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Park SH, Siddiqi H, Castro DV, De Angelis AA, Oom AL, Stoneham CA, Lewinski MK, Clark AE, Croker BA, Carlin AF, Guatelli J, Opella SJ. Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. PLoS Pathog 2021; 17:e1009519. [PMID: 34003853 PMCID: PMC8184013 DOI: 10.1371/journal.ppat.1009519] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/07/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. The novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Haley Siddiqi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniela V. Castro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Anna A. De Angelis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Aaron L. Oom
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Charlotte A. Stoneham
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Mary K. Lewinski
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - John Guatelli
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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2
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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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3
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DeLisle CF, Malooley AL, Banerjee I, Lorieau JL. Pro-islet amyloid polypeptide in micelles contains a helical prohormone segment. FEBS J 2020; 287:4440-4457. [PMID: 32077246 DOI: 10.1111/febs.15253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 01/17/2020] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
Pro-islet amyloid polypeptide (proIAPP) is the prohormone precursor molecule to IAPP, also known as amylin. IAPP is a calcitonin family peptide hormone that is cosecreted with insulin, and largely responsible for hunger satiation and metabolic homeostasis. Amyloid plaques containing mixtures of mature IAPP and misprocessed proIAPP deposit on, and destroy pancreatic β-cell membranes, and they are recognized as a clinical hallmark of type 2 diabetes mellitus. In order to better understand the interaction with cellular membranes, we solved the solution NMR structure of proIAPP bound to dodecylphosphocholine micelles at pH 4.5. We show that proIAPP is a dynamic molecule with four α-helices. The first two helices are contained within the mature IAPP sequence, while the second two helices are part of the C-terminal prohormone segment (Cpro). We mapped the membrane topology of the amphipathic helices by paramagnetic relaxation enhancement, and we used CD and diffusion-ordered spectroscopy to identify environmental factors that impact proIAPP membrane affinity. We discuss how our structural results relate to prohormone processing based on the varied pH environments and lipid compositions of organelle membranes within the regulated secretory pathway, and the likelihood of Cpro survival for cosecretion with IAPP. DATABASE: The assigned resonances have been deposited in the Biological Magnetic Resonance Bank (BMRB) with accession numbers 50007 and 50019 for proIAPP and Cpro, respectively. The lowest energy structures have been deposited in the Protein Data Bank (PDB) with access codes 6UCJ and 6UCK.
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Affiliation(s)
- Charles F DeLisle
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Indrani Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
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4
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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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5
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Computational Study of HCV p7 Channel: Insight into a New Strategy for HCV Inhibitor Design. Interdiscip Sci 2018; 11:292-299. [PMID: 30194627 DOI: 10.1007/s12539-018-0306-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/23/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
HCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydrated cations. The binding pocket for the channel blockers, e.g., amantadine and rimantadine, was composed of residues 20-26 in H2 helix and 52-60 in H3 helix in i + 2 monomer. However, the molecular volumes for both amantadine and rimantadine were too small for the binding pocket of HCV p7 channel. Thus, designing a compound similar with rimantadine and having much larger volume would be an effective strategy for discovering inhibitors against HCV p7 channel. To achieve this point, we used rimantadine as a structural template to search ChEMBL database for the candidates employing favorable binding affinities to HCV p7 channel. As a result, six candidates were identified to have potential to be novel inhibitors against HCV p7 channel.
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6
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Cao Y, Dong Y, Chou JJ. Structural and Functional Properties of Viral Membrane Proteins. ADVANCES IN MEMBRANE PROTEINS 2018. [PMCID: PMC7122571 DOI: 10.1007/978-981-13-0532-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Viruses have developed a large variety of transmembrane proteins to carry out their infectious cycles. Some of these proteins are simply anchored to membrane via transmembrane helices. Others, however, adopt more interesting structures to perform tasks such as mediating membrane fusion and forming ion-permeating channels. Due to the dynamic or plastic nature shown by many of the viral membrane proteins, structural and mechanistic understanding of these proteins has lagged behind their counterparts in prokaryotes and eukaryotes. This chapter provides an overview of the use of NMR spectroscopy to unveil the transmembrane and membrane-proximal regions of viral membrane proteins, as well as their interactions with potential therapeutics.
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Affiliation(s)
- Yu Cao
- Institute of Precision Medicine, The Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Chen W, Dev J, Mezhyrova J, Pan L, Piai A, Chou JJ. The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure 2018; 26:627-634.e4. [PMID: 29551287 PMCID: PMC5884736 DOI: 10.1016/j.str.2018.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/24/2018] [Accepted: 02/09/2018] [Indexed: 01/14/2023]
Abstract
The p7 protein of the hepatitis C virus (HCV) can oligomerize in membrane to form cation channels. Previous studies showed that the channel assembly in detergent micelles adopts a unique flower-shaped oligomer, but the unusual architecture also presented problems for understanding how this viroporin resides in the membrane. Moreover, the oligomeric state of p7 remains controversial, as both hexamer and heptamer have been proposed. Here we address the above issues using p7 reconstituted in bicelles that mimic a lipid bilayer. We found, using a recently developed oligomer-labeling method, that p7 forms hexamers in the bicelles. Solvent paramagnetic relaxation enhancement analyses showed that the bilayer thickness around the HCV ion channel is substantially smaller than expected, and thus a significant portion of the previously assigned membrane-embedded region is solvent exposed. Our study provides an effective approach for characterizing the transmembrane partition of small ion channels in near lipid bilayer environment.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jyoti Dev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Liqiang Pan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, China.
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8
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Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study. Biophys Chem 2018; 233:47-54. [DOI: 10.1016/j.bpc.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022]
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9
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Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity. Biophys J 2017; 113:2311-2315. [PMID: 29056231 PMCID: PMC5722206 DOI: 10.1016/j.bpj.2017.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/12/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022] Open
Abstract
Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.
