1
|
Devantier K, Kjær VMS, Griffin S, Kragelund BB, Rosenkilde MM. Advancing the field of viroporins-Structure, function and pharmacology: IUPHAR Review X. Br J Pharmacol 2024. [PMID: 39224966 DOI: 10.1111/bph.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 09/04/2024] Open
Abstract
Viroporins possess important potential as antiviral targets due to their critical roles during virus life cycles, spanning from virus entry to egress. Although the antiviral amantadine targets the M2 viroporin of influenza A virus, successful progression of other viroporin inhibitors into clinical use remains challenging. These challenges relate in varying proportions to a lack of reliable full-length 3D-structures, difficulties in functionally characterising individual viroporins, and absence of verifiable direct binding between inhibitor and viroporin. This review offers perspectives to help overcome these challenges. We provide a comprehensive overview of the viroporin family, including their structural and functional features, highlighting the moldability of their energy landscapes and actions. To advance the field, we suggest a list of best practices to aspire towards unambiguous viroporin identification and characterisation, along with considerations of potential pitfalls. Finally, we present current and future scenarios of, and prospects for, viroporin targeting drugs.
Collapse
Affiliation(s)
- Kira Devantier
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Viktoria M S Kjær
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen Griffin
- Leeds Institute of Medical Research, St James' University Hospital, School of Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette M Rosenkilde
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
2
|
Xing G, Zheng Q. Insights into the specific feature of the electrostatic recognition binding mechanism between BM2 and BM1: a molecular dynamics simulation study. Phys Chem Chem Phys 2024; 26:22726-22738. [PMID: 39161312 DOI: 10.1039/d4cp01936a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Matrix protein 2 (M2) and matrix protein 1 (M1) of the influenza B virus are two important proteins, and the interactions between BM2 and BM1 play an important role in the process of virus assembly and replication. However, the interaction details between BM2 and BM1 are still unclear at the atomic level. Here, we constructed the BM2-BM1 complex system using homology modelling and molecular docking methods. Molecular dynamics (MD) simulations were used to illustrate the binding mechanism between BM2 and BM1. The results identify that the eight polar residues (E88B, E89B, H119BM1, E94B, R101BM1, K102BM1, R105BM1, and E104B) play an important role in stabilizing the binding through the formation of hydrogen bond networks and salt-bridge interactions at the binding interface. Furthermore, based on the simulation results and the experimental facts, the mutation experiments were designed to verify the influence of the mutation of residues both within and outside the effector domain. The mutations directly or indirectly disrupt interactions between polar residues, thus affecting viral assembly and replication. The results could help us understand the details of the interactions between BM2 and BM1 and provide useful information for the anti-influenza drug design.
Collapse
Affiliation(s)
- Guixuan Xing
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| |
Collapse
|
3
|
Pankratova Y, McKay MJ, Ma C, Tan H, Wang J, Hong M. Structure and dynamics of the proton-selective histidine and the gating tryptophan in an inward rectifying hybrid influenza B and A virus M2 proton channel. Phys Chem Chem Phys 2024; 26:20629-20644. [PMID: 39037444 PMCID: PMC11290064 DOI: 10.1039/d4cp01648c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The M2 proteins of influenza A and B viruses form acid-activated proton channels that are essential for the virus lifecycle. Proton selectivity is achieved by a transmembrane (TM) histidine whereas gating is achieved by a tryptophan residue. Although this functional apparatus is conserved between AM2 and BM2 channels, AM2 conducts protons exclusively inward whereas BM2 conducts protons in either direction depending on the pH gradient. Previous studies showed that in AM2, mutations of D44 abolished inward rectification of AM2, suggesting that the tryptophan gate is destabilized. To elucidate how charged residues C-terminal to the tryptophan regulates channel gating, here we investigate the structure and dynamics of H19 and W23 in a BM2 mutant, GDR-BM2, in which three BM2 residues are mutated to the corresponding AM2 residues, S16G, G26D and H27R. Whole-cell electrophysiological data show that GDR-BM2 conducts protons with inward rectification, identical to wild-type (WT) AM2 but different from WT-BM2. Solid-state NMR 15N and 13C spectra of H19 indicate that the mutant BM2 channel contains higher populations of cationic histidine and neutral τ tautomers compared to WT-BM2 at acidic pH. Moreover, 19F NMR spectra of 5-19F-labeled W23 resolve three peaks at acidic pH, suggesting three tryptophan sidechain conformations. Comparison of these spectra with the tryptophan spectra of other M2 peptides suggests that these indole sidechain conformations arise from interactions with the C-terminal charged residues and with the N-terminal cationic histidine. Taken together, these solid-state NMR data show that inward rectification in M2 proton channels is accomplished by tryptophan interactions with charged residues on both its C-terminal and N-terminal sides. Gating of these M2 proton channels is thus accomplished by a multi-residue complex with finely tuned electrostatic and aromatic interactions.
Collapse
Affiliation(s)
- Yanina Pankratova
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, 85721, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| |
Collapse
|
4
|
Yue Z, Wu J, Teng D, Wang Z, Voth GA. Activation of the influenza B M2 proton channel (BM2). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605324. [PMID: 39091734 PMCID: PMC11291123 DOI: 10.1101/2024.07.26.605324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Influenza B viruses have co-circulated during most seasonal flu epidemics and can cause significant human morbidity and mortality due to their rapid mutation, emerging drug resistance, and severe impact on vulnerable populations. The influenza B M2 proton channel (BM2) plays an essential role in viral replication, but the mechanisms behind its symmetric proton conductance and the involvement of a second histidine (His27) cluster remain unclear. Here we perform the membrane-enabled continuous constant-pH molecular dynamics simulations on wildtype BM2 and a key H27A mutant to explore its pH-dependent conformational switch. Simulations capture the activation as the first histidine (His19) protonates and reveal the transition at lower pH values compared to AM2 is a result of electrostatic repulsions between His19 and pre-protonated His27. Crucially, we provide an atomic-level understanding of the symmetric proton conduction by identifying pre-activating channel hydration in the C-terminal portion. This research advances our understanding of the function of BM2 function and lays the groundwork for further chemically reactive modeling of the explicit proton transport process as well as possible anti-flu drug design efforts.
