscopy, structural mass spectrometry and small angle scattering, have been explored to complement X-ray crystallography in studying degraders and their ternary complexes. Together the studies covered in this review make a case for the invaluable perspectives that integrative structural biology techniques in solution can bring to understanding ternary complexes and designing degraders.
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Affiliation(s)
- Kevin Haubrich
- Centre for Targeted Protein Degradation & Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK. https://twitter.com/KevinHaubrich1
| | - Valentina A Spiteri
- Centre for Targeted Protein Degradation & Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK. https://twitter.com/val_spiteri
| | - William Farnaby
- Centre for Targeted Protein Degradation & Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK. https://twitter.com/farnaby84
| | - Frank Sobott
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK. https://twitter.com/FrankSobott
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation & Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.
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6
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Asadollahi K, Scott DJ, Gooley PR. NMR applications to GPCR recognition by peptide ligands. Curr Opin Pharmacol 2023; 70:102366. [PMID: 37003111 DOI: 10.1016/j.coph.2023.102366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 04/03/2023]
Abstract
Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo significant conformational changes upon binding that is essential for receptor recognition and activation. Conformational selection and induced fit are the extreme mechanisms of coupled folding and binding that can be distinguished by analysis of binding pathways by methods that include NMR. However, the large size of GPCRs in membrane-mimetic environments limits NMR applications. In this review, we highlight advances in the field that can be adopted to address coupled folding and binding of peptide ligands to their cognate receptors.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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7
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Nedielkov R, Möller HM. Detecting and Characterizing Interactions of Metabolites with Proteins by Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Spectroscopy. Methods Mol Biol 2023; 2554:123-139. [PMID: 36178624 DOI: 10.1007/978-1-0716-2624-5_9] [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] [Indexed: 06/16/2023]
Abstract
Saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy is an established technique for detecting and characterizing the binding of small molecules, such as metabolites, to biological macromolecules like proteins and nucleic acids. STD NMR allows detection of binding in complex mixtures of potential ligands, which is often used for library screening in the pharmaceutical industry but may also be beneficial for binding studies with metabolite mixtures. The nature of the ligand is normally restricted to small molecules in terms of NMR spectroscopy, and the size of the macromolecule on the other side should be larger than 10-15 kDa. This technique is especially applicable to detecting binders of intermediate to low affinity with the dissociation constant (KD) above 1 μM. In this chapter, we focus on recent developments and the applications of STD NMR to studying interactions of natural products and metabolites, in particular. The reader is also referred to excellent reviews of the field and the literature cited therein. This chapter also provides a detailed experimental protocol for performing the STD NMR measurement based on the example of the subunit A of the Na+-transporting NADH/ubiquinone oxidoreductase (Na+-NQR) from V. cholerae interacting with its natural quinone substrate and inhibitors.
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Affiliation(s)
- Ruslan Nedielkov
- University of Potsdam, Institute for Chemistry, Potsdam, Germany.
| | - Heiko M Möller
- University of Potsdam, Institute for Chemistry, Potsdam, Germany
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8
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Toyama Y, Harkness RW, Kay LE. Structural basis of protein substrate processing by human mitochondrial high-temperature requirement A2 protease. Proc Natl Acad Sci U S A 2022; 119:e2203172119. [PMID: 35452308 DOI: 10.1073/pnas.2203172119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/18/2022] Open
Abstract
Protein aggregates are often toxic, leading to impaired cellular activities and disease. The human HtrA2 trimeric enzyme cleaves such aggregates, and mutations in HtrA2 are causative for various neurodegenerative disorders, such as Parkinson’s disease and essential tremor. The mechanism by which cleavage occurs has been studied using small peptides, but little information is available as to how HtrA2 protects cells from the pathologic effects of aggregation involving protein molecules that can form well-folded structures. Using solution NMR spectroscopy, we investigated the structural dynamics of the interaction between HtrA2 and a model protein substrate, demonstrating that HtrA2 preferentially binds to an unfolded substrate ensemble and providing insights into how HtrA2 function is regulated. The human high-temperature requirement A2 (HtrA2) protein is a trimeric protease that cleaves misfolded proteins to protect cells from stresses caused by toxic, proteinaceous aggregates, and the aberrant function of HtrA2 is closely related to the onset of neurodegenerative disorders. Our methyl-transverse relaxation optimized spectroscopy (TROSY)–based NMR studies using small-peptide ligands have previously revealed a stepwise activation mechanism involving multiple distinct conformational states. However, very little is known about how HtrA2 binds to protein substrates and if the distinct conformational states observed in previous peptide studies might be involved in the processing of protein clients. Herein, we use solution-based NMR spectroscopy to investigate the interaction between the N-terminal Src homology 3 domain from downstream of receptor kinase (drk) with an added C-terminal HtrA2-binding motif (drkN SH3-PDZbm) that exhibits marginal folding stability and serves as a mimic of a physiological protein substrate. We show that drkN SH3-PDZbm binds to HtrA2 via a two-pronged interaction, involving both its C-terminal PDZ-domain binding motif and a central hydrophobic region, with binding occurring preferentially via an unfolded ensemble of substrate molecules. Multivalent interactions between several clients and a single HtrA2 trimer significantly stimulate the catalytic activity of HtrA2, suggesting that binding avidity plays an important role in regulating substrate processing. Our results provide a thermodynamic, kinetic, and structural description of the interaction of HtrA2 with protein substrates and highlight the importance of a trimeric architecture for function as a stress-protective protease that mitigates aggregation.
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9
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Abstract
Because of the key relevance of protein–protein interactions (PPI) in diseases, the modulation of protein-protein complexes is of relevant clinical significance. The successful design of binding compounds modulating PPI requires a detailed knowledge of the involved protein-protein system at molecular level, and investigation of the structural motifs that drive the association of the proteins at the recognition interface. These elements represent hot spots of the protein binding free energy, define the complex lifetime and possible modulation strategies. Here, we review the advanced technologies used to map the PPI involved in human diseases, to investigate the structure-function features of protein complexes, and to discover effective ligands that modulate the PPI for therapeutic intervention.
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Affiliation(s)
- Elisa Martino
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy
| | - Sara Chiarugi
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy.,BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
| | | | - Gianpiero Garau
- BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
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10
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Liu CH, Huang SJ, Yu TY. Cholesterol Modulates the Interaction between HIV-1 Viral Protein R and Membrane. Membranes (Basel) 2021; 11:784. [PMID: 34677550 PMCID: PMC8539443 DOI: 10.3390/membranes11100784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022]
Abstract
Being a major metabolite for maintaining cellular homeostasis, as well as an important structural component in lipid membrane, cholesterol also plays critical roles in the life cycles of some viruses, including human immunodeficiency virus-1 (HIV-1). The involvement of cholesterol in HIV-1 infectivity, assembly and budding has made it an important research target. Viral protein R (Vpr) is an accessory protein of HIV-1, which is involved in many major events in the life cycle of HIV-1. In addition to its multi-functional roles in the HIV-1 life cycle, it is shown to interact with lipid membrane and form a cation-selective channel. In this work, we examined the effect of cholesterol on the interaction of Vpr and lipid membrane. Using calcein release assay, we found that the membrane permeability induced by the membrane binding of Vpr was significantly reduced in the presence of cholesterol in membrane. In addition, using solid-state NMR (ssNMR) spectroscopy, Vpr was shown to experience multiple chemical environments in lipid membrane, as indicated by the broad line shape of carbonyl 13C resonance of Cys-76 residue ranging from 165-178 ppm, which can be attributed to the existence of complex Vpr-membrane environments. We further showed that the presence of cholesterol in membrane will alter the distribution of Vpr in the complex membrane environments, which may explain the change of the Vpr induced membrane permeability in the presence of cholesterol.