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Affiliation(s)
- François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Paul Schanda
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Grenoble, France.
| | - Martin S King
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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10
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Non-Enveloped Virus Entry: Structural Determinants and Mechanism of Functioning of a Viral Lytic Peptide. J Mol Biol 2016; 428:3540-56. [DOI: 10.1016/j.jmb.2016.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 11/20/2022]
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11
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Holzmann N, Chipot C, Penin F, Dehez F. Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments. Bioorg Med Chem 2016; 24:4920-4927. [PMID: 27501910 DOI: 10.1016/j.bmc.2016.07.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
The viroporin p7 of the hepatitis C virus forms multimeric channels eligible for ion transport across the endoplasmic reticulum membrane. Currently the subject of many studies and discussion, the molecular assembly of the ion channel and the structural characteristics of the p7 monomer are not yet fully understood. Structural investigation of p7 has been carried out only in detergent environments, making the interpretation of the experimental results somewhat questionable. Here, we analyze by means of molecular dynamics simulations the structure of the p7 monomer as a function of its sequence, initial conformation and environment. We investigate the conductance properties of three models of a hexameric p7 ion channel by examining ion translocation in a pure lipid bilayer. It is noteworthy that although none of the models reflects the experimentally observed trend to conduct preferentially cations, we were able to identify the position and orientation of titratable acidic or basic residues playing a crucial role in ion selectivity and in the overall conductance of the channel. In addition, too compact a packing of the monomers leads to channel collapse rather than formation of a reasonable pore, amenable to ion translocation. The present findings are envisioned to help assess the physiological relevance of p7 ion channel models consisting of multimeric structures obtained in non-native environments.
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Affiliation(s)
- Nicole Holzmann
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Christophe Chipot
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Penin
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, UMR 5086, Université de Lyon, 69367 Lyon, France; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, UMR 5086, CNRS, 69367 Lyon, France
| | - François Dehez
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France.
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12
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Laasch N, Kalita MM, Griffin S, Fischer WB. Small molecule ligand docking to genotype specific bundle structures of hepatitis C virus (HCV) p7 protein. Comput Biol Chem 2016; 64:56-63. [PMID: 27258799 DOI: 10.1016/j.compbiolchem.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 04/28/2016] [Indexed: 01/26/2023]
Abstract
The genome of hepatitis C virus encodes for an essential 63 amino acid polytopic protein p7 of most likely two transmembrane domains (TMDs). The protein is identified to self-assemble thereby rendering lipid membranes permeable to ions. A series of small molecules such as adamantanes, imino sugars and guanidinium compounds are known to interact with p7. A set of 9 of these small molecules is docked against hexameric bundles of genotypes 5a (bundle-5a) and 1b (bundle-1b) using LeadIT. Putative sites for bundle-5a are identified within the pore and at pockets on the outside of the bundle. For bundle-1b preferred sites are found at the site of the loops. Binding energies are in favour of the guanidinium compounds. Rescoring of the identified poses with HYDE reveals a dehydration penalty for the guanidinium compounds, leaving the adamantanes and imino sugar in a better position. Binding energies calculated by HYDE and those by LeadIT indicate that all compounds are moderate binders.
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Affiliation(s)
- Niklas Laasch
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Stephen Griffin
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
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13
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Padhi S, Priyakumar UD. Cooperation of Hydrophobic Gating, Knock-on Effect, and Ion Binding Determines Ion Selectivity in the p7 Channel. J Phys Chem B 2016; 120:4351-6. [DOI: 10.1021/acs.jpcb.6b00684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Siladitya Padhi
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - U. Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
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14
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Kalita MM, Fischer WB. Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1462-70. [PMID: 27079148 DOI: 10.1016/j.bbamem.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/01/2023]
Abstract
Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
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15
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Jovanovic-Cupic S, Glisic S, Stanojevic M, Nozic D, Petrovic N, Mandusic V, Krajnovic M. The influence of host factors and sequence variability of the p7 region on the response to pegylated interferon/ribavirin therapy for chronic hepatitis C genotype 1b in patients from Serbia. Arch Virol 2016; 161:1189-98. [PMID: 26860912 DOI: 10.1007/s00705-016-2777-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/27/2016] [Indexed: 12/31/2022]
Abstract
The goal of this study was to identify host and viral factors affecting the response to pegylated interferon/ribavirin (PEG-IFN/RBV) treatment in patients with chronic hepatitis C genotype 1b. Baseline characteristics of the patients and sequences within the p7 region were analyzed in pre-treatment serum samples from 53 individuals with chronic hepatitis C genotype 1b and related to the outcome of therapy. We found a significant correlation between age and response to therapy (p < 0.001). Furthermore, the pre-treatment viral load was closely associated with the stage of liver fibrosis (p < 0.001). The presence of fewer than 4 mutations and age above 40 were significantly associated with non-response (NR) (p < 0.001). Our findings may be useful for estimating the likelihood of achieving a sustained virologic response (SVR) in patients who are chronically infected with hepatitis C virus genotype 1b.
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Affiliation(s)
- Snezana Jovanovic-Cupic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia.
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
| | - Darko Nozic
- Clinics of Infectious and Tropical Diseases, Military Medical Academy, 11000, Belgrade, Serbia
| | - Nina Petrovic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Vesna Mandusic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Milena Krajnovic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
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16
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Fischer WB, Kalita MM, Heermann D. Viral channel forming proteins--How to assemble and depolarize lipid membranes in silico. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1710-21. [PMID: 26806161 PMCID: PMC7094687 DOI: 10.1016/j.bbamem.2016.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/23/2023]
Abstract
Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug–protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Early references about the discovery of viral channel forming proteins. Latest structural information about the class of proteins. Identification of structural motifs, assembly mechanism of function and drug action using computational methods. Outlook for the use of coarse grained techniques to address assembly and integration into cellular processes.
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Affiliation(s)
- Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Dieter Heermann
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
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17
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Abstract
Since the discovery that certain small viral membrane proteins, collectively termed as viroporins, can permeabilize host cellular membranes and also behave as ion channels, attempts have been made to link this feature to specific biological roles. In parallel, most viroporins identified so far are virulence factors, and interest has focused toward the discovery of channel inhibitors that would have a therapeutic effect, or be used as research tools to understand the biological roles of viroporin ion channel activity. However, this paradigm is being shifted by the difficulties inherent to small viral membrane proteins, and by the realization that protein-protein interactions and other diverse roles in the virus life cycle may represent an equal, if not, more important target. Therefore, although targeting the channel activity of viroporins can probably be therapeutically useful in some cases, the focus may shift to their other functions in following years. Small-molecule inhibitors have been mostly developed against the influenza A M2 (IAV M2 or AM2). This is not surprising since AM2 is the best characterized viroporin to date, with a well-established biological role in viral pathogenesis combined the most extensive structural investigations conducted, and has emerged as a validated drug target. For other viroporins, these studies are still mostly in their infancy, and together with those for AM2, are the subject of the present review.