Collapse
Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jiangbo Wu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Da Teng
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | | | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
5
|
Liu A, Zhang H, Zheng Q, Wang S. The Potential of Cyclodextrins as Inhibitors for the BM2 Protein: An In Silico Investigation. Molecules 2024; 29:620. [PMID: 38338365 PMCID: PMC10856705 DOI: 10.3390/molecules29030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The influenza BM2 transmembrane domain (BM2TM), an acid-activated proton channel, is an attractive antiviral target due to its essential roles during influenza virus replication, whereas no effective inhibitors have been reported for BM2. In this study, we draw inspiration from the properties of cyclodextrins (CDs) and hypothesize that CDs of appropriate sizes may possess the potential to act as inhibitors of the BM2TM proton channel. To explore this possibility, molecular dynamics simulations were employed to assess their inhibitory capabilities. Our findings reveal that CD4, CD5, and CD6 are capable of binding to the BM2TM proton channel, resulting in disrupted water networks and reduced hydrogen bond occupancy between H19 and the solvent within the BM2TM channel necessary for proton conduction. Notably, CD4 completely obstructs the BM2TM water channel. Based on these observations, we propose that CD4, CD5, and CD6 individually contribute to diminishing the proton transfer efficiency of the BM2 protein, and CD4 demonstrates promising potential as an inhibitor for the BM2 proton channel.
Collapse
Affiliation(s)
- Aijun Liu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| | - Hao Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Song Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| |
Collapse
|
6
|
Din GU, Hasham K, Amjad MN, Hu Y. Natural History of Influenza B Virus-Current Knowledge on Treatment, Resistance and Therapeutic Options. Curr Issues Mol Biol 2023; 46:183-199. [PMID: 38248316 PMCID: PMC10814056 DOI: 10.3390/cimb46010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Influenza B virus (IBV) significantly impacts the health and the economy of the global population. WHO global health estimates project 1 billion flu cases annually, with 3 to 5 million resulting in severe disease and 0.3 to 0.5 million influenza-related deaths worldwide. Influenza B virus epidemics result in significant economic losses due to healthcare expenses, reduced workforce productivity, and strain on healthcare systems. Influenza B virus epidemics, such as the 1987-1988 Yamagata lineage outbreak and the 2001-2002 Victoria lineage outbreak, had a significant global impact. IBV's fast mutation and replication rates facilitate rapid adaptation to the environment, enabling the evasion of existing immunity and the development of resistance to virus-targeting treatments. This leads to annual outbreaks and necessitates the development of new vaccination formulations. This review aims to elucidate IBV's evolutionary genomic organization and life cycle and provide an overview of anti-IBV drugs, resistance, treatment options, and prospects for IBV biology, emphasizing challenges in preventing and treating IBV infection.
Collapse
Affiliation(s)
- Ghayyas Ud Din
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
| | - Kinza Hasham
- Sundas Molecular Analysis Center, Sundas Foundation Gujranwala Punjab Pakistan, Gujranwala 50250, Pakistan
| | - Muhammad Nabeel Amjad
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
| | - Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
| |
Collapse
|
7
|
Chowdhury UD, Bhargava BL. Understanding the conformational changes in the influenza B M2 ion channel at various protonation states. Biophys Chem 2022; 289:106859. [PMID: 35905599 DOI: 10.1016/j.bpc.2022.106859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
The characterization of influenza (A/B M2) ion channels is very important as they are potential binding sites for the drugs. We report the all-atom molecular dynamics study of the influenza B M2 ion channel in the presence of explicit solvent and lipid bilayers using the high resolution solid-state NMR structures. The importance of the various protonation states of histidine in the activation of the ion channel is discussed. The conformational changes at the closed and the open structures clearly show that the increase in tilt angle is necessary for the activation of the ion channel. Additionally, the free energy surfaces of the eight systems show the importance of the protonation state of the histidine residues in the activation of the influenza B M2 ion channel. The protonation of the histidine residues increases the tilt angle and the intra-helix distance which is evident from the superimposition of the structures corresponding to the maxima and the minima in the free energy landscape. The findings imply differences in the singly protonated and double protonated conformational states of BM2 ion channel and provide insights to help further studies of these ion channels as the drug targets for the influenza virus.
Collapse
Affiliation(s)
- Unmesh D Chowdhury
- School of Chemical Sciences, National Institute of Science Education & Research - Bhubaneswar, an OCC of Homi Bhabha National Institute, P.O.Jatni, Khurda, Odisha 752050, India
| | - B L Bhargava
- School of Chemical Sciences, National Institute of Science Education & Research - Bhubaneswar, an OCC of Homi Bhabha National Institute, P.O.Jatni, Khurda, Odisha 752050, India.
| |
Collapse
|
8
|
Zhang X, Abel T, Su S, Herrmann A, Ludwig K, Veit M. Structural and functional analysis of the roles of influenza C virus membrane proteins in assembly and budding. J Biol Chem 2022; 298:101727. [PMID: 35157850 PMCID: PMC8914389 DOI: 10.1016/j.jbc.2022.101727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/24/2022] Open
Abstract
Assembly and budding of the influenza C virus is mediated by three membrane proteins: the hemagglutinin-esterase-fusion glycoprotein (HEF), the matrix protein (CM1), and the ion channel (CM2). Here we investigated whether the formation of the hexagonal HEF arrangement, a distinctive feature of influenza C virions is important for virus budding. We used super resolution microscopy and found 250-nm sized HEF clusters at the plasma membrane of transfected cells, which were insensitive to cholesterol extraction and cytochalasin treatment. Overexpression of either CM1, CM2, or HEF caused the release of membrane-enveloped particles. Cryo-electron microscopy of the latter revealed spherical vesicles exhibiting the hexagonal HEF clusters. We subsequently used reverse genetics to identify elements in HEF required for this clustering. We found that deletion of the short cytoplasmic tail of HEF reduced virus titer and hexagonal HEF arrays, suggesting that an interaction with CM1 stabilizes the HEF clusters. In addition, we substituted amino acids at the surface of the closed HEF conformation and identified specific mutations that prevented virus rescue, others reduced virus titers and the number of HEF clusters in virions. Finally, mutation of two regions that mediate contacts between trimers in the in-situ structure of HEF was shown to prevent rescue of infectious virus particles. Mutations at residues thought to mediate lateral interactions were revealed to promote intracellular trafficking defects. Taken together, we propose that lateral interactions between the ectodomains of HEF trimers are a driving force for virus budding, although CM2 and CM1 also play important roles in this process.