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Affiliation(s)
- Chun-Hao Liu
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan;
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu 300044, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei 10617, Taiwan
| | - Tsyr-Yan Yu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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11
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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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12
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Di Muzio M, Wildner S, Huber S, Hauser M, Vejvar E, Auzinger W, Regl C, Laimer J, Zennaro D, Wopfer N, Huber CG, van Ree R, Mari A, Lackner P, Ferreira F, Schubert M, Gadermaier G. Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins. J Biol Chem 2021; 295:17398-17410. [PMID: 33453986 DOI: 10.1074/jbc.ra120.014243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Indexed: 01/30/2023] Open
Abstract
Identification of antibody-binding epitopes is crucial to understand immunological mechanisms. It is of particular interest for allergenic proteins with high cross-reactivity as observed in the lipid transfer protein (LTP) syndrome, which is characterized by severe allergic reactions. Art v 3, a pollen LTP from mugwort, is frequently involved in this cross-reactivity, but no antibody-binding epitopes have been determined so far. To reveal human IgE-binding regions of Art v 3, we produced three murine high-affinity mAbs, which showed 70-90% coverage of the allergenic epitopes from mugwort pollen-allergic patients. As reliable methods to determine structural epitopes with tightly interacting intact antibodies under native conditions are lacking, we developed a straightforward NMR approach termed hydrogen/deuterium exchange memory (HDXMEM). It relies on the slow exchange between the invisible antigen-mAb complex and the free 15N-labeled antigen whose 1H-15N correlations are detected. Due to a memory effect, changes of NH protection during antibody binding are measured. Differences in H/D exchange rates and analyses of mAb reactivity to homologous LTPs revealed three structural epitopes: two partially cross-reactive regions around α-helices 2 and 4 as well as a novel Art v 3-specific epitope at the C terminus. Protein variants with exchanged epitope residues confirmed the antibody-binding sites and revealed strongly reduced IgE reactivity. Using the novel HDXMEM for NMR epitope mapping allowed identification of the first structural epitopes of an allergenic pollen LTP. This knowledge enables improved cross-reactivity prediction for patients suffering from LTP allergy and facilitates design of therapeutics.
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Affiliation(s)
- Martina Di Muzio
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Sabrina Wildner
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Sara Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Michael Hauser
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Eva Vejvar
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Werner Auzinger
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Josef Laimer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Danila Zennaro
- Centri Associati di Allergologica Molecolare (CAAM), Latina, Italy
| | - Nicole Wopfer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Ronald van Ree
- Department of Experimental Immunology and of Otorhinolaryngology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Adriano Mari
- Centri Associati di Allergologica Molecolare (CAAM), Latina, Italy
| | - Peter Lackner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
| | - Gabriele Gadermaier
- Department of Biosciences, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
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13
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Feng W, Nguyen H, Shen D, Deng H, Jiang Z, Podolnikova N, Ugarova T, Wang X. Structural Characterization of the Interaction between the α MI-Domain of the Integrin Mac-1 (α Mβ 2) and the Cytokine Pleiotrophin. Biochemistry 2021; 60:182-193. [PMID: 33427449 DOI: 10.1021/acs.biochem.0c00700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Integrin Mac-1 (αMβ2) is an adhesion receptor vital to many functions of myeloid leukocytes. It is also the most promiscuous member of the integrin family capable of recognizing a broad range of ligands. In particular, its ligand-binding αMI-domain is known to bind cationic proteins/peptides depleted in acidic residues. This contradicts the canonical ligand-binding mechanism of αI-domains, which requires an acidic amino acid in the ligand to coordinate the divalent cation within the metal ion-dependent adhesion site (MIDAS) of αI-domains. The lack of acidic amino acids in the αMI-domain-binding sequences suggests the existence of an as-yet uncharacterized interaction mechanism. In the present study, we analyzed interactions of the αMI-domain with a representative Mac-1 ligand, the cationic cytokine pleiotrophin (PTN). Through NMR chemical shift perturbation analysis, cross saturation, NOESY, and mutagenesis studies, we found the interaction between the αMI-domain and PTN is divalent cation-independent and mediated mostly by hydrophobic contacts between the N-terminal domain of PTN and residues in the α5-β5 loop of αMI-domain. The observation that increased ionic strength weakens the interaction between the proteins indicates electrostatic forces may also play a significant role in the binding. On the basis of the results from these experiments, we formulated a model of the interaction between the αMI-domain and PTN.
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14
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Hossain MA, Larrous F, Rawlinson SM, Zhan J, Sethi A, Ibrahim Y, Aloi M, Lieu KG, Mok YF, Griffin MDW, Ito N, Ose T, Bourhy H, Moseley GW, Gooley PR. Structural Elucidation of Viral Antagonism of Innate Immunity at the STAT1 Interface. Cell Rep 2020; 29:1934-1945.e8. [PMID: 31722208 DOI: 10.1016/j.celrep.2019.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 11/30/2018] [Revised: 07/16/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022] Open
Abstract
To evade immunity, many viruses express interferon antagonists that target STAT transcription factors as a major component of pathogenesis. Because of a lack of direct structural data, these interfaces are poorly understood. We report the structural analysis of full-length STAT1 binding to an interferon antagonist of a human pathogenic virus. The interface revealed by transferred cross-saturation NMR is complex, involving multiple regions in both the viral and cellular proteins. Molecular mapping analysis, combined with biophysical characterization and in vitro/in vivo functional assays, indicates that the interface is significant in disease caused by a pathogenic field-strain lyssavirus, with critical roles for contacts between the STAT1 coiled-coil/DNA-binding domains and specific regions within the viral protein. These data elucidate the potentially complex nature of IFN antagonist/STAT interactions, and the spatial relationship of protein interfaces that mediate immune evasion and replication, providing insight into how viruses can regulate these essential functions via single multifunctional proteins.
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Affiliation(s)
- Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Florence Larrous
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Stephen M Rawlinson
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Jingyu Zhan
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Youssef Ibrahim
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Maria Aloi
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Kim G Lieu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, 060-0810 Sapporo, Japan
| | - Hervé Bourhy
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia.