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18
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"Too little, too late?" Will inhibitors of the hepatitis C virus p7 ion channel ever be used in the clinic? Future Med Chem 2015; 6:1893-907. [PMID: 25495983 DOI: 10.4155/fmc.14.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is a virus-coded ion channel, or 'viroporin'. p7 is an essential HCV protein, promoting infectious virion production, and this process can be blocked by prototypic p7 inhibitors. However, prototype potency is weak and effects in clinical trials are unsatisfactory. Nevertheless, recent structural studies render p7 amenable to modern drug discovery, with studies supporting that effective drug-like molecules should be achievable. However, burgeoning HCV therapies clear infection in the majority of treated patients. This perspective summarizes current understanding of p7 channel function and structure, pertaining to the development of improved p7 inhibitors. We ask, 'is this too little, too late', or could p7 inhibitors play a role in the long-term management of HCV disease?
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19
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Hong W, Lang Y, Li T, Zeng Z, Song Y, Wu Y, Li W, Cao Z. A p7 Ion Channel-derived Peptide Inhibits Hepatitis C Virus Infection in Vitro. J Biol Chem 2015; 290:23254-63. [PMID: 26251517 DOI: 10.1074/jbc.m115.662452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 11/06/2022] Open
Abstract
Viral infection is an early stage of its life cycle and represents a promising target for antiviral drug development. Here we designed and characterized three peptide inhibitors of hepatitis C virus (HCV) infection based on the structural features of the membrane-associated p7 polypeptide of HCV. The three peptides exhibited low toxicity and high stability while potently inhibiting initial HCV infection and suppressed established HCV infection at non-cytotoxic concentrations in vitro. The most efficient peptide (designated H2-3), which is derived from the H2 helical region of HCV p7 ion channel, inhibited HCV infection by inactivating both intracellular and extracellular viral particles. The H2-3 peptide inactivated free HCV with an EC50 (50% effective concentration) of 82.11 nm, which is >1000-fold lower than the CC50 (50% cytotoxic concentration) of Huh7.5.1 cells. H2-3 peptide also bound to cell membrane and protected host cells from viral infection. The peptide H2-3 did not alter the normal electrophysiological profile of the p7 ion channel or block viral release from Huh7.5.1 cells. Our work highlights a new anti-viral peptide design strategy based on ion channel, giving the possibility that ion channels are potential resources to generate antiviral peptides.
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Affiliation(s)
- Wei Hong
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yange Lang
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tian Li
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhengyang Zeng
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Song
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingliang Wu
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxin Li
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhijian Cao
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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20
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Opella SJ. Relating structure and function of viral membrane-spanning miniproteins. Curr Opin Virol 2015; 12:121-5. [PMID: 26057606 DOI: 10.1016/j.coviro.2015.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/25/2022]
Abstract
Many viruses express small hydrophobic membrane proteins. These proteins are often referred to as viroporins because they exhibit ion channel activity. However, the channel activity has not been definitively associated with a biological function in all cases. More generally, protein-protein and protein-phospholipid interactions have been associated with specific biological activities of these proteins. As research has progressed there is a decreased emphasis on potential roles of the channel activity, and increased research on multiple other biological functions. This being the case, it may be more appropriate to refer to them as 'viral membrane-spanning miniproteins'. Structural studies are illustrated with Vpu from HIV-1 and p7 from HCV.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA.
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21
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Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
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Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
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22
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Padhi S, Priyakumar UD. Ion Hydration Dynamics in Conjunction with a Hydrophobic Gating Mechanism Regulates Ion Permeation in p7 Viroporin from Hepatitis C Virus. J Phys Chem B 2015; 119:6204-10. [DOI: 10.1021/acs.jpcb.5b02759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Siladitya Padhi
- Centre for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - U. Deva Priyakumar
- Centre for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
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23
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Dev J, Brüschweiler S, Ouyang B, Chou JJ. Transverse relaxation dispersion of the p7 membrane channel from hepatitis C virus reveals conformational breathing. JOURNAL OF BIOMOLECULAR NMR 2015; 61:369-78. [PMID: 25724842 PMCID: PMC4398636 DOI: 10.1007/s10858-015-9912-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/20/2015] [Indexed: 05/22/2023]
Abstract
The p7 membrane protein encoded by hepatitis C virus (HCV) assembles into a homo-hexamer that selectively conducts cations. An earlier solution NMR structure of the hexameric complex revealed a funnel-like architecture and suggests that a ring of conserved asparagines near the narrow end of the funnel are important for cation interaction. NMR based drug-binding experiments also suggest that rimantadine can allosterically inhibit ion conduction via a molecular wedge mechanism. These results suggest the presence of dilation and contraction of the funnel tip that are important for channel activity and that the action of the drug is attenuating this motion. Here, we determined the conformational dynamics and solvent accessibility of the p7 channel. The proton exchange measurements show that the cavity-lining residues are largely water accessible, consistent with the overall funnel shape of the channel. Our relaxation dispersion data show that residues Val7 and Leu8 near the asparagine ring are subject to large chemical exchange, suggesting significant intrinsic channel breathing at the tip of the funnel. Moreover, the hinge regions connecting the narrow and wide regions of the funnel show strong relaxation dispersion and these regions are the binding sites for rimantadine. Presence of rimantadine decreases the conformational dynamics near the asparagine ring and the hinge area. Our data provide direct observation of μs-ms dynamics of the p7 channel and support the molecular wedge mechanism of rimantadine inhibition of the HCV p7 channel.