Collapse
Affiliation(s)
- Xu Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Tim Abel
- Institut für Biologie/Molekulare Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
| | - Andreas Herrmann
- Institut für Biologie/Molekulare Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany; Biophysikalische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Kai Ludwig
- Department of Chemistry and Biochemistry and Core Facility BioSupraMol, Research Center of Electron Microscopy, Free University Berlin, Berlin, Germany
| | - Michael Veit
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
9
|
Döring K, Langeder J, Duwe S, Tahir A, Grienke U, Rollinger JM, Schmidtke M. Insights into the direct anti-influenza virus mode of action of Rhodiola rosea. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 96:153895. [PMID: 35026524 DOI: 10.1016/j.phymed.2021.153895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/24/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The anti-influenza A virus activities and contents of previously isolated most active flavonoids (rhodiosin and tricin) from a standardized hydro-ethanolic R. rosea root and rhizome extract (SHR-5®), did not fully explain the efficacy of SHR-5®. Moreover, the mode of antiviral action of SHR-5® is unknown. PURPOSE To determine the anti-influenza viral principle of SHR-5® we evaluated i) the combined anti-influenza virus effect of rhodiosin and tricin, ii) the impact of its tannin-enriched fraction (TE), iii) its antiviral spectrum and mode of action, and iv) its propensity for resistance development in vitro. METHODS The combined anti-influenza virus effect of rhodiosin and tricin and the impact of TE were investigated with cytopathic effect (CPE)-inhibition assays in MDCK cells. A tannin-depleted fraction (TD) and TE were prepared by polyamide column chromatography and dereplicated by LC-MS. Plaque-reduction assays provided insights into the anti-influenza virus profile, the mode of action, and the propensity for resistance development of SHR-5®. RESULTS Our results i) did not reveal synergistic anti-influenza A virus effects of rhodiosin and tricin, but ii) proved a strong impact of TE mainly composed of prodelphinidin gallate oligomers. iii) TE inhibited the plaque-production of influenza virus A(H1N1)pdm09, A(H3N2), and B (Victoria and Yamagata) isolates (including isolates resistant to neuraminidase and/or M2 ion channel inhibitors) with 50% inhibitory concentration values between 0.12 - 0.53 µg/ml similar to SHR-5®. Mechanistic studies proved a virucidal activity, inhibition of viral adsorption, viral neuraminidase activity, and virus spread by SHR-5® and TE. iv) No resistance development was observed in vitro. CONCLUSION For the first time a comprehensive analysis of the anti-influenza virus profile of a hydro-ethanolic R. rosea extract (SHR-5®) was assessed in vitro. The results demonstrating broad-spectrum multiple direct anti-influenza virus activities, and a lack of resistance development to SHR-5® together with its known augmentation of host defense, support its potential role as an adaptogen against influenza virus infection.
Collapse
Affiliation(s)
- Kristin Döring
- Section of Experimental Virology, Department of Medical Microbiology, Jena University Hospital, Hans-Knöll-Str. 2, d-07745 Jena, Germany
| | - Julia Langeder
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Susanne Duwe
- Robert Koch Institute, Unit 17: Influenza and Other Respiratory Viruses, National Reference Centre for Influenza, Seestr. 10, d-13353 Berlin, Germany
| | - Ammar Tahir
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Ulrike Grienke
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Judith M Rollinger
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria.
| | - Michaela Schmidtke
- Section of Experimental Virology, Department of Medical Microbiology, Jena University Hospital, Hans-Knöll-Str. 2, d-07745 Jena, Germany.
| |
Collapse
|
10
|
Cao Y, Yang R, Lee I, Zhang W, Sun J, Wang W, Meng X. Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Sci 2021; 30:1114-1130. [PMID: 33813796 PMCID: PMC8138525 DOI: 10.1002/pro.4075] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.
Collapse
Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| | - Rui Yang
- Department of Infection and ImmunityTianjin Union Medical Center, Nankai University Affiliated HospitalTianjinPeople's Republic of China
| | - Imshik Lee
- College of PhysicsNankai UniversityTianjinPeople's Republic of China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Xiangfei Meng
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| |
Collapse
|
11
|
Duwe SC, Schmidt B, Gärtner BC, Timm J, Adams O, Fickenscher H, Schmidtke M. Prophylaxis and treatment of influenza: options, antiviral susceptibility, and existing recommendations. GMS INFECTIOUS DISEASES 2021; 9:Doc02. [PMID: 34113534 PMCID: PMC8165743 DOI: 10.3205/id000071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Influenza viruses of types A and B attack 5-10% of adults and 20-30% of children, thereby causing millions of acute respiratory infections in Germany annually. A significant number of these infections are associated with complications such as pneumonia and bacterial superinfections that need hospitalization and might lead to death. In addition to vaccines, drugs were developed that might support influenza prevention and that can be used to treat influenza patients. The timely application of anti-influenza drugs can inhibit virus replication, help reduce and shorten the symptoms, and prevent death as well as virus transmission. This review concisely describes the mechanism of action, the potential for prophylactic and therapeutic use, and the knowledge on resistance of anti-influenza drugs approved today. However, the main aim is to give an overview on the recommendations available in Germany for the proper use of these drugs. In doing so, the recommendations published in statements and guidelines of medical societies as well as the German influenza pandemic preparedness plan are summarized with the consideration of specific circumstances and groups of patients.