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15
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Chu N, Viennet T, Bae H, Salguero A, Boeszoermenyi A, Arthanari H, Cole PA. The structural determinants of PH domain-mediated regulation of Akt revealed by segmental labeling. eLife 2020; 9:e59151. [PMID: 32744507 PMCID: PMC7438110 DOI: 10.7554/elife.59151] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 05/20/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022] Open
Abstract
Akt is a critical protein kinase that governs cancer cell growth and metabolism. Akt appears to be autoinhibited by an intramolecular interaction between its N-terminal pleckstrin homology (PH) domain and kinase domain, which is relieved by C-tail phosphorylation, but the precise molecular mechanisms remain elusive. Here, we use a combination of protein semisynthesis, NMR, and enzymological analysis to characterize structural features of the PH domain in its autoinhibited and activated states. We find that Akt autoinhibition depends on the length/flexibility of the PH-kinase linker. We identify a role for a dynamic short segment in the PH domain that appears to regulate autoinhibition and PDK1-catalyzed phosphorylation of Thr308 in the activation loop. We determine that Akt allosteric inhibitor MK2206 drives distinct PH domain structural changes compared to baseline autoinhibited Akt. These results highlight how the conformational plasticity of Akt governs the delicate control of its catalytic properties.
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Affiliation(s)
- Nam Chu
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Biology, Dana-Farber Cancer InstituteBostonUnited States
| | - Hwan Bae
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Antonieta Salguero
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Biology, Dana-Farber Cancer InstituteBostonUnited States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Biology, Dana-Farber Cancer InstituteBostonUnited States
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
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16
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McRae EKS, Davidson DE, McKenna SA. 2D Saturation Transfer Difference NMR for Determination of Protein Binding Sites on RNA Guanine Quadruplexes. Methods Mol Biol 2020; 2161:101-13. [PMID: 32681509 DOI: 10.1007/978-1-0716-0680-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Saturation transfer difference (STD) NMR is a technique that provides information on the intermolecular interfaces of heterogenous complexes by cross-saturation from one molecule to the other. In this case, selective saturation of protein protons is applied, and the cross-relaxation to the RNA sample results in a reduction of the peak intensities in the measured H1-H1 NOESY spectrum. This allows for a relatively rapid and simple method of identifying the protein binding interface of an RNA with assigned chemical shift data.
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17
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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18
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Piserchio A, Will N, Giles DH, Hajredini F, Dalby KN, Ghose R. Solution Structure of the Carboxy-Terminal Tandem Repeat Domain of Eukaryotic Elongation Factor 2 Kinase and Its Role in Substrate Recognition. J Mol Biol 2019; 431:2700-2717. [PMID: 31108082 PMCID: PMC6599559 DOI: 10.1016/j.jmb.2019.05.019] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/15/2019] [Accepted: 05/12/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K), an atypical calmodulin-activated protein kinase, regulates translational elongation by phosphorylating its substrate, eukaryotic elongation factor 2 (eEF-2), thereby reducing its affinity for the ribosome. The activation and activity of eEF-2K are critical for survival under energy-deprived conditions and is implicated in a variety of essential physiological processes. Previous biochemical experiments have indicated that the binding site for the substrate eEF-2 is located in the C-terminal domain of eEF-2K, a region predicted to harbor several α-helical repeats. Here, using NMR methodology, we have determined the solution structure of a C-terminal fragment of eEF-2K, eEF-2K562-725 that encodes two α-helical repeats. The structure of eEF-2K562-725 shows signatures characteristic of TPR domains and of their SEL1-like sub-family. Furthermore, using the analyses of NMR spectral perturbations and ITC measurements, we have localized the eEF-2 binding site on eEF-2K562-725. We find that eEF-2K562-725 engages eEF-2 with an affinity comparable to that of the full-length enzyme. Furthermore, eEF-2K562-725 is able to inhibit the phosphorylation of eEF-2 by full-length eEF-2K in trans. Our present studies establish that eEF-2K562-725 encodes the major elements necessary to enable the eEF-2K/eEF-2 interactions.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA
| | - Nathan Will
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - David H Giles
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Kevin N Dalby
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA.
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19
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Mallis RJ, Brazin KN, Duke-Cohan JS, Hwang W, Wang JH, Wagner G, Arthanari H, Lang MJ, Reinherz EL. NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology. J Biomol NMR 2019; 73:319-332. [PMID: 30815789 PMCID: PMC6693947 DOI: 10.1007/s10858-019-00234-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/28/2018] [Accepted: 02/06/2019] [Indexed: 05/05/2023]
Abstract
Early studies of T cell structural biology using X-ray crystallography, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) focused on a picture of the αβT cell receptor (αβTCR) component domains and their cognate ligands (peptides bound to MHC molecules, i.e. pMHCs) as static interaction partners. Moving forward requires integrating this corpus of data with dynamic technologies such as NMR, molecular dynamics (MD) simulations and real-time single molecule (SM) studies exemplified by optical tweezers (OT). NMR bridges relevant timescales and provides the potential for an all-atom dynamic description of αβTCR components prior to and during interactions with binding partners. SM techniques have opened up vistas in understanding the non-equilibrium nature of T cell signaling through the introduction of force-mediated binding measurements into the paradigm for T cell function. In this regard, bioforces consequent to T-lineage cell motility are now perceived as placing piconewton (pN)-level loads on single receptor-pMHC bonds to impact structural change and αβT-lineage biology, including peptide discrimination, cellular activation, and developmental progression. We discuss herein essential NMR technologies in illuminating the role of ligand binding in the preT cell receptor (preTCR), the αβTCR developmental precursor, and convergence of NMR, SM and MD data in advancing our comprehension of T cell development. More broadly we review the central hypothesis that the αβTCR is a mechanosensor, fostered by breakthrough NMR-based structural insights. Collectively, elucidating dynamic aspects through the integrative use of NMR, SM, and MD shall advance fundamental appreciation of the mechanism of T cell signaling as well as inform translational efforts in αβTCR and chimeric T cell (CAR-T) immunotherapies and T cell vaccinology.
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Affiliation(s)
- Robert J Mallis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kristine N Brazin
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, 77843, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea
| | - Jia-Huai Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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20
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Shang K, Song S, Cheng Y, Guo L, Pei Y, Lv X, Aastrup T, Pei Z. Fabrication of Carbohydrate Chips Based on Polydopamine for Real-Time Determination of Carbohydrate⁻Lectin Interactions by QCM Biosensor. Polymers (Basel) 2018; 10:E1275. [PMID: 30961200 PMCID: PMC6401853 DOI: 10.3390/polym10111275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 10/17/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
A novel approach for preparing carbohydrate chips based on polydopamine (PDA) surface to study carbohydrate⁻lectin interactions by quartz crystal microbalance (QCM) biosensor instrument has been developed. The amino-carbohydrates were immobilized on PDA-coated quartz crystals via Schiff base reaction and/or Michael addition reaction. The resulting carbohydrate-chips were applied to QCM biosensor instrument with flow-through system for real-time detection of lectin⁻carbohydrate interactions. A series of plant lectins, including wheat germ agglutinin (WGA), concanavalin A (Con A), Ulex europaeus agglutinin I (UEA-I), soybean agglutinin (SBA), and peanut agglutinin (PNA), were evaluated for the binding to different kinds of carbohydrate chips. Clearly, the results show that the predicted lectin selectively binds to the carbohydrates, which demonstrates the applicability of the approach. Furthermore, the kinetics of the interactions between Con A and mannose, WGA and N-Acetylglucosamine were studied, respectively. This study provides an efficient approach to preparing carbohydrate chips based on PDA for the lectin⁻carbohydrate interactions study.