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Affiliation(s)
- Jyoti Dev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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24
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Kalita MM, Griffin S, Chou JJ, Fischer WB. Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1383-92. [PMID: 25772504 PMCID: PMC7094707 DOI: 10.1016/j.bbamem.2015.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/12/2015] [Accepted: 03/06/2015] [Indexed: 12/12/2022]
Abstract
The 63 amino acid polytopic membrane protein, p7, encoded by hepatitis C virus (HCV) is involved in the modulation of electrochemical gradients across membranes within infected cells. Structural information relating to p7 from multiple genotypes has been generated in silico (e.g. genotype (GT) 1a), as well as obtained from experiments in form of monomeric and hexameric structures (GTs 1b and 5a, respectively). However, sequence diversity and structural differences mean that comparison of their channel gating behaviour has not thus far been simulated. Here, a molecular model of the monomeric GT 1a protein is optimized and assembled into a hexameric bundle for comparison with both the 5a hexamer structure and another hexameric bundle generated using the GT 1b monomer structure. All bundles tend to turn into a compact structure during molecular dynamics (MD) simulations (Gromos96 (ffG45a3)) in hydrated lipid bilayers, as well as when simulated at 'low pH', which may trigger channel opening according to some functional studies. Both GT 1a and 1b channel models are gated via movement of the parallel aligned helices, yet the scenario for the GT 5a protein is more complex, with a short N-terminal helix being involved. However, all bundles display pulsatile dynamics identified by monitoring water dynamics within the pore.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, TW
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology, Faculty of Medicine and Health, St James' University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, UK
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, TW.
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25
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Das BB, Park SH, Opella SJ. Membrane protein structure from rotational diffusion. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:229-45. [PMID: 24747039 PMCID: PMC4201901 DOI: 10.1016/j.bbamem.2014.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/02/2014] [Indexed: 02/02/2023]
Abstract
The motional averaging of powder pattern line shapes is one of the most fundamental aspects of sold-state NMR. Since membrane proteins in liquid crystalline phospholipid bilayers undergo fast rotational diffusion, all of the signals reflect the angles of the principal axes of their dipole-dipole and chemical shift tensors with respect to the axis defined by the bilayer normal. The frequency span and sign of the axially symmetric powder patterns that result from motional averaging about a common axis provide sufficient structural restraints for the calculation of the three-dimensional structure of a membrane protein in a phospholipid bilayer environment. The method is referred to as rotationally aligned (RA) solid-state NMR and demonstrated with results on full-length, unmodified membrane proteins with one, two, and seven trans-membrane helices. RA solid-state NMR is complementary to other solid-state NMR methods, in particular oriented sample (OS) solid-state NMR of stationary, aligned samples. Structural distortions of membrane proteins from the truncations of terminal residues and other sequence modifications, and the use of detergent micelles instead of phospholipid bilayers have also been demonstrated. Thus, it is highly advantageous to determine the structures of unmodified membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. RA solid-state NMR provides a general method for obtaining accurate and precise structures of membrane proteins under near-native conditions.
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Affiliation(s)
- Bibhuti B Das
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA.
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26
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Ion-dynamics in hepatitis C virus p7 helical transmembrane domains — a molecular dynamics simulation study. Biophys Chem 2014; 192:33-40. [DOI: 10.1016/j.bpc.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/31/2022]
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27
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Fan X, Xue B, Dolan PT, LaCount DJ, Kurgan L, Uversky VN. The intrinsic disorder status of the human hepatitis C virus proteome. MOLECULAR BIOSYSTEMS 2014; 10:1345-63. [PMID: 24752801 DOI: 10.1039/c4mb00027g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many viral proteins or their biologically important regions are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions do not possess unique structures and possess functions that complement the functional repertoire of "normal" ordered proteins and domains, with many protein functional classes being heavily dependent on the intrinsic disorder. Viruses commonly use these highly flexible regions to invade the host organisms and to hijack various host systems. These disordered regions also help viruses in adapting to their hostile habitats and to manage their economic usage of genetic material. In this article, we focus on the structural peculiarities of proteins from human hepatitis C virus (HCV) and use a wide spectrum of bioinformatics techniques to evaluate the abundance of intrinsic disorder in the completed proteomes of several human HCV genotypes, to analyze the peculiarities of disorder distribution within the individual HCV proteins, and to establish potential roles of the structural disorder in functions of ten HCV proteins. We show that the intrinsic disorder or increased flexibility is not only abundant in these proteins, but is also absolutely necessary for their functions, playing a crucial role in the proteolytic processing of the HCV polyprotein, the maturation of the individual HCV proteins, and being related to the posttranslational modifications of these proteins and their interactions with DNA, RNA, and various host proteins.
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Affiliation(s)
- Xiao Fan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta AB T6G 2V4, Canada.
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28
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Foster TL, Thompson GS, Kalverda AP, Kankanala J, Bentham M, Wetherill LF, Thompson J, Barker AM, Clarke D, Noerenberg M, Pearson AR, Rowlands DJ, Homans SW, Harris M, Foster R, Griffin S. Structure-guided design affirms inhibitors of hepatitis C virus p7 as a viable class of antivirals targeting virion release. Hepatology 2014; 59:408-22. [PMID: 24022996 PMCID: PMC4298801 DOI: 10.1002/hep.26685] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 08/07/2013] [Indexed: 01/02/2023]
Abstract
UNLABELLED Current interferon-based therapy for hepatitis C virus (HCV) infection is inadequate, prompting a shift toward combinations of direct-acting antivirals (DAA) with the first protease-targeted drugs licensed in 2012. Many compounds are in the pipeline yet primarily target only three viral proteins, namely, NS3/4A protease, NS5B polymerase, and NS5A. With concerns growing over resistance, broadening the repertoire for DAA targets is a major priority. Here we describe the complete structure of the HCV p7 protein as a monomeric hairpin, solved using a novel combination of chemical shift and nuclear Overhauser effect (NOE)-based methods. This represents atomic resolution information for a full-length virus-coded ion channel, or "viroporin," whose essential functions represent a clinically proven class of antiviral target exploited previously for influenza A virus therapy. Specific drug-protein interactions validate an allosteric site on the channel periphery and its relevance is demonstrated by the selection of novel, structurally diverse inhibitory small molecules with nanomolar potency in culture. Hit compounds represent a 10,000-fold improvement over prototypes, suppress rimantadine resistance polymorphisms at submicromolar concentrations, and show activity against other HCV genotypes. CONCLUSION This proof-of-principle that structure-guided design can lead to drug-like molecules affirms p7 as a much-needed new target in the burgeoning era of HCV DAA.