Collapse
Affiliation(s)
- Susanne C Duwe
- Robert Koch Institute, Unit 17: Influenza and Other Respiratory Viruses, National Reference Centre for Influenza, Berlin, Germany
| | - Barbara Schmidt
- Institute for Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
| | - Barbara C Gärtner
- Institute of Medical Microbiology & Hygiene, Saarland University Medical Center, Homburg, Germany
| | - Jörg Timm
- Institute for Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Germany
| | - Ortwin Adams
- Institute for Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michaela Schmidtke
- Section Experimental Virology, Department of Medical Microbiology, Jena University Hospital, Germany
| |
Collapse
|
12
|
Zhang Y, Zheng QC. In Silico Analysis Revealed a Unique Binding but Ineffective Mode of Amantadine to Influenza Virus B M2 Channel. J Phys Chem Lett 2021; 12:1169-1174. [PMID: 33480694 DOI: 10.1021/acs.jpclett.0c03560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The M2 proton channel of influenza A (AM2) and B (BM2) have a highly conserved function motif, considered as the effective target. As yet, there is no effective drug against BM2. Research showed that AM2 channel blocker, amantadine (AMT), was able to bind to BM2 channel, but AMT lacked inhibition against BM2. Nevertheless, the study of the binding but ineffective mode of AMT to BM2 is challenging. To resolve the challenge and obtain more information for drug design of inhibitors targeting BM2, multiple molecular dynamics simulations were performed. We discovered AMT mainly adopted up binding mode in BM2, involved in a transition flipping from down mode to up mode. Furthermore, we discovered a new key factor to explain ineffective inhibition of AMT to BM2 because of the unmatched spatial geometry between AMT and BM2. Our work could enrich structural feature information on BM2 and provide a new perspective for rational drug design of anti-influenza B.
Collapse
Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China
| |
Collapse
|
13
|
Abstract
This article summarizes current knowledge on the related influenza B and C viruses and considers the few studies on the recently identified influenza D virus. We focus on the particular viral genome organizations, the viral propagation cycles, as well as structural and functional insight into the encoded viral gene products. This is complemented with comprehensive sections that address the evolutionary strategies and the epidemiological significance of these influenza virus types, as well as the current state of interventions available for their control.
Collapse
|
14
|
Lamb RA. The Structure, Function, and Pathobiology of the Influenza A and B Virus Ion Channels. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038505. [PMID: 31988204 DOI: 10.1101/cshperspect.a038505] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Influenza A virus AM2 protein is an integral membrane protein that is an ion channel (also known as a viroporin). The channel has 24 extracellular residues, 19 residues that span the membrane once and acts as both the channel pore and also the membrane anchoring domain, and a 54-residue cytoplasmic tail. The M2 protein has four identical chains linked via two disulfide bonds that form a four-helix bundle that is 107-108 more permeable to protons than Na+ ions. The M2 channel is activated by low pH, His residue 37 is the pH sensor, and Trp residue 41 is the channel gate. The channel is blocked by the antiviral drug amantadine hydrochloride. The influenza B virus BM2 protein does not have homology with the AM2 channel, but BM2 does have the His proton sensor, Trp gate, and is activated by low pH. It is thought that the AM2 and BM2 proteins have common functions in the influenza A and B virus life cycles. Both BM2 and AM2 also facilitate virus budding. The amphipathic helix in the AM2 cytoplasmic tail has an important role in the assembly of the virus, and functional AM2 protein makes the virus independent of the "endosomal sorting complex required for transport" (ESCRT) complex scission.
Collapse
Affiliation(s)
- Robert A Lamb
- Department of Molecular Biosciences, Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois 60208-3500, USA
| |
Collapse
|
15
|
de Vlugt JE, Xiao P, Munro R, Charchoglyan A, Brewer D, Al-Abdul-Wahid MS, Brown LS, Ladizhansky V. Identifying lipids tightly bound to an integral membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183345. [DOI: 10.1016/j.bbamem.2020.183345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023]
|
16
|
Núñez-Ramírez R, Huesa J, Bel Y, Ferré J, Casino P, Arias-Palomo E. Molecular architecture and activation of the insecticidal protein Vip3Aa from Bacillus thuringiensis. Nat Commun 2020; 11:3974. [PMID: 32769995 PMCID: PMC7414852 DOI: 10.1038/s41467-020-17758-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/08/2020] [Indexed: 12/27/2022] Open
Abstract
Bacillus thuringiensis Vip3 (Vegetative Insecticidal Protein 3) toxins are widely used in biotech crops to control Lepidopteran pests. These proteins are produced as inactive protoxins that need to be activated by midgut proteases to trigger cell death. However, little is known about their three-dimensional organization and activation mechanism at the molecular level. Here, we have determined the structures of the protoxin and the protease-activated state of Vip3Aa at 2.9 Å using cryo-electron microscopy. The reconstructions show that the protoxin assembles into a pyramid-shaped tetramer with the C-terminal domains exposed to the solvent and the N-terminal region folded into a spring-loaded apex that, after protease activation, drastically remodels into an extended needle by a mechanism akin to that of influenza haemagglutinin. These results provide the molecular basis for Vip3 activation and function, and serves as a strong foundation for the development of more efficient insecticidal proteins.
Collapse
Affiliation(s)
- Rafael Núñez-Ramírez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain
| | - Juanjo Huesa
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
| | - Yolanda Bel
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
- Department of Genetics, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
| | - Juan Ferré
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
- Department of Genetics, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
| | - Patricia Casino
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain.
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain.