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Affiliation(s)
- Kun Shang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Siyu Song
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yaping Cheng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Lili Guo
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yuxin Pei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Xiaomeng Lv
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | | | - Zhichao Pei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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21
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Becker W, Bhattiprolu KC, Gubensäk N, Zangger K. Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy. Chemphyschem 2018; 19:895-906. [PMID: 29314603 PMCID: PMC5915746 DOI: 10.1002/cphc.201701253] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [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: 11/20/2017] [Revised: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution.
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Affiliation(s)
- Walter Becker
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | | | - Nina Gubensäk
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Klaus Zangger
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
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22
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Martin T, Lou YC, Chou CC, Wei SY, Sadotra S, Cho CC, Lin MH, Tai JH, Hsu CH, Chen C. Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis. Sci Rep 2018; 8:5410. [PMID: 29615721 DOI: 10.1038/s41598-018-23821-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/21/2018] [Indexed: 11/08/2022] Open
Abstract
Cyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme. Here, we determined the crystal structures of TvCyP1 and its complex with the minimum TvCyP1-binding sequence of Myb1 (Myb1104-111), where TvCyP1 formed a homodimer, unlike other single domain cyclophilins. In the complex structure, one Myb1104-111 peptide was bound to each TvCyP1 protomer, with G106-P107 and Y105 fitting well into the active site and auxiliary S2 pocket, respectively. NMR data further showed that TvCyP1 can catalyze the cis/trans isomerization of P107 in Myb1104-111. Interestingly, in the well-folded Myb1 protein (Myb135-141), the minimum binding sequence adopted a different conformation from that of unstructured Myb1104-111 peptide, that could make P107 binding to the active site of TvCyP1 difficult. However, NMR studies showed that similar to Myb1104-111 peptide, Myb135-141 also interacted with the active site of TvCyP1 and the dynamics of the Myb135-141 residues near P107 was reduced upon interaction. Together, the structure of TvCyP1 and detailed structural insights on TvCyP1-Myb1 interaction provided here could pave the way for newer drugs to treat drug-resistant strains.
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23
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Abstract
Understanding the changes in the macro-structure of amphiphilic pH-responsive polymers remains a relevant issue due to their potential use as drug delivery carriers. Since some of the amphiphilic polymers are known to exchange hydrogen ions with an aqueous solvent, we monitor the effective change of the surface to volume ratio of such polymer aggregates using solution-state nuclear magnetic resonance (NMR) spectroscopy. The surface to volume ratio with the help of UV-visible spectroscopy is shown to yield the average diameter of the polymer aggregates. We show that the proposed method not only satisfactorily corroborates the existing notions of how the aggregation of these polymers takes place as a function of pH, but also provides a quantitative estimate of the size of the aggregates.
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Affiliation(s)
- Ipsita Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur - 741246, India.
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24
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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Abstract
A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data. The results with the HDGB model compare favorably with predictions from methods used in the Orientations of Proteins in Membranes (OPM) and Protein Data Bank of Transmembrane Proteins (PDB-TM) databases.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University , 603 Wilson Road, Room BCH, 218, East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , 603 Wilson Road, Room BCH, 218, East Lansing, Michigan 48824, United States
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26
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Minato Y, Ueda T, Machiyama A, Iwaï H, Shimada I. Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR. Sci Rep 2017; 7:16462. [PMID: 29184123 DOI: 10.1038/s41598-017-16755-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
Bacteria utilize thermotaxis signal transduction proteins, including CheA, and CheY, to switch the direction of the cell movement. However, the thermally responsive machinery enabling warm-seeking behavior has not been identified. Here we examined the effects of temperature on the structure and dynamics of the full-length CheA and CheY complex, by NMR. Our studies revealed that the CheA-CheY complex exists in equilibrium between multiple states, including one state that is preferable for the autophosphorylation of CheA, and another state that is preferable for the phosphotransfer from CheA to CheY. With increasing temperature, the equilibrium shifts toward the latter state. The temperature-dependent population shift of the dynamic domain arrangement of the CheA-CheY complex induced changes in the concentrations of phosphorylated CheY that are comparable to those induced by chemical attractants or repellents. Therefore, the dynamic domain arrangement of the CheA-CheY complex functions as the primary thermally responsive machinery in warm-seeking behavior.
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Toyama Y, Mase Y, Kano H, Yokogawa M, Osawa M, Shimada I. Nuclear Magnetic Resonance Approaches for Characterizing Protein-Protein Interactions. Methods Mol Biol 2018; 1684:115-28. [PMID: 29058188 DOI: 10.1007/978-1-4939-7362-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The gating of potassium ion (K+) channels is regulated by various kinds of protein-protein interactions (PPIs). Structural investigations of these PPIs provide useful information not only for understanding the gating mechanisms of K+ channels, but also for developing the pharmaceutical compounds targeting K+ channels. Here, we describe a nuclear magnetic resonance spectroscopic method, termed the cross saturation (CS) method, to accurately determine the binding surfaces of protein complexes, and its application to the investigation of the interaction between a G protein-coupled inwardly rectifying K+ channel and a G protein α subunit.
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28
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Song S, Lu Y, Li X, Cao S, Pei Y, Aastrup T, Pei Z. Optimization of 3D Surfaces of Dextran with Different Molecule Weights for Real-Time Detection of Biomolecular Interactions by a QCM Biosensor. Polymers (Basel) 2017; 9:E409. [PMID: 30965713 PMCID: PMC6418631 DOI: 10.3390/polym9090409] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/15/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023] Open
Abstract
Quartz crystal microbalance (QCM) has been extensively applied in real-time and label-free biomolecular interaction studies. However, the sensitive detection by QCM technology remains challenging, mainly due to the limited surface immobilization capacity. Here, a three-dimensional (3D) carboxymethyl dextran coated gold sensor chip surface was successfully fabricated with dextran of different molecular weight (100, 500 and 2000 kDa, respectively). To evaluate the 3D carboxymethyl dextran surface immobilization capacity, the 3D surface was used for studying antigen⁻antibody interactions on the QCM biosensor. The results showed that the protein immobilization capacity of the 3D carboxymethyl dextran (2000 kDa) surface exceeded more than 4 times the capacity of the 2D carboxyl surface, and 2 times the capacity of the traditional 3D carboxymethyl dextran (500 kDa) surface. Furthermore, the kinetic and affinity properties of antigen⁻antibody interactions were performed. Most notably, the optimized 3D carboxymethyl dextran (2000 kDa) surface could be used for small molecule detection, where the binding of biotinylated oligo (0.67 kDa) reached 8.1 Hz. The results confirmed that a 3D carboxymethyl dextran (2000 kDa) surface can be exploited for sensitive detection of low molecular weight analytes, which have great potential applications for characterizing the interactions between small molecule drugs and proteins.