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Affiliation(s)
- Toshana L Foster
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK,School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Gary S Thompson
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Arnout P Kalverda
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Jayakanth Kankanala
- School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Matthew Bentham
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK
| | - Laura F Wetherill
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK
| | - Joseph Thompson
- School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Amy M Barker
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Dean Clarke
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Marko Noerenberg
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Arwen R Pearson
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - David J Rowlands
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Steven W Homans
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Mark Harris
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Richard Foster
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK,School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK,Address reprint requests to: Stephen Griffin, Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St. James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire, LS9 7TF, UK. E-mail: ; fax: (+44)113 3438501
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK,School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
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29
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Two different conformations in hepatitis C virus p7 protein account for proton transport and dye release. PLoS One 2014; 9:e78494. [PMID: 24409277 PMCID: PMC3883635 DOI: 10.1371/journal.pone.0078494] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 10/18/2013] [Indexed: 12/28/2022] Open
Abstract
The p7 protein from the hepatitis C virus (HCV) is a 63 amino acid long polypeptide that is essential for replication, and is involved in protein trafficking and proton transport. Therefore, p7 is a possible target for antivirals. The consensus model for the channel formed by p7 protein is a hexameric or heptameric oligomer of α-helical hairpin monomers, each having two transmembrane domains, TM1 and TM2, where the N-terminal TM1 would face the lumen of this channel. A reported high-throughput functional assay to search for p7 channel inhibitors is based on carboxyfluorescein (CF) release from liposomes after p7 addition. However, the rationale for the dual ability of p7 to serve as an ion or proton channel in the infected cell, and to permeabilize membranes to large molecules like CF is not clear. We have recreated both activities in vitro, examining the conformation present in these assays using infrared spectroscopy. Our results indicate that an α-helical form of p7, which can transport protons, is not able to elicit CF release. In contrast, membrane permeabilization to CF is observed when p7 contains a high percentage of β-structure, or when using a C-terminal fragment of p7, encompassing TM2. We propose that the reported inhibitory effect of some small compounds, e.g., rimantadine, on both CF release and proton transport can be explained via binding to the membrane-inserted C-terminal half of p7, increasing its rigidity, in a similar way to the influenza A M2-rimantadine interaction.
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30
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Largo E, Gladue DP, Huarte N, Borca MV, Nieva JL. Pore-forming activity of pestivirus p7 in a minimal model system supports genus-specific viroporin function. Antiviral Res 2013; 101:30-6. [PMID: 24189547 DOI: 10.1016/j.antiviral.2013.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/03/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
Abstract
Viroporins are small integral membrane proteins functional in viral assembly and egress by promoting permeabilization. Blocking of viroporin function therefore constitutes a target for antiviral development. Classical swine fever virus (CSFV) protein p7 has been recently regarded as a class II viroporin. Here, we sought to establish the determinants of the CSFV p7 permeabilizing activity in a minimal model system. Assessment of an overlapping peptide library mapped the porating domain to the C-terminal hydrophobic stretch (residues 39-67). Pore-opening dependence on pH or sensitivity to channel blockers observed for the full protein required the inclusion of a preceding polar sequence (residues 33-38). Effects of lipid composition and structural data further support that the resulting peptide (residues 33-67), may comprise a bona fide surrogate to assay p7 activity in model membranes. Our observations imply that CSFV p7 relies on genus-specific structures-mechanisms to perform its viroporin function.
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Affiliation(s)
- Eneko Largo
- Biophysics Unit (CSIC-UPV/EHU) and Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Douglas P Gladue
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - Nerea Huarte
- Biophysics Unit (CSIC-UPV/EHU) and Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Manuel V Borca
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - José L Nieva
- Biophysics Unit (CSIC-UPV/EHU) and Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain.
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Wang Y, Park SH, Tian Y, Opella SJ. Impact of histidine residues on the transmembrane helices of viroporins. Mol Membr Biol 2013; 30:360-9. [PMID: 24102567 DOI: 10.3109/09687688.2013.842657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Abstract The role of histidine in channel-forming transmembrane (TM) helices was investigated by comparing the TM helices from Virus protein 'u' (Vpu) and the M2 proton channel. Both proteins are members of the viroporin family of small membrane proteins that exhibit ion channel activity, and have a single TM helix that is capable of forming oligomers. The TM helices from both proteins have a conserved tryptophan towards the C-terminus. Previously, alanine 18 of Vpu was mutated to histidine in order to artificially introduce the same HXXXW motif that is central to the proton channel activity of M2. Interestingly, the mutated Vpu TM resulted in an increase in helix tilt angle of 11° in lipid bilayers compared to the wild-type Vpu TM. Here, we find the reverse, when histidine 37 of the HXXXW motif in M2 was mutated to alanine, it decreased the helix tilt by 10° from that of wild-type M2. The tilt change is independent of both the helix length and the presence of tryptophan. In addition, compared to wild-type M2, the H37A mutant displayed lowered sensitivity to proton concentration. We also found that the solvent accessibility of histidine-containing M2 is greater than without histidine. This suggests that the TM helix may increase the solvent exposure by changing its tilt angle in order to accommodate a polar/charged residue within the hydrophobic membrane region. The comparative results of M2, Vpu and their mutants demonstrated the significance of histidine in a transmembrane helix and the remarkable plasticity of the function and structure of ion channels stemming from changes at a single amino acid site.
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Affiliation(s)
- Yan Wang
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92037-0307 , USA
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32
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Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
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Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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33
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The minimalist architectures of viroporins and their therapeutic implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1058-67. [PMID: 24055819 PMCID: PMC3943691 DOI: 10.1016/j.bbamem.2013.09.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/03/2013] [Accepted: 09/08/2013] [Indexed: 11/23/2022]
Abstract
Many viral genomes encode small, integral membrane proteins that form homo-oligomeric channels in membrane, and they transport protons, cations, and other molecules across the membrane barrier to aid various steps of viral entry and maturation. These viral proteins, collectively named viroporins, are crucial for viral pathogenicity. In the past five years, structures obtained by nuclear magnetic resonance (NMR), X-ray crystallography, and electron microscopy (EM) showed that viroporins often adopt minimalist architectures to achieve their functions. A number of small molecules have been identified to interfere with their channel activities and thereby inhibit viral infection, making viroporins potential drug targets for therapeutic intervention. The known architectures and inhibition mechanisms of viroporins differ significantly from each other, but some common principles are shared between them. This review article summarizes the recent developments in the structural investigation of viroporins and their inhibition by antiviral compounds. This article is part of a Special Issue entitled: Viral Membrane Proteins-Channels for Cellular Networking.