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain.
| | - Ernesto Arias-Palomo
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain.
| |
Collapse
|
17
|
Zhang Y, Zhang HX, Zheng QC. In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel. J Chem Inf Model 2020; 60:3603-3615. [PMID: 32589410 DOI: 10.1021/acs.jcim.0c00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in silico. The appearance of several important hydrogen-bond networks has been discovered, as the addition of negatively charged lipid palmitoyloleoyl phosphatidylglycerol (POPG) and cholesterol reduces membrane fluidity and augments membrane rigidity. A more rigid membrane environment is beneficial to expand the channel, allow more water to enter the channel, promote channel hydration, and then even affect the proton conduction facilitated by the hydrated channel. Thus, membrane environment could be identified as an important influence factor of conformation and hydration of BM2. These findings can provide a unique perspective for understanding the mechanism of membrane lipid composition regulating conformation and hydration of BM2 and have important significance to the further study of anti-influenza virus B drugs.
Collapse
Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China
| |
Collapse
|
18
|
Chou KC. An Insightful 10-year Recollection Since the Emergence of the 5-steps Rule. Curr Pharm Des 2020; 25:4223-4234. [PMID: 31782354 DOI: 10.2174/1381612825666191129164042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE One of the most challenging and also the most difficult problems is how to formulate a biological sequence with a vector but considerably keep its sequence order information. METHODS To address such a problem, the approach of Pseudo Amino Acid Components or PseAAC has been developed. RESULTS AND CONCLUSION It has become increasingly clear via the 10-year recollection that the aforementioned proposal has been indeed very powerful.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, Massachusetts 02478, United States.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
19
|
|
20
|
Zheng L, Huang S, Mu N, Zhang H, Zhang J, Chang Y, Yang L, Zuo Y. RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5650975. [PMID: 31802128 PMCID: PMC6893003 DOI: 10.1093/database/baz131] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
By reducing amino acid alphabet, the protein complexity can be significantly simplified, which could improve computational efficiency, decrease information redundancy and reduce chance of overfitting. Although some reduced alphabets have been proposed, different classification rules could produce distinctive results for protein sequence analysis. Thus, it is urgent to construct a systematical frame for reduced alphabets. In this work, we constructed a comprehensive web server called RAACBook for protein sequence analysis and machine learning application by integrating reduction alphabets. The web server contains three parts: (i) 74 types of reduced amino acid alphabet were manually extracted to generate 673 reduced amino acid clusters (RAACs) for dealing with unique protein problems. It is easy for users to select desired RAACs from a multilayer browser tool. (ii) An online tool was developed to analyze primary sequence of protein. The tool could produce K-tuple reduced amino acid composition by defining three correlation parameters (K-tuple, g-gap, λ-correlation). The results are visualized as sequence alignment, mergence of RAA composition, feature distribution and logo of reduced sequence. (iii) The machine learning server is provided to train the model of protein classification based on K-tuple RAAC. The optimal model could be selected according to the evaluation indexes (ROC, AUC, MCC, etc.). In conclusion, RAACBook presents a powerful and user-friendly service in protein sequence analysis and computational proteomics. RAACBook can be freely available at http://bioinfor.imu.edu.cn/raacbook. Database URL: http://bioinfor.imu.edu.cn/raacbook
Collapse
Affiliation(s)
- Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Shenghui Huang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Nengjiang Mu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Haoyue Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Jiayu Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Yu Chang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road No.157, Harbin 150081, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| |
Collapse
|
21
|
Saelens X. The Role of Matrix Protein 2 Ectodomain in the Development of Universal Influenza Vaccines. J Infect Dis 2020; 219:S68-S74. [PMID: 30715367 PMCID: PMC6452325 DOI: 10.1093/infdis/jiz003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The influenza A virus matrix protein 2 ectodomain (M2e) is a universal influenza A vaccine candidate. Numerous studies in laboratory mice, but very few in natural influenza A virus hosts, have demonstrated that M2e-based vaccines can provide protection against any influenza A virus challenge. M2e-based immunity is largely accomplished by IgG and early stage clinical studies have demonstrated that the vaccine is safe. Yet M2e is considered a difficult target to develop as a vaccine: it does not offer sterilizing immunity and its mode of action relies on Fcγ receptor-mediated effector mechanisms, most likely in concert with alveolar macrophages. In a human challenge study with an H3N2 virus, treatment with a monoclonal M2e-specific human IgG was associated with a faster recovery compared to placebo treatment. If the universal influenza vaccine field incorporates this antigen into next generation vaccines, M2e could prove its merit when the next influenza pandemic strikes.
Collapse
Affiliation(s)
- Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, Ghent.,Department of Biomedical Molecular Biology, Ghent University, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| |
Collapse
|
22
|
Identifying FL11 subtype by characterizing tumor immune microenvironment in prostate adenocarcinoma via Chou's 5-steps rule. Genomics 2020; 112:1500-1515. [DOI: 10.1016/j.ygeno.2019.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/03/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
|
23
|
Mandala VS, Loftis AR, Shcherbakov AA, Pentelute BL, Hong M. Atomic structures of closed and open influenza B M2 proton channel reveal the conduction mechanism. Nat Struct Mol Biol 2020; 27:160-167. [PMID: 32015551 PMCID: PMC7641042 DOI: 10.1038/s41594-019-0371-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
The influenza B M2 (BM2) proton channel is activated by acidic pH to mediate virus uncoating. Unlike influenza A M2 (AM2), which conducts protons with strong inward rectification, BM2 conducts protons both inward and outward. Here we report 1.4- and 1.5-Å solid-state NMR structures of the transmembrane domain of the closed and open BM2 channels in a phospholipid environment. Upon activation, the transmembrane helices increase the tilt angle by 6° and the average pore diameter enlarges by 2.1 Å. BM2 thus undergoes a scissor motion for activation, which differs from the alternating-access motion of AM2. These results indicate that asymmetric proton conduction requires a backbone hinge motion, whereas bidirectional conduction is achieved by a symmetric scissor motion. The proton-selective histidine and gating tryptophan in the open BM2 reorient on the microsecond timescale, similar to AM2, indicating that side chain dynamics are the essential driver of proton shuttling.