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Affiliation(s)
- Siyu Song
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yuchao Lu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Xueming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Shoupeng Cao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yuxin Pei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | | | - Zhichao Pei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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Natarajan K, McShan AC, Jiang J, Kumirov VK, Wang R, Zhao H, Schuck P, Tilahun ME, Boyd LF, Ying J, Bax A, Margulies DH, Sgourakis NG. An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role. Nat Commun 2017; 8:15260. [PMID: 28508865 PMCID: PMC5440810 DOI: 10.1038/ncomms15260] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022] Open
Abstract
The molecular mechanism through which the interaction of a clonotypic αβ T-cell receptor (TCR) with a peptide-loaded major histocompatibility complex (p/MHC) leads to T-cell activation is not yet fully understood. Here we exploit a high-affinity TCR (B4.2.3) to examine the structural changes that accompany binding to its p/MHC ligand (P18-I10/H2-Dd). In addition to conformational changes in complementarity-determining regions (CDRs) of the TCR seen in comparison of unliganded and bound X-ray structures, NMR characterization of the TCR β-chain dynamics reveals significant chemical shift effects in sites removed from the MHC-binding site. Remodelling of electrostatic interactions near the Cβ H3 helix at the membrane-proximal face of the TCR, a region implicated in interactions with the CD3 co-receptor, suggests a possible role for an allosteric mechanism in TCR signalling. The contribution of these TCR residues to signal transduction is supported by mutagenesis and T-cell functional assays.
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MESH Headings
- Allosteric Site/immunology
- Animals
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/metabolism
- Crystallography, X-Ray
- Major Histocompatibility Complex/immunology
- Mice
- Molecular Dynamics Simulation
- Mutagenesis
- Peptides/metabolism
- Protein Binding/immunology
- Protein Domains/immunology
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Signal Transduction/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew C. McShan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Rui Wang
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Huaying Zhao
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter Schuck
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mulualem E. Tilahun
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nikolaos G. Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA
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30
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Abstract
Fourier transform NMR spectroscopy has provided unprecedented insight into the structure, interaction and dynamic motion of proteins and nucleic acids. Conventional biomolecular NMR relies on the acquisition of three-dimensional and four-dimensional (4D) data matrices to establish correlations between chemical shifts in the frequency domains F 1, F 2, F 3 and F 1, F 2, F 3, F 4 respectively. While rich in information, these datasets require a substantial amount of acquisition time, are visually highly unintuitive, require expert knowledge to process, and sample dark and bright regions of the frequency domains equally. Here, we present an alternative approach to obtain multidimensional chemical shift correlations for biomolecules. This strategy focuses on one narrow frequency range, F 1 F 2, at a time and records the resulting F 3 F 4 correlation spectrum by two-dimensional NMR. As a result, only regions of the frequency domain that contain signals in F 1 F 2 ("bright regions") are sampled. F 1 F 2 selection is achieved by Hartmann-Hahn cross-polarization using weak radio frequency fields. This approach reveals information equivalent to that of a conventional 4D experiment, while the dimensional reduction may shorten the total acquisition time and simplifies spectral processing, interpretation and comparative analysis. Potential applicability of the F 1 F 2-selective approach is illustrated by de novo assignment, structural and dynamics studies of ubiquitin and fatty-acid binding protein 4 (FABP4). Further extension of this concept may spawn new selective NMR experiments to aid studies of site-specific structural dynamics, protein-protein interactions and allosteric modulation of protein structure.
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Affiliation(s)
- Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-ku Yoshida Konoe-cho, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku Kyoto-Daigaku Katsura, Kyoto, 615-8510, Japan.
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Agwa AJ, Henriques ST, Schroeder CI. Gating modifier toxin interactions with ion channels and lipid bilayers: Is the trimolecular complex real? Neuropharmacology 2017; 127:32-45. [PMID: 28400258 DOI: 10.1016/j.neuropharm.2017.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 02/14/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 11/15/2022]
Abstract
Spider peptide toxins have attracted attention because of their ability to target voltage-gated ion channels, which are involved in several pathologies including chronic pain and some cardiovascular conditions. A class of these peptides acts by modulating the gating mechanism of voltage-gated ion channels and are thus called gating modifier toxins (GMTs). In addition to their interactions with voltage-gated ion channels, some GMTs have affinity for lipid bilayers. This review discusses the potential importance of the cell membrane on the mode of action of GMTs. We propose that peptide-membrane interactions can anchor GMTs at the cell surface, thereby increasing GMT concentration in the vicinity of the channel binding site. We also propose that modulating peptide-membrane interactions might be useful for increasing the therapeutic potential of spider toxins. Furthermore, we explore the advantages and limitations of the methodologies currently used to examine peptide-membrane interactions. Although GMT-lipid membrane binding does not appear to be a requirement for the activity of all GMTs, it is an important feature, and future studies with GMTs should consider the trimolecular peptide-lipid membrane-channel complex. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Akello J Agwa
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia T Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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32
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Vallurupalli P, Sekhar A, Yuwen T, Kay LE. Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer. J Biomol NMR 2017; 67:243-271. [PMID: 28317074 DOI: 10.1007/s10858-017-0099-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [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: 01/04/2017] [Accepted: 02/20/2017] [Indexed: 05/25/2023]
Abstract
Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.
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Affiliation(s)
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada.
- Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, ON, Canada.
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33
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Puglisi R, Yan R, Adinolfi S, Pastore A. A New Tessera into the Interactome of the isc Operon: A Novel Interaction between HscB and IscS. Front Mol Biosci 2016; 3:48. [PMID: 27730125 PMCID: PMC5037179 DOI: 10.3389/fmolb.2016.00048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 07/30/2016] [Accepted: 08/22/2016] [Indexed: 12/05/2022] Open
Abstract
Iron sulfur clusters are essential universal prosthetic groups which can be formed inorganically but, in biology, are bound to proteins and produced enzymatically. Most of the components of the machine that produces the clusters are conserved throughout evolution. In bacteria, they are encoded in the isc operon. Previous reports provide information on the role of specific components but a clear picture of how the whole machine works is still missing. We have carried out a study of the effects of the co-chaperone HscB from the model system E. coli. We document a previously undetected weak interaction between the chaperone HscB and the desulfurase IscS, one of the two main players of the machine. The binding site involves a region of HscB in the longer stem of the approximately L-shaped molecule, whereas the interacting surface of IscS overlaps with the surface previously involved in binding other proteins, such as ferredoxin and frataxin. Our findings provide an entirely new perspective to our comprehension of the role of HscB and propose this protein as a component of the IscS complex.