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34
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Viral channel proteins in intracellular protein-protein communication: Vpu of HIV-1, E5 of HPV16 and p7 of HCV. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1113-21. [PMID: 24035804 DOI: 10.1016/j.bbamem.2013.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/06/2013] [Accepted: 08/09/2013] [Indexed: 01/20/2023]
Abstract
Viral channel forming proteins are known for their capability to make the lipid membrane of the host cell and its subcellular compartments permeable to ions and small compounds. There is increasing evidence that some of the representatives of this class of proteins are also strongly interacting with host proteins and the effectiveness of this interaction seems to be high. Interaction of viral channel proteins with host factors has been proposed by bioinformatics approaches and has also been identified experimentally. An overview of the interactions with host proteins is given for Vpu from HIV-1, E5 from HPV-16 and p7 from HCV. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking.
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35
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Gomes-Neto F, Valente AP, Almeida FCL. Modeling the interaction of dodecylphosphocholine micelles with the anticoccidial peptide PW2 guided by NMR data. Molecules 2013; 18:10056-80. [PMID: 23966088 PMCID: PMC6270265 DOI: 10.3390/molecules180810056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticoccidial peptide PW2, we performed molecular dynamics (MD) simulations guided by NMR experimental data, focusing on strategies to explore the transient nature of micelles, which rearrange on a millisecond to second timescale. We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. The simulation with spontaneous micelle formation provided the adequate environment which replicated the experimental data. The unrestrained MD simulations reproduced the NMR structure for the entire 100 ns MD simulation time. Hidden discrete conformational states could be described. Coulomb interactions are important for initial approximation and hydrogen bonds for floating the aromatic region at the interface, being essential for the stabilization of the interaction. Arg9 is strongly attached with phosphate. We observed a helix elongation process stabilized by the intermolecular peptide-micelle association. Full association that mimics the experimental data only happens after complete micelle re-association. Fast micelle dynamics without dissociation of surfactants leads to only superficial binding.
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Affiliation(s)
- Francisco Gomes-Neto
- Laboratory of Toxinology, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21045-900, Brazil; E-Mail:
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Ana Paula Valente
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Fabio C. L. Almeida
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-21-3104-2326; Fax: +55-21-3104-2326
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36
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Cook GA, Dawson LA, Tian Y, Opella SJ. Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance. Biochemistry 2013; 52:5295-303. [PMID: 23841474 DOI: 10.1021/bi4006623] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hepatitis C virus (HCV) protein p7 plays an important role in the assembly and release of mature virus particles. This small 63-residue membrane protein has been shown to induce channel activity, which may contribute to its functions. p7 is highly conserved throughout the entire range of HCV genotypes, which contributes to making p7 a potential target for antiviral drugs. The secondary structure of p7 from the J4 genotype and the tilt angles of the helices within bilayers have been previously characterized by nuclear magnetic resonance (NMR). Here we describe the three-dimensional structure of p7 in short chain phospholipid (1,2-dihexanoyl-sn-glycero-3-phosphocholine) micelles, which provide a reasonably effective membrane-mimicking environment that is compatible with solution NMR experiments. Using a combination of chemical shifts, residual dipolar couplings, and PREs, we determined the structure of p7 using an implicit membrane potential combining both CS-Rosetta decoys and Xplor-NIH refinement. The final set of structures has a backbone root-mean-square deviation of 2.18 Å. Molecular dynamics simulations in NAMD indicate that several side chain interactions might be taking place and that these could affect the dynamics of the protein. In addition to probing the dynamics of p7, we evaluated several drug-protein and protein-protein interactions. Established channel-blocking compounds such as amantadine, hexamethylene amiloride, and long alkyl chain iminosugar derivatives inhibit the ion channel activity of p7. It has also been shown that the protein interacts with HCV nonstructural protein 2 at the endoplasmic reticulum and that this interaction may be important for the infectivity of the virus. Changes in the chemical shift frequencies of solution NMR spectra identify the residues taking part in these interactions.
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Affiliation(s)
- Gabriel A Cook
- Department of Chemistry and Biochemistry, University of California at San Diego , La Jolla, California 92093, United States
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37
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Wang YT, Hsu HJ, Fischer WB. Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs. SPRINGERPLUS 2013; 2:324. [PMID: 23961398 PMCID: PMC3724979 DOI: 10.1186/2193-1801-2-324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/11/2013] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus p7 protein is a 63 amino acid polytopic protein with two transmembrane domains (TMDs) and one of the prime targets for anti HCV drug development. A bio-inspired modeling pathway is used to generate plausible computational models of the two TMDs forming the monomeric protein model. A flexible region between Leu-13 and Gly-15 is identified for TMD11-32 and a region around Gly-46 to Trp-48 for TMD236-58. Mutations of the tyrosine residues in TMD236-58 into phenylalanine and serine are simulated to identify their role in shaping TMD2. Lowest energy structures of the two TMDs connected with the loop residues are used for a posing study in which small molecule drugs BIT225, amantadine, rimantadine and NN-DNJ, are identified to bind to the loop region. BIT225 is identified to interact with the backbone of the functionally important residues Arg-35 and Trp-36.