Collapse
Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander R Loftis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
24
|
Gronnier J, Legrand A, Loquet A, Habenstein B, Germain V, Mongrand S. Mechanisms governing subcompartmentalization of biological membranes. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:114-123. [PMID: 31546133 DOI: 10.1016/j.pbi.2019.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Membranes show a tremendous variety of lipids and proteins operating biochemistry, transport and signalling. The dynamics and the organization of membrane constituents are regulated in space and time to execute precise functions. Our understanding of the molecular mechanisms that shape and govern membrane subcompartmentalization and inter-organelle contact sites still remains limited. Here, we review some reported mechanisms implicated in regulating plant membrane domains including those of plasma membrane, plastids, mitochondria and endoplasmic reticulum. Finally, we discuss several state-of-the-art methods that allow nowadays researchers to decipher the architecture of these structures at the molecular and atomic level.
Collapse
Affiliation(s)
- Julien Gronnier
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Anthony Legrand
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France; Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Véronique Germain
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France
| | - Sébastien Mongrand
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France.
| |
Collapse
|
25
|
Chou KC. Impacts of Pseudo Amino Acid Components and 5-steps Rule to Proteomics and Proteome Analysis. Curr Top Med Chem 2019; 19:2283-2300. [DOI: 10.2174/1568026619666191018100141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023]
Abstract
Stimulated by the 5-steps rule during the last decade or so, computational proteomics has achieved remarkable progresses in the following three areas: (1) protein structural class prediction; (2) protein subcellular location prediction; (3) post-translational modification (PTM) site prediction. The results obtained by these predictions are very useful not only for an in-depth study of the functions of proteins and their biological processes in a cell, but also for developing novel drugs against major diseases such as cancers, Alzheimer’s, and Parkinson’s. Moreover, since the targets to be predicted may have the multi-label feature, two sets of metrics are introduced: one is for inspecting the global prediction quality, while the other for the local prediction quality. All the predictors covered in this review have a userfriendly web-server, through which the majority of experimental scientists can easily obtain their desired data without the need to go through the complicated mathematics.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| |
Collapse
|
26
|
Xie NZ, Li JX, Huang RB. Biological Production of (S)-acetoin: A State-of-the-Art Review. Curr Top Med Chem 2019; 19:2348-2356. [PMID: 31648637 DOI: 10.2174/1568026619666191018111424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/24/2022]
Abstract
Acetoin is an important four-carbon compound that has many applications in foods, chemical synthesis, cosmetics, cigarettes, soaps, and detergents. Its stereoisomer (S)-acetoin, a high-value chiral compound, can also be used to synthesize optically active drugs, which could enhance targeting properties and reduce side effects. Recently, considerable progress has been made in the development of biotechnological routes for (S)-acetoin production. In this review, various strategies for biological (S)- acetoin production are summarized, and their constraints and possible solutions are described. Furthermore, future prospects of biological production of (S)-acetoin are discussed.
Collapse
Affiliation(s)
- Neng-Zhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Jian-Xiu Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China
| |
Collapse
|
27
|
Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
Collapse
Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| |
Collapse
|
28
|
Mezhenskaya D, Isakova-Sivak I, Rudenko L. M2e-based universal influenza vaccines: a historical overview and new approaches to development. J Biomed Sci 2019; 26:76. [PMID: 31629405 PMCID: PMC6800501 DOI: 10.1186/s12929-019-0572-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/01/2019] [Indexed: 01/04/2023] Open
Abstract
The influenza A virus was isolated for the first time in 1931, and the first attempts to develop a vaccine against the virus began soon afterwards. In addition to causing seasonal epidemics, influenza viruses can cause pandemics at random intervals, which are very hard to predict. Vaccination is the most effective way of preventing the spread of influenza infection. However, seasonal vaccination is ineffective against pandemic influenza viruses because of antigenic differences, and it takes approximately six months from isolation of a new virus to develop an effective vaccine. One of the possible ways to fight the emergence of pandemics may be by using a new type of vaccine, with a long and broad spectrum of action. The extracellular domain of the M2 protein (M2e) of influenza A virus is a conservative region, and an attractive target for a universal influenza vaccine. This review gives a historical overview of the study of M2 protein, and summarizes the latest developments in the preparation of M2e-based universal influenza vaccines.
Collapse
Affiliation(s)
- Daria Mezhenskaya
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia.
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia
| |
Collapse
|
29
|
Liang R, Xie J, Zhang C, Zhang M, Huang H, Huo H, Cao X, Niu B. Identifying Cancer Targets Based on Machine Learning Methods via Chou's 5-steps Rule and General Pseudo Components. Curr Top Med Chem 2019; 19:2301-2317. [PMID: 31622219 DOI: 10.2174/1568026619666191016155543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 07/19/2019] [Accepted: 08/26/2019] [Indexed: 01/09/2023]
Abstract
In recent years, the successful implementation of human genome project has made people realize that genetic, environmental and lifestyle factors should be combined together to study cancer due to the complexity and various forms of the disease. The increasing availability and growth rate of 'big data' derived from various omics, opens a new window for study and therapy of cancer. In this paper, we will introduce the application of machine learning methods in handling cancer big data including the use of artificial neural networks, support vector machines, ensemble learning and naïve Bayes classifiers.