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Affiliation(s)
- Rita Puglisi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Robert Yan
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Salvatore Adinolfi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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34
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Huang S, Umemoto R, Tamura Y, Kofuku Y, Uyeda TQ, Nishida N, Shimada I. Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin. Sci Rep 2016; 6:33690. [PMID: 27654858 DOI: 10.1038/srep33690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/23/2016] [Indexed: 11/08/2022] Open
Abstract
Actin cytoskeleton dynamics are controlled by various actin binding proteins (ABPs) that modulate the polymerization of the monomeric G-actin and the depolymerization of filamentous F-actin. Although revealing the structures of the actin/ABP complexes is crucial to understand how the ABPs regulate actin dynamics, the X-ray crystallography and cryoEM methods are inadequate to apply for the ABPs that interact with G- or F-actin with lower affinity or multiple binding modes. In this study, we aimed to establish the alternative method to build a structural model of G-actin/ABP complexes, utilizing the paramagnetic relaxation enhancement (PRE) experiments. Thymosin β4 (Tβ4) was used as a test case for validation, since its structure in complex with G-actin was reported recently. Recombinantly expressed G-actin, containing a cysteine mutation, was conjugated with a nitroxyl spin label at the specific site. Based on the intensity ratio of the 1H-15N HSQC spectra of Tβ4 in the complex with G-actin in the paramagnetic and diamagnetic states, the distances between the amide groups of Tβ4 and the spin label of G-actin were estimated. Using the PRE-derived distance constraints, we were able to compute a well-converged docking structure of the G-actin/Tβ4 complex that shows great accordance with the reference structure.
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35
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36
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Ferrage F, Dutta K, Cowburn D. Identification of Hydrophobic Interfaces in Protein-Ligand Complexes by Selective Saturation Transfer NMR Spectroscopy. Molecules 2015; 20:21992-9. [PMID: 26690112 PMCID: PMC6332028 DOI: 10.3390/molecules201219824] [Citation(s) in RCA: 2] [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: 05/06/2015] [Revised: 09/17/2015] [Accepted: 11/26/2015] [Indexed: 11/28/2022] Open
Abstract
The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase.
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Affiliation(s)
- Fabien Ferrage
- New York Structural Biology Center, New York, NY 10027, USA.
- Department of Chemistry, École Normale Supérieure-PSL Research University, 24 rue Lhomond, 75005 Paris, France.
- LBM, Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, F-75005 Paris, France.
- UMR 7203 LBM, CNRS, F-75005 Paris, France.
| | - Kaushik Dutta
- New York Structural Biology Center, New York, NY 10027, USA.
| | - David Cowburn
- New York Structural Biology Center, New York, NY 10027, USA.
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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37
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Mallis RJ, Bai K, Arthanari H, Hussey RE, Handley M, Li Z, Chingozha L, Duke-Cohan JS, Lu H, Wang JH, Zhu C, Wagner G, Reinherz EL. Pre-TCR ligand binding impacts thymocyte development before αβTCR expression. Proc Natl Acad Sci U S A 2015; 112:8373-8. [PMID: 26056289 DOI: 10.1073/pnas.1504971112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Adaptive cellular immunity requires accurate self- vs. nonself-discrimination to protect against infections and tumorous transformations while at the same time excluding autoimmunity. This vital capability is programmed in the thymus through selection of αβT-cell receptors (αβTCRs) recognizing peptides bound to MHC molecules (pMHC). Here, we show that the pre-TCR (preTCR), a pTα-β heterodimer appearing before αβTCR expression, directs a previously unappreciated initial phase of repertoire selection. Contrasting with the ligand-independent model of preTCR function, we reveal through NMR and bioforce-probe analyses that the β-subunit binds pMHC using Vβ complementarity-determining regions as well as an exposed hydrophobic Vβ patch characteristic of the preTCR. Force-regulated single bonds akin to those of αβTCRs but with more promiscuous ligand specificity trigger calcium flux. Thus, thymic development involves sequential β- and then, αβ-repertoire tuning, whereby preTCR interactions with self pMHC modulate early thymocyte expansion, with implications for β-selection, immunodominant peptide recognition, and germ line-encoded MHC interaction.
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38
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Bardelli M, Livoti E, Simonelli L, Pedotti M, Moraes A, Valente AP, Varani L. Epitope mapping by solution NMR spectroscopy: EPITOPE MAPPING BY SOLUTION NMR SPECTROSCOPY. J Mol Recognit 2015; 28:393-400. [DOI: 10.1002/jmr.2454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/21/2014] [Accepted: 11/25/2014] [Indexed: 11/07/2022]
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39
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Faggiano S, Menon RP, Kelly GP, Todi SV, Scaglione KM, Konarev PV, Svergun DI, Paulson HL, Pastore A. Allosteric regulation of deubiquitylase activity through ubiquitination. Front Mol Biosci 2015; 2:2. [PMID: 25988170 PMCID: PMC4428445 DOI: 10.3389/fmolb.2015.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 10/22/2014] [Accepted: 01/07/2015] [Indexed: 12/28/2022] Open
Abstract
Ataxin-3, the protein responsible for spinocerebellar ataxia type-3, is a cysteine protease that specifically cleaves poly-ubiquitin chains and participates in the ubiquitin proteasome pathway. The enzymatic activity resides in the N-terminal Josephin domain. An unusual feature of ataxin-3 is its low enzymatic activity especially for mono-ubiquitinated substrates and short ubiquitin chains. However, specific ubiquitination at lysine 117 in the Josephin domain activates ataxin-3 through an unknown mechanism. Here, we investigate the effects of K117 ubiquitination on the structure and enzymatic activity of the protein. We show that covalently linked ubiquitin rests on the Josephin domain, forming a compact globular moiety and occupying a ubiquitin binding site previously thought to be essential for substrate recognition. In doing so, ubiquitination enhances enzymatic activity by locking the enzyme in an activated state. Our results indicate that ubiquitin functions both as a substrate and as an allosteric regulatory factor. We provide a novel example in which a conformational switch controls the activity of an enzyme that mediates deubiquitination.