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Affiliation(s)
- Yi-Ting Wang
- Department of Life Science, Tzu Chi University, Hualien, 970 Taiwan
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38
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Unusual architecture of the p7 channel from hepatitis C virus. Nature 2013; 498:521-5. [PMID: 23739335 PMCID: PMC3725310 DOI: 10.1038/nature12283] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/22/2013] [Indexed: 12/19/2022]
Abstract
The hepatitis C virus (HCV) has developed a small membrane protein, p7, which remarkably can self-assemble into a large channel complex that selectively conducts cations. We wanted to examine the structural solution that the viroporin adopts in order to achieve selective cation conduction, because p7 has no homology with any of the known prokaryotic or eukaryotic channel proteins. The activity of p7 can be inhibited by amantadine and rimantadine, which are potent blockers of the influenza M2 channel and licensed drugs against influenza infections. The adamantane derivatives have been used in HCV clinical trials, but large variation in drug efficacy among the various HCV genotypes has been difficult to explain without detailed molecular structures. Here we determine the structures of this HCV viroporin as well as its drug-binding site using the latest nuclear magnetic resonance (NMR) technologies. The structure exhibits an unusual mode of hexameric assembly, where the individual p7 monomers, i, not only interact with their immediate neighbours, but also reach farther to associate with the i+2 and i+3 monomers, forming a sophisticated, funnel-like architecture. The structure also points to a mechanism of cation selection: an asparagine/histidine ring that constricts the narrow end of the funnel serves as a broad cation selectivity filter, whereas an arginine/lysine ring that defines the wide end of the funnel may selectively allow cation diffusion into the channel. Our functional investigation using whole-cell channel recording shows that these residues are critical for channel activity. NMR measurements of the channel-drug complex revealed six equivalent hydrophobic pockets between the peripheral and pore-forming helices to which amantadine or rimantadine binds, and compound binding specifically to this position may allosterically inhibit cation conduction by preventing the channel from opening. Our data provide a molecular explanation for p7-mediated cation conductance and its inhibition by adamantane derivatives.
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39
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Probing the orientational distribution of dyes in membranes through multiphoton microscopy. Biophys J 2013; 103:907-17. [PMID: 23009840 DOI: 10.1016/j.bpj.2012.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/23/2012] [Accepted: 08/01/2012] [Indexed: 11/21/2022] Open
Abstract
Numerous dyes are available or under development for probing the structural and functional properties of biological membranes. Exogenous chromophores adopt a range of orientations when bound to membranes, which have a drastic effect on their biophysical behavior. Here, we present a method that employs optical anisotropy data from three polarization-imaging techniques to establish the distribution of orientations adopted by molecules in monolayers and bilayers. The resulting probability density functions, which contain the preferred molecular tilt μ and distribution breadth γ, are more informative than an average tilt angle [φ]. We describe a methodology for the extraction of anisotropy data through an image-processing technology that decreases the error in polarization measurements by about a factor of four. We use this technique to compare di-4-ANEPPS and di-8-ANEPPS, both dipolar dyes, using data from polarized 1-photon, 2-photon fluorescence and second-harmonic generation imaging. We find that di-8-ANEPPS has a lower tilt but the same distributional width. We find the distribution of tilts taken by di-4-ANEPPS in two phospholipid membrane models: giant unilamellar vesicles and water-in-oil droplet monolayers. Both models result in similar distribution functions with average tilts of 52° and 47°, respectively.
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40
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Tierney DL. Jahn-Teller dynamics in a series of high-symmetry Co(II) chelates determine paramagnetic relaxation enhancements. J Phys Chem A 2012; 116:10959-72. [PMID: 23095055 DOI: 10.1021/jp309245e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR paramagnetic relaxation enhancements (PREs) of a series of structurally characterized, trigonal bis-trispyrazolylborate (Tp) chelates of high-spin Co(II), spanning 100-850 MHz in field, are reported. Prior knowledge of the metal-nucleus distances allows numerical extraction of position-dependent electron spin relaxation rates (τ(c)(-1)) from direct measurement of the individual PREs of the four symmetry distinct protons in Co(Tp)(2), using available closed-form expressions. The data for this electronically complex system where spin-orbit coupling defines the ground state electronic structure are analyzed in terms of the Solomon-Bloembergen-Morgan (SBM) relations, as well as available zero-field splitting limit theories. A simple angular correction is shown to be sufficient to reconcile the individual τ(c)(T) data for the four classes of protons. The data identify a previously unrecognized dynamic Jahn-Teller effect in these historically important complexes, with a barrier of ~230 cm(-1), pointing to a level of dynamics in trispyrazolylborate chemistry that has not been described before, and further show that it is the Jahn-Teller that is responsible for the PREs in fluid solution. A field-dependent component is also identified for the two protons nearest g(//), which is suggested to arise due to Zeeman mixing of excited state character into the ground level.
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Affiliation(s)
- David L Tierney
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States.
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41
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Dürr UN, Gildenberg M, Ramamoorthy A. The magic of bicelles lights up membrane protein structure. Chem Rev 2012; 112:6054-74. [PMID: 22920148 PMCID: PMC3497859 DOI: 10.1021/cr300061w] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 12/12/2022]
Affiliation(s)
| | - Melissa Gildenberg
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
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42
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Chandler DE, Penin F, Schulten K, Chipot C. The p7 protein of hepatitis C virus forms structurally plastic, minimalist ion channels. PLoS Comput Biol 2012; 8:e1002702. [PMID: 23028296 PMCID: PMC3447957 DOI: 10.1371/journal.pcbi.1002702] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/27/2012] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is a membrane-associated oligomeric protein harboring ion channel activity. It is essential for effective assembly and release of infectious HCV particles and an attractive target for antiviral intervention. Yet, the self-assembly and molecular mechanism of p7 ion channelling are currently only partially understood. Using molecular dynamics simulations (aggregate time 1.2 µs), we show that p7 can form stable oligomers of four to seven subunits, with a bias towards six or seven subunits, and suggest that p7 self-assembles in a sequential manner, with tetrameric and pentameric complexes forming as intermediate states leading to the final hexameric or heptameric assembly. We describe a model of a hexameric p7 complex, which forms a transiently-open channel capable of conducting ions in simulation. We investigate the ability of the hexameric model to flexibly rearrange to adapt to the local lipid environment, and demonstrate how this model can be reconciled with low-resolution electron microscopy data. In the light of these results, a view of p7 oligomerization is proposed, wherein hexameric and heptameric complexes may coexist, forming minimalist, yet robust functional ion channels. In the absence of a high-resolution p7 structure, the models presented in this paper can prove valuable as a substitute structure in future studies of p7 function, or in the search for p7-inhibiting drugs.
