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Alzahrani N, Wu MJ, Sousa CF, Kalinina OV, Welsch C, Yi M. SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency. PLoS Pathog 2022; 18:e1010310. [PMID: 35130329 PMCID: PMC8853643 DOI: 10.1371/journal.ppat.1010310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/17/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
Recent studies identified signal peptidase complex subunit 1 (SPCS1) as a proviral host factor for Flaviviridae viruses, including HCV. One of the SPCS1’s roles in flavivirus propagation was attributed to its regulation of signal peptidase complex (SPC)-mediated processing of flavivirus polyprotein, especially C-prM junction. However, whether SPCS1 also regulates any SPC-mediated processing sites within HCV polyprotein remains unclear. In this study, we determined that loss of SPCS1 specifically impairs the HCV E2-p7 processing by the SPC. We also determined that efficient separation of E2 and p7, regardless of its dependence on SPC-mediated processing, leads to SPCS1 dispensable for HCV assembly These results suggest that SPCS1 regulates HCV assembly by facilitating the SPC-mediated processing of E2-p7 precursor. Structural modeling suggests that intrinsically delayed processing of the E2-p7 is likely caused by the structural rigidity of p7 N-terminal transmembrane helix-1 (p7/TM1/helix-1), which has mostly maintained membrane-embedded conformations during molecular dynamics (MD) simulations. E2-p7-processing-impairing p7 mutations narrowed the p7/TM1/helix-1 bending angle against the membrane, resulting in closer membrane embedment of the p7/TM1/helix-1 and less access of E2-p7 junction substrate to the catalytic site of the SPC, located well above the membrane in the ER lumen. Based on these results we propose that the key mechanism of action of SPCS1 in HCV assembly is to facilitate the E2-p7 processing by enhancing the E2-p7 junction site presentation to the SPC active site. By providing evidence that SPCS1 facilitates HCV assembly by regulating SPC-mediated cleavage of E2-p7 junction, equivalent to the previously established role of this protein in C-prM junction processing in flavivirus, this study establishes the common role of SPCS1 in Flaviviridae family virus propagation as to exquisitely regulate the SPC-mediated processing of specific, suboptimal target sites.
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Affiliation(s)
- Nabeel Alzahrani
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Ming-Jhan Wu
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Carla F. Sousa
- Drug Bioinformatics Group, HIPS, HZI, Saarbrücken, Germany
| | - Olga V. Kalinina
- Drug Bioinformatics Group, HIPS, HZI, Saarbrücken, Germany
- Medical Faculty, Saarland University, Homburg, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital, Frankfurt am Main, Germany
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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2
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Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. ENTROPY 2021; 23:e23050571. [PMID: 34066581 PMCID: PMC8148522 DOI: 10.3390/e23050571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions.
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Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
- Correspondence: ; Tel.: +1-650-604-5759
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3
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Gilbert RJC. Electron microscopy as a critical tool in the determination of pore forming mechanisms in proteins. Methods Enzymol 2021; 649:71-102. [PMID: 33712203 DOI: 10.1016/bs.mie.2021.01.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Electron microscopy has consistently played an important role in the description of pore-forming protein systems. The discovery of pore-forming proteins has depended on visualization of the structural pores formed by their oligomeric protein complexes, and as electron microscopy has advanced technologically so has the degree of insight it has been able to give. This review considers a large number of published studies of pore-forming complexes in prepore and pore states determined using single-particle cryo-electron microscopy. Sample isolation and preparation, imaging and image analysis, structure determination and optimization of results are all discussed alongside challenges which pore-forming proteins particularly present. The review also considers the use made of cryo-electron tomography to study pores within their membrane environment and which will prove an increasingly important approach for the future.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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4
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Yeh V, Goode A, Bonev BB. Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR. BIOLOGY 2020; 9:E396. [PMID: 33198410 PMCID: PMC7697852 DOI: 10.3390/biology9110396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022]
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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Affiliation(s)
| | | | - Boyan B. Bonev
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (V.Y.); (A.G.)
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5
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Shaw J, Gosain R, Kalita MM, Foster TL, Kankanala J, Mahato DR, Abas S, King BJ, Scott C, Brown E, Bentham MJ, Wetherill L, Bloy A, Samson A, Harris M, Mankouri J, Rowlands DJ, Macdonald A, Tarr AW, Fischer WB, Foster R, Griffin S. Rationally derived inhibitors of hepatitis C virus (HCV) p7 channel activity reveal prospect for bimodal antiviral therapy. eLife 2020; 9:e52555. [PMID: 33169665 PMCID: PMC7714397 DOI: 10.7554/elife.52555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
Since the 1960s, a single class of agent has been licensed targeting virus-encoded ion channels, or 'viroporins', contrasting the success of channel blocking drugs in other areas of medicine. Although resistance arose to these prototypic adamantane inhibitors of the influenza A virus (IAV) M2 proton channel, a growing number of clinically and economically important viruses are now recognised to encode essential viroporins providing potential targets for modern drug discovery. We describe the first rationally designed viroporin inhibitor with a comprehensive structure-activity relationship (SAR). This step-change in understanding not only revealed a second biological function for the p7 viroporin from hepatitis C virus (HCV) during virus entry, but also enabled the synthesis of a labelled tool compound that retained biological activity. Hence, p7 inhibitors (p7i) represent a unique class of HCV antiviral targeting both the spread and establishment of infection, as well as a precedent for future viroporin-targeted drug discovery.