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Affiliation(s)
- Serena Faggiano
- National Institute for Medical Research, Medical Research Council London, UK
| | - Rajesh P Menon
- National Institute for Medical Research, Medical Research Council London, UK
| | - Geoff P Kelly
- Medical Research Council Biomedical NMR Centre, National Institute for Medical Research, Medical Research Council London, UK
| | - Sokol V Todi
- Department of Pharmacology and Department of Neurology, Wayne State University School of Medicine Detroit, MI, USA
| | - K Matthew Scaglione
- Department of Biochemistry and The Neuroscience Research Center, Medical College of Wisconsin Milwaukee, WI, USA
| | - Petr V Konarev
- European Molecular Biology Laboratory Hamburg, Germany ; Laboratory of Reflectometry and Small-Angle Scattering, Institute of Crystallography Russian Academy of Sciences Moscow, Russia
| | | | - Henry L Paulson
- Department of Neurology, University of Michigan Medical School Ann Arbor, MI, USA
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London London, UK
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40
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Tsutsumi N, Kimura T, Arita K, Ariyoshi M, Ohnishi H, Yamamoto T, Zuo X, Maenaka K, Park EY, Kondo N, Shirakawa M, Tochio H, Kato Z. The structural basis for receptor recognition of human interleukin-18. Nat Commun 2014; 5:5340. [PMID: 25500532 PMCID: PMC4275594 DOI: 10.1038/ncomms6340] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/20/2014] [Indexed: 12/25/2022] Open
Abstract
Interleukin (IL)-18 is a proinflammatory cytokine that belongs to the IL-1 family and plays an important role in inflammation. The uncontrolled release of this cytokine is associated with severe chronic inflammatory disease. IL-18 forms a signalling complex with the IL-18 receptor α (Rα) and β (Rβ) chains at the plasma membrane, which induces multiple inflammatory cytokines. Here, we present a crystal structure of human IL-18 bound to the two receptor extracellular domains. Generally, the receptors' recognition mode for IL-18 is similar to IL-1β; however, certain notable differences were observed. The architecture of the IL-18 receptor second domain (D2) is unique among the other IL-1R family members, which presumably distinguishes them from the IL-1 receptors that exhibit a more promiscuous ligand recognition mode. The structures and associated biochemical and cellular data should aid in developing novel drugs to neutralize IL-18 activity.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Kimura
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Kyohei Arita
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Takahiro Yamamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, , Kita-12, Nishi-6, Kita-ki, Sapporo 060-0812, Japan
| | - Enoch Y. Park
- Research Institute of Green Science and Technology, Department of Bioscience, Graduate school of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
- Heisei College of Health Sciences, 180 Kurono, Gifu 501-1131, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core Research of Evolution Science (CREST), Japan Sciences and Technology Agency, Tokyo 102-0076, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
- Biomedical Informatics, Medical Information Sciences Division, The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1194, Japan
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41
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Esaki K, Yoshinaga S, Tsuji T, Toda E, Terashima Y, Saitoh T, Kohda D, Kohno T, Osawa M, Ueda T, Shimada I, Matsushima K, Terasawa H. Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT. FEBS J 2014; 281:5552-66. [DOI: 10.1111/febs.13096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 09/09/2014] [Accepted: 09/30/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Kaori Esaki
- Department of Structural BioImaging; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
| | - Sosuke Yoshinaga
- Department of Structural BioImaging; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
| | - Tatsuichiro Tsuji
- Department of Structural BioImaging; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
| | - Etsuko Toda
- Department of Molecular Preventive Medicine; Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Yuya Terashima
- Department of Molecular Preventive Medicine; Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Takashi Saitoh
- Division of Structural Biology; Medical Institute of Bioregulation; Kyushu University; Fukuoka Japan
| | - Daisuke Kohda
- Division of Structural Biology; Medical Institute of Bioregulation; Kyushu University; Fukuoka Japan
| | - Toshiyuki Kohno
- Department of Biochemistry; Kitasato University School of Medicine; Kanagawa Japan
| | - Masanori Osawa
- Division of Physical Chemistry; Graduate School of Pharmaceutical Sciences; The University of Tokyo; Tokyo Japan
| | - Takumi Ueda
- Division of Physical Chemistry; Graduate School of Pharmaceutical Sciences; The University of Tokyo; Tokyo Japan
| | - Ichio Shimada
- Division of Physical Chemistry; Graduate School of Pharmaceutical Sciences; The University of Tokyo; Tokyo Japan
| | - Kouji Matsushima
- Department of Molecular Preventive Medicine; Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Hiroaki Terasawa
- Department of Structural BioImaging; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
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42
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Iqbal Z, Hoessli DC, Qazi WM, Ahmad M, Shakoori AR, Nasir-ud-Din. Exploring the sequence context of phosphorylatable amino acids: the contribution of the upgraded MAPRes tool. J Cell Biochem 2014; 116:370-9. [PMID: 25258092 DOI: 10.1002/jcb.24983] [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: 07/23/2014] [Accepted: 09/19/2014] [Indexed: 11/10/2022]
Abstract
Several models that predict where post-translational modifications are likely to occur and formulate the corresponding association rules are available to analyze the functional potential of a protein sequence, but an algorithm incorporating the functional groups of the involved amino acids in the sequence analyses process is not yet available. In its previous version, MAPRes was utilized to investigate the influence of the surrounding amino acids of post- translationally and co-translationally modifiable sites. The MAPRes has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post- translational modifications (PTMs). In the present study, the upgraded version of MAPRes was implemented on phosphorylated Ser/Thr/Tyr data by considering the polarity and charge of the surrounding amino acids. The patterns mined by MAPRes incorporating structural information on polarity and charge of amino acids suggest distinct structure-function relationships for phosphorylated serines in a multifunctional protein such as the insulin-receptor substrate-1 (IRS-1) protein. The new version of MAPRes is freely available at http://www.imsb.edu.pk/Database.htm.
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Affiliation(s)
- Zeeshan Iqbal
- Institute of Molecular Sciences and Bioinformatics, Lahore, Pakistan
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43
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Sher I, Chang SC, Li Y, Chhabra S, Palmer AG, Norton RS, Chill JH. Conformational flexibility in the binding surface of the potassium channel blocker ShK. Chembiochem 2014; 15:2402-10. [PMID: 25236806 DOI: 10.1002/cbic.201402295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 06/08/2014] [Indexed: 01/27/2023]
Abstract
ShK is a 35-residue peptide that binds with high affinity to human voltage-gated potassium channels through a conserved K-Y dyad. Here we have employed NMR measurements of backbone-amide (15)N spin-relaxation rates to investigate motions of the ShK backbone. Although ShK is rigid on the ps to ns timescale, increased linewidths observed for 11 backbone-amide (15)N resonances identify chemical or conformational exchange contributions to the spin relaxation. Relaxation dispersion profiles indicate that exchange between major and minor conformers occurs on the sub-millisecond timescale. Affected residues are mostly clustered around the central helix-kink-helix structure and the critical K22-Y23 motif. We suggest that the less structured minor conformer increases the exposure of Y23, known to contribute to binding affinity and selectivity, thereby facilitating its interaction with potassium channels. These findings have potential implications for the design of new channel blockers based on ShK.
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Affiliation(s)
- Inbal Sher
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900 (Israel)
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44
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Chu BCH, Otten R, Krewulak KD, Mulder FAA, Vogel HJ. The solution structure, binding properties, and dynamics of the bacterial siderophore-binding protein FepB. J Biol Chem 2014; 289:29219-34. [PMID: 25173704 DOI: 10.1074/jbc.m114.564021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 12/20/2022] Open
Abstract
The periplasmic binding protein (PBP) FepB plays a key role in transporting the catecholate siderophore ferric enterobactin from the outer to the inner membrane in Gram-negative bacteria. The solution structures of the 34-kDa apo- and holo-FepB from Escherichia coli, solved by NMR, represent the first solution structures determined for the type III class of PBPs. Unlike type I and II PBPs, which undergo large "Venus flytrap" conformational changes upon ligand binding, both forms of FepB maintain similar overall folds; however, binding of the ligand is accompanied by significant loop movements. Reverse methyl cross-saturation experiments corroborated chemical shift perturbation results and uniquely defined the binding pocket for gallium enterobactin (GaEnt). NMR relaxation experiments indicated that a flexible loop (residues 225-250) adopted a more rigid and extended conformation upon ligand binding, which positioned residues for optimal interactions with the ligand and the cytoplasmic membrane ABC transporter (FepCD), respectively. In conclusion, this work highlights the pivotal role that structural dynamics plays in ligand binding and transporter interactions in type III PBPs.