Collapse
Affiliation(s)
- Ruirui Liang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jiayang Xie
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Chi Zhang
- Foshan Huaxia Eye Hospital, Huaxia Eye Hospital Group, Foshan 528000, China
| | - Mengying Zhang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Hai Huang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Haizhong Huo
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xin Cao
- Zhongshan Hospital, Institute of Clinical Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bing Niu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| |
Collapse
|
30
|
Identifying DNase I hypersensitive sites using multi-features fusion and F-score features selection via Chou's 5-steps rule. Biophys Chem 2019; 253:106227. [DOI: 10.1016/j.bpc.2019.106227] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023]
|
31
|
|
32
|
Fu Q, Piai A, Chen W, Xia K, Chou JJ. Structure determination protocol for transmembrane domain oligomers. Nat Protoc 2019; 14:2483-2520. [PMID: 31270510 DOI: 10.1038/s41596-019-0188-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
The transmembrane (TM) anchors of cell surface proteins have been one of the 'blind spots' in structural biology because they are generally very hydrophobic, sometimes dynamic, and thus difficult targets for structural characterization. A plethora of examples show these membrane anchors are not merely anchors but can multimerize specifically to activate signaling receptors on the cell surface or to stabilize envelope proteins in viruses. Through a series of studies of the TM domains (TMDs) of immune receptors and viral membrane proteins, we have established a robust protocol for determining atomic-resolution structures of TM oligomers by NMR in bicelles that closely mimic a lipid bilayer. Our protocol overcomes hurdles typically encountered by structural biology techniques such as X-ray crystallography and cryo-electron microscopy (cryo-EM) when studying small TMDs. Here, we provide the details of the protocol, covering five major technical aspects: (i) a general method for producing isotopically labeled TM or membrane-proximal (MP) protein fragments that involves expression of the protein (which is fused to TrpLE) into inclusion bodies and releasing the target protein by cyanogen bromide (CNBr) cleavage; (ii) determination of the oligomeric state of TMDs in bicelles; (iii) detection of intermolecular contacts using nuclear Overhauser effect (NOE) experiments; (iv) structure determination; and (v) paramagnetic probe titration (PPT) to characterize the membrane partition of the TM oligomers. This protocol is broadly applicable for filling structural gaps of many type I/II membrane proteins. The procedures may take 3-6 months to complete, depending on the complexity and stability of the protein sample.
Collapse
Affiliation(s)
- Qingshan Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
33
|
Bai X, Chen X. Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia. J Theor Biol 2019; 473:44-51. [DOI: 10.1016/j.jtbi.2019.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/17/2019] [Accepted: 03/23/2019] [Indexed: 10/27/2022]
|
34
|
To J, Torres J. Viroporins in the Influenza Virus. Cells 2019; 8:cells8070654. [PMID: 31261944 PMCID: PMC6679168 DOI: 10.3390/cells8070654] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022] Open
Abstract
Influenza is a highly contagious virus that causes seasonal epidemics and unpredictable pandemics. Four influenza virus types have been identified to date: A, B, C and D, with only A–C known to infect humans. Influenza A and B viruses are responsible for seasonal influenza epidemics in humans and are responsible for up to a billion flu infections annually. The M2 protein is present in all influenza types and belongs to the class of viroporins, i.e., small proteins that form ion channels that increase membrane permeability in virus-infected cells. In influenza A and B, AM2 and BM2 are predominantly proton channels, although they also show some permeability to monovalent cations. By contrast, M2 proteins in influenza C and D, CM2 and DM2, appear to be especially selective for chloride ions, with possibly some permeability to protons. These differences point to different biological roles for M2 in types A and B versus C and D, which is also reflected in their sequences. AM2 is by far the best characterized viroporin, where mechanistic details and rationale of its acid activation, proton selectivity, unidirectionality, and relative low conductance are beginning to be understood. The present review summarizes the biochemical and structural aspects of influenza viroporins and discusses the most relevant aspects of function, inhibition, and interaction with the host.
Collapse
Affiliation(s)
- Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| |
Collapse
|
35
|
Behzadi MA, Leyva-Grado VH. Overview of Current Therapeutics and Novel Candidates Against Influenza, Respiratory Syncytial Virus, and Middle East Respiratory Syndrome Coronavirus Infections. Front Microbiol 2019; 10:1327. [PMID: 31275265 PMCID: PMC6594388 DOI: 10.3389/fmicb.2019.01327] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/28/2019] [Indexed: 01/26/2023] Open
Abstract
Emergence and re-emergence of respiratory virus infections represent a significant threat to global public health, as they occur seasonally and less frequently (such as in the case of influenza virus) as pandemic infections. Some of these viruses have been in the human population for centuries and others had recently emerged as a public health problem. Influenza viruses have been affecting the human population for a long time now; however, their ability to rapidly evolve through antigenic drift and antigenic shift causes the emergence of new strains. A recent example of these events is the avian-origin H7N9 influenza virus outbreak currently undergoing in China. Human H7N9 influenza viruses are resistant to amantadines and some strains are also resistant to neuraminidase inhibitors greatly limiting the options for treatment. Respiratory syncytial virus (RSV) may cause a lower respiratory tract infection characterized by bronchiolitis and pneumonia mainly in children and the elderly. Infection with RSV can cause severe disease and even death, imposing a severe burden for pediatric and geriatric health systems worldwide. Treatment for RSV is mainly supportive since the only approved therapy, a monoclonal antibody, is recommended for prophylactic use in high-risk patients. The Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging respiratory virus. The virus was first recognized in 2012 and it is associated with a lower respiratory tract disease that is more severe in patients with comorbidities. No licensed vaccines or antivirals have been yet approved for the treatment of MERS-CoV in humans. It is clear that the discovery and development of novel antivirals that can be used alone or in combination with existing therapies to treat these important respiratory viral infections are critical. In this review, we will describe some of the novel therapeutics currently under development for the treatment of these infections.