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Affiliation(s)
- Joseph Shaw
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Rajendra Gosain
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Monoj Mon Kalita
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Toshana L Foster
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jayakanth Kankanala
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - D Ram Mahato
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Sonia Abas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Barnabas J King
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | - Claire Scott
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Emma Brown
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Matthew J Bentham
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Laura Wetherill
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Abigail Bloy
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Adel Samson
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
| | - Mark Harris
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jamel Mankouri
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Andrew Macdonald
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Alexander W Tarr
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | | | - Richard Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Stephen Griffin
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
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6
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Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies. Viruses 2020; 12:v12101069. [PMID: 32987909 PMCID: PMC7599928 DOI: 10.3390/v12101069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.
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7
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Alam I, Kamau AA, Kulmanov M, Jaremko Ł, Arold ST, Pain A, Gojobori T, Duarte CM. Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2. Front Cell Infect Microbiol 2020; 10:405. [PMID: 32850499 PMCID: PMC7396417 DOI: 10.3389/fcimb.2020.00405] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social, and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells. The S proteins from SARS and SARS-CoV-2 are similar, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-specific neutralizing antibodies to inhibit SARS-CoV-2. Here we used comparative pangenomic analysis of all sequenced reference Betacoronaviruses, complemented with functional and structural analyses. This analysis reveals that, among all core gene clusters present in these viruses, the envelope protein E shows a variant cluster shared by SARS and SARS-CoV-2 with two completely-conserved key functional features, namely an ion-channel, and a PDZ-binding motif (PBM). These features play a key role in the activation of the inflammasome causing the acute respiratory distress syndrome, the leading cause of death in SARS and SARS-CoV-2 infections. Together with functional pangenomic analysis, mutation tracking, and previous evidence, on E protein as a determinant of pathogenicity in SARS, we suggest E protein as an alternative therapeutic target to be considered for further studies to reduce complications of SARS-CoV-2 infections in COVID-19.
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Affiliation(s)
- Intikhab Alam
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Allan A. Kamau
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maxat Kulmanov
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Arnab Pain
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takashi Gojobori
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M. Duarte
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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8
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Puthenveetil R, Vinogradova O. Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments. J Biol Chem 2019; 294:15914-15931. [PMID: 31551353 DOI: 10.1074/jbc.rev119.009178] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.
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Affiliation(s)
- Robbins Puthenveetil
- Department of Molecular and Cell Biology, college of liberal arts and sciences, University of Connecticut at Storrs, Storrs, Connecticut 06269
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, Connecticut 06269
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9
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Chen W, OuYang B, Chou JJ. Critical Effect of the Detergent:Protein Ratio on the Formation of the Hepatitis C Virus p7 Channel. Biochemistry 2019; 58:3834-3837. [PMID: 31468972 DOI: 10.1021/acs.biochem.9b00636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The p7 protein encoded by the hepatitis C virus forms a cation-selective viroporin in the membrane. One of the most intriguing findings about the p7 viroporin is its unique hexameric structure in dodecylphosphocholine (DPC) micelles determined by nuclear magnetic resonance (NMR), but the hexameric structure was recently challenged by another NMR study of p7, also in DPC detergent, which claimed that the p7 in this detergent is monomeric. Here, we show that p7 oligomerization is highly sensitive to the detergent:protein ratio used in protein reconstitution and that the 40-fold difference in this ratio between the two studies was the cause of their different conclusions. In addition, we have performed extensive measurements of interchain paramagnetic relaxation enhancements (PREs) for p7 hexamers reconstituted in DPC micelles and in 1,2-dimyristoyl-sn-glycero-3-phosphocholine/1,2-dihexanoyl-sn-glycero-3-phosphocholine bicelles. In both cases, interchain PREs are overall consistent with the hexameric structure determined in micelles. Our data validate the overall architecture of the p7 hexamer while highlighting the importance of the detergent:protein ratio in membrane protein sample preparation.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 201203 , China
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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10
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Oestringer BP, Bolivar JH, Claridge JK, Almanea L, Chipot C, Dehez F, Holzmann N, Schnell JR, Zitzmann N. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features. Sci Rep 2019; 9:8383. [PMID: 31182749 PMCID: PMC6557816 DOI: 10.1038/s41598-019-44413-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
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Affiliation(s)
- Benjamin P Oestringer
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RY, United Kingdom
| | - Juan H Bolivar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Jolyon K Claridge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Latifah Almanea
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Chris Chipot
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois, 61801, United States
| | - François Dehez
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Nicole Holzmann
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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