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Affiliation(s)
- Byron C H Chu
- From the Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Renee Otten
- the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, and
| | - Karla D Krewulak
- From the Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Frans A A Mulder
- the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, and the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, 8000 Aarhus C, Denmark
| | - Hans J Vogel
- From the Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada,
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45
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Dias DM, Ciulli A. NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes. Prog Biophys Mol Biol 2014; 116:101-12. [PMID: 25175337 PMCID: PMC4261069 DOI: 10.1016/j.pbiomolbio.2014.08.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/06/2014] [Accepted: 08/19/2014] [Indexed: 01/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets.
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Affiliation(s)
- David M Dias
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alessio Ciulli
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, DD1 5EH, Dundee, UK.
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46
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Shalom-Elazari H, Zazrin-Greenspon H, Shaked H, Chill JH. Global fold and backbone dynamics of the hepatitis C virus E2 glycoprotein transmembrane domain determined by NMR. Biochim Biophys Acta 2014; 1838:2919-28. [PMID: 25109935 DOI: 10.1016/j.bbamem.2014.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 06/30/2014] [Accepted: 07/22/2014] [Indexed: 01/13/2023]
Abstract
E1 and E2 are two hepatitis C viral envelope glycoproteins that assemble into a heterodimer that is essential for membrane fusion and penetration into the target cell. Both extracellular and transmembrane (TM) glycoprotein domains contribute to this interaction, but study of TM-TM interactions has been limited because synthesis and structural characterization of these highly hydrophobic segments present significant challenges. In this NMR study, by successful expression and purification of the E2 transmembrane domain as a fusion construct we have determined the global fold and characterized backbone motions for this peptide incorporated in phospholipid micelles. Backbone resonance frequencies, relaxation rates and solvent exposure measurements concur in showing this domain to adopt a helical conformation, with two helical segments spanning residues 717-726 and 732-746 connected by an unstructured linker containing the charged residues D728 and R730 involved in E1 binding. Although this linker exhibits increased local motions on the ps timescale, the dominating contribution to its relaxation is the global tumbling motion with an estimated correlation time of 12.3ns. The positioning of the helix-linker-helix architecture within the mixed micelle was established by paramagnetic NMR spectroscopy and phospholipid-peptide cross relaxation measurements. These indicate that while the helices traverse the hydrophobic interior of the micelle, the linker lies closer to the micelle perimeter to accommodate its charged residues. These results lay the groundwork for structure determination of the E1/E2 complex and a molecular understanding of glycoprotein heterodimerization.
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Affiliation(s)
| | | | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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47
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. Prog Nucl Magn Reson Spectrosc 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [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: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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48
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Ueda T, Takeuchi K, Nishida N, Stampoulis P, Kofuku Y, Osawa M, Shimada I. Cross-saturation and transferred cross-saturation experiments. Q Rev Biophys 2014; 47:143-87. [PMID: 24780282 DOI: 10.1017/S0033583514000043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Structural analyses of protein-protein interactions are required to reveal their functional mechanisms, and accurate protein-protein complex models, based on experimental results, are the starting points for drug development. In addition, structural information about proteins under physiologically relevant conditions is crucially important for understanding biological events. However, for proteins such as those embedded in lipid bilayers and transiently complexed with their effectors under physiological conditions, structural analyses by conventional methods are generally difficult, due to their large molecular weights and inhomogeneity. We have developed the cross-saturation (CS) method, which is an nuclear magnetic resonance measurement technique for the precise identification of the interfaces of protein-protein complexes. In addition, we have developed an extended version of the CS method, termed transferred cross-saturation (TCS), which enables the identification of the residues of protein ligands in close proximity to huge (>150 kDa) and heterogeneous complexes under fast exchange conditions (>0.1 s(-1)). Here, we discuss the outline, basic theory, and practical considerations of the CS and TCS methods. In addition, we will review the recent progress in the construction of models of protein-protein complexes, based on CS and TCS experiments, and applications of TCS to in situ analyses of biologically and medically important proteins in physiologically relevant states.
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49
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Carlomagno T. Present and future of NMR for RNA-protein complexes: a perspective of integrated structural biology. J Magn Reson 2014; 241:126-136. [PMID: 24656085 DOI: 10.1016/j.jmr.2013.10.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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: 08/13/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 06/03/2023]
Abstract
Nucleic acids are gaining enormous importance as key molecules in almost all biological processes. Most nucleic acids do not act in isolation but are generally associated with proteins to form high-molecular-weight nucleoprotein complexes. In this perspective article I focus on the structural studies of supra-molecular ribonucleoprotein (RNP) assemblies in solution by a combination of state-of-the-art TROSY-based NMR experiments and other structural biology techniques. I discuss ways how to combine sparse NMR data with low-resolution structural information from small-angle scattering, fluorescence and electron paramagnetic resonance spectroscopy to obtain the structure of large RNP particles by an integrated structural biology approach. In the last section I give a perspective for the study of RNP complexes by solid-state NMR.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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50
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Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP. Competitive and cooperative interactions mediate RNA transfer from herpesvirus saimiri ORF57 to the mammalian export adaptor ALYREF. PLoS Pathog 2014; 10:e1003907. [PMID: 24550725 DOI: 10.1371/journal.ppat.1003907] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 12/16/2013] [Indexed: 01/08/2023] Open
Abstract
The essential herpesvirus adaptor protein HVS ORF57, which has homologs in all other herpesviruses, promotes viral mRNA export by utilizing the cellular mRNA export machinery. ORF57 protein specifically recognizes viral mRNA transcripts, and binds to proteins of the cellular transcription-export (TREX) complex, in particular ALYREF. This interaction introduces viral mRNA to the NXF1 pathway, subsequently directing it to the nuclear pore for export to the cytoplasm. Here we have used a range of techniques to reveal the sites for direct contact between RNA and ORF57 in the absence and presence of ALYREF. A binding site within ORF57 was characterized which recognizes specific viral mRNA motifs. When ALYREF is present, part of this ORF57 RNA binding site, composed of an α-helix, binds preferentially to ALYREF. This competitively displaces viral RNA from the α-helix, but contact with RNA is still maintained by a flanking region. At the same time, the flexible N-terminal domain of ALYREF comes into contact with the viral RNA, which becomes engaged in an extensive network of synergistic interactions with both ALYREF and ORF57. Transfer of RNA to ALYREF in the ternary complex, and involvement of individual ORF57 residues in RNA recognition, were confirmed by UV cross-linking and mutagenesis. The atomic-resolution structure of the ORF57-ALYREF interface was determined, which noticeably differed from the homologous ICP27-ALYREF structure. Together, the data provides the first site-specific description of how viral mRNA is locked by a herpes viral adaptor protein in complex with cellular ALYREF, giving herpesvirus access to the cellular mRNA export machinery. The NMR strategy used may be more generally applicable to the study of fuzzy protein-protein-RNA complexes which involve flexible polypeptide regions.
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