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Affiliation(s)
- Danielle E. Chandler
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - François Penin
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Université Lyon 1, Univ Lyon, France; CNRS, UMR 5086, Lyon, France
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Christophe Chipot
- Beckman Institute, University of Illinois at Urbana-Champaign Urbana, Illinois, United States of America
- Équipe de Dynamique des Assemblages Membranaires UMR 7565, Université de Lorraine, Vanduvre-lès-Nancy, France
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43
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Schindler C, Fischer WB. Sequence alignment of viral channel proteins with cellular ion channels. J Comput Biol 2012; 19:1060-72. [PMID: 22891808 DOI: 10.1089/cmb.2011.0297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sequence alignment is an important tool for identifying regions of similarities among proteins and for, thus, establishing functional and structural relationships between different proteins. Here, alignments of transmembrane domains (TMDs) of viral channel forming proteins with host ion channels and toxins are evaluated. The following representatives of polytopic viral channel proteins are chosen: (i) p7 of HCV and 2B of Polio virus (two TMDs) and (ii) 3a of SARS-CoV (three TMDs). Using ClustalW2, each of the TMDs of the viral channels is aligned, and the overlap is mapped onto structural models of the host channels and toxins focusing on the pore-lining TMDs. The analysis reveals that p7 and 2B TMDs align with the pore-facing TMD of MscL, and 3a-TMDs align with those of ligand-gated ion channels. Possible implications concerning the mechanism of function of the viral proteins are discussed.
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Affiliation(s)
- Christina Schindler
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
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44
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Abstract
Viroporins are small virally encoded hydrophobic proteins that oligomerize in the membrane of host cells, leading to the formation of hydrophilic pores. This activity modifies several cellular functions, including membrane permeability, Ca2+ homeostasis, membrane remodelling and glycoprotein trafficking. A classification scheme for viroporins is proposed on the basis of their structure and membrane topology. Thus, class I and class II viroporins are defined according to the number of transmembrane domains in the protein (one and two, respectively), and subclasses are defined according to their orientation in the membrane. The main function of viroporins during viral replication is to participate in virion morphogenesis and release from host cells. In addition, some viroporins are involved in viral entry and genome replication. The structure and activity of several viroporins, such as picornavirus protein 2B (P2B), influenza A virus matrix protein 2 (M2), hepatitis C virus p7 and HIV-1 viral protein U (Vpu), have been analysed in detail. New members of this expanding family of viral proteins have been described, from both RNA and DNA viruses. In addition to having a common general structure, all of these new viroporins have the ability to increase membrane permeability. Viroporins represent ideal targets to block viral replication and the spread of infection. Although a number of selective inhibitors of viroporin ion channels have been analysed in detail, optimized screening systems promise to provide new and more potent antiviral compounds in the near future.
Viroporins belong to a growing family of virally encoded proteins that form aqueous channels in the membranes of host cells. Here, Carrasco and colleagues review the structure and diverse biological functions of these proteins during the viral life cycle, as well as their potential as antiviral therapeutic targets. Viroporins are small, hydrophobic proteins that are encoded by a wide range of clinically relevant animal viruses. When these proteins oligomerize in host cell membranes, they form hydrophilic pores that disrupt a number of physiological properties of the cell. Viroporins are crucial for viral pathogenicity owing to their involvement in several diverse steps of the viral life cycle. Thus, these viral proteins, which include influenza A virus matrix protein 2 (M2), HIV-1 viral protein U (Vpu) and hepatitis C virus p7, represent ideal targets for therapeutic intervention, and several compounds that block their pore-forming activity have been identified. Here, we review recent studies in the field that have advanced our knowledge of the structure and function of this expanding family of viral proteins.
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45
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Li H, Atkins E, Bruckner J, McArdle S, Qiu WC, Thomassen LV, Scott J, Shuhart MC, Livingston S, Townshend-Bulson L, McMahon BJ, Harris M, Griffin S, Gretch DR. Genetic and functional heterogeneity of the hepatitis C virus p7 ion channel during natural chronic infection. Virology 2012; 423:30-7. [DOI: 10.1016/j.virol.2011.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/01/2011] [Accepted: 11/11/2011] [Indexed: 01/19/2023]
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46
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Son WS, Park SH, Nothnagel HJ, Lu GJ, Wang Y, Zhang H, Cook GA, Howell SC, Opella SJ. 'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:111-8. [PMID: 22079194 PMCID: PMC3257358 DOI: 10.1016/j.jmr.2011.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/07/2011] [Accepted: 10/18/2011] [Indexed: 05/13/2023]
Abstract
'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (∼10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.
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Fischer WB, Wang YT, Schindler C, Chen CP. Mechanism of function of viral channel proteins and implications for drug development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 294:259-321. [PMID: 22364876 PMCID: PMC7149447 DOI: 10.1016/b978-0-12-394305-7.00006-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo.
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Affiliation(s)
- Wolfgang B. Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Yi-Ting Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Christina Schindler
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Chin-Pei Chen
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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Cook GA, Zhang H, Park SH, Wang Y, Opella SJ. Comparative NMR studies demonstrate profound differences between two viroporins: p7 of HCV and Vpu of HIV-1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:554-60. [PMID: 20727848 DOI: 10.1016/j.bbamem.2010.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 10/19/2022]
Abstract
The p7 protein from hepatitis C virus and the Vpu protein from HIV-1 are members of the viroporin family of small viral membrane proteins. It is essential to determine their structures in order to obtain an understanding of their molecular mechanisms and to develop new classes of anti-viral drugs. Because they are membrane proteins, it is challenging to study them in their native phospholipid bilayer environments by most experimental methods. Here we describe applications of NMR spectroscopy to both p7 and Vpu. Isotopically labeled p7 and Vpu samples were prepared by heterologous expression in bacteria, initial isolation as fusion proteins, and final purification by chromatography. The purified proteins were studied in the model membrane environments of micelles by solution NMR spectroscopy and in aligned phospholipid bilayers by solid-state NMR spectroscopy. The resulting structural findings enable comparisons to be made between the two proteins, demonstrating that they have quite different architectures. Most notably, Vpu has one trans-membrane helix and p7 has two trans-membrane helices; in addition, there are significant differences in the structures and dynamics of their internal loop and terminal regions.
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Affiliation(s)
- Gabriel A Cook
- Department of Chemistry and Biochemistry, University of California, San Diego, Lajolla, CA 92093, USA
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