Collapse
Affiliation(s)
- Mohammad Amin Behzadi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Victor H Leyva-Grado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
36
|
Kwon B, Roos M, Mandala VS, Shcherbakov AA, Hong M. Elucidating Relayed Proton Transfer through a His-Trp-His Triad of a Transmembrane Proton Channel by Solid-State NMR. J Mol Biol 2019; 431:2554-2566. [PMID: 31082440 DOI: 10.1016/j.jmb.2019.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/13/2019] [Accepted: 05/05/2019] [Indexed: 01/02/2023]
Abstract
Proton transfer through membrane-bound ion channels is mediated by both water and polar residues of proteins, but the detailed molecular mechanism is challenging to determine. The tetrameric influenza A and B virus M2 proteins form canonical proton channels that use an HxxxW motif for proton selectivity and gating. The BM2 channel also contains a second histidine (His), H27, equidistant from the gating tryptophan, which leads to a symmetric H19xxxW23xxxH27 motif. The proton-dissociation constants (pKa's) of H19 in BM2 were found to be much lower than the pKa's of H37 in AM2. To determine if the lower pKa's result from H27-facilitated proton dissociation of H19, we have now investigated a H27A mutant of BM2 using solid-state NMR. 15N NMR spectra indicate that removal of the second histidine converted the protonation and tautomeric equilibria of H19 to be similar to the H37 behavior in AM2, indicating that the peripheral H27 is indeed the origin of the low pKa's of H19 in wild-type BM2. Measured interhelical distances between W23 sidechains indicate that the pore constriction at W23 increases with the H19 tetrad charge but is independent of the H27A mutation. These results indicate that H27 both accelerates proton dissociation from H19 to increase the inward proton conductance and causes the small reverse conductance of BM2. The proton relay between H19 and H27 is likely mediated by the intervening gating tryptophan through cation-π interactions. This relayed proton transfer may exist in other ion channels and has implications for the design of imidazole-based synthetic proton channels.
Collapse
Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Matthias Roos
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| |
Collapse
|
37
|
Messerli MA, Sarkar A. Advances in Electrochemistry for Monitoring Cellular Chemical Flux. Curr Med Chem 2019; 26:4984-5002. [PMID: 31057100 DOI: 10.2174/0929867326666190506111629] [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: 09/28/2018] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/22/2022]
Abstract
The transport of organic and inorganic molecules, along with inorganic ions across the plasma membrane results in chemical fluxes that reflect the cellular function in healthy and diseased states. Measurement of these chemical fluxes enables the characterization of protein function and transporter stoichiometry, characterization of a single cell and embryo viability prior to implantation, and screening of pharmaceutical agents. Electrochemical sensors emerge as sensitive and non-invasive tools for measuring chemical fluxes immediately outside the cells in the boundary layer, that are capable of monitoring a diverse range of transported analytes including inorganic ions, gases, neurotransmitters, hormones, and pharmaceutical agents. Used on their own or in combination with other methods, these sensors continue to expand our understanding of the function of rare cells and small tissues. Advances in sensor construction and detection strategies continue to improve sensitivity under physiological conditions, diversify analyte detection, and increase throughput. These advances will be discussed in the context of addressing technical challenges to measuring chemical flux in the boundary layer of cells and measuring the resultant changes to the chemical concentration in the bulk media.
Collapse
Affiliation(s)
- Mark A Messerli
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD. United States
| | - Anyesha Sarkar
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD. United States
| |
Collapse
|
38
|
Zhang Y, Zheng QC. What are the effects of the serine triad on proton conduction of an influenza B M2 channel? An investigation by molecular dynamics simulations. Phys Chem Chem Phys 2019; 21:8820-8826. [PMID: 30968902 DOI: 10.1039/c9cp00612e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The tetrameric influenza B M2 channel (BM2), an acid activated proton channel, is important in the influenza virus B lifecycle. A conserved HxxxW motif is responsible for proton conduction and channel gating. In this study, to explore the effects of the serine triad (S9, S12 and S16) on proton conduction, we performed classical molecular dynamics (CMD) simulations and adaptive steered molecular dynamics (ASMD) simulations at different protonation states of the H19 tetrad. The results of the pore radius and the C-terminal tilt angle show that the electrostatic repulsion induced by protonated H19 is the key driving force for opening the BM2 channel. The open states could be stabilized by the hydrogen bonds between S16 and protonated H19. The solvent accessible surface area and water density indicate that the polar hydrophilic environment provided by the serine triad facilitates the formation of a water wire, and then exhibits favourable effects on proton conduction. The mutant research verifies and supports these views. Our work clarifies the effects of the serine triad on proton conduction in the BM2 channel, which would help us deeply understand the proton conduction mechanism in BM2 and provides a new perspective for antiviral drug design against BM2.
Collapse
Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People's Republic of China.
| | | |
Collapse
|
39
|
Piepenbrink MS, Nogales A, Basu M, Fucile CF, Liesveld JL, Keefer MC, Rosenberg AF, Martinez-Sobrido L, Kobie JJ. Broad and Protective Influenza B Virus Neuraminidase Antibodies in Humans after Vaccination and their Clonal Persistence as Plasma Cells. mBio 2019; 10:e00066-19. [PMID: 30862743 PMCID: PMC6414695 DOI: 10.1128/mbio.00066-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 12/14/2022] Open
Abstract
Although most seasonal inactivated influenza vaccines (IIV) contain neuraminidase (NA), the extent and mechanisms of action of protective human NA-specific humoral responses induced by vaccination are poorly resolved. Due to the propensity of influenza virus for antigenic drift and shift and its tendency to elicit predominantly strain-specific antibodies, humanity remains susceptible to waves of new strains of seasonal viruses and is at risk from viruses with pandemic potential for which limited or no immunity may exist. Here we demonstrate that the use of IIV results in increased levels of influenza B virus (IBV) NA-specific serum antibodies. Detailed analysis of the IBV NA B cell response indicates concurrent expansion of IBV NA-specific peripheral blood plasmablasts 7 days after IIV immunization which express monoclonal antibodies with broad and potent antiviral activity against both IBV Victoria and Yamagata lineages and prophylactic and therapeutic activity in mice. These IBV NA-specific B cell clonal lineages persisted in CD138+ long-lived bone marrow plasma cells. These results represent the first demonstration that IIV-induced NA human antibodies can protect and treat influenza virus infection in vivo and suggest that IIV can induce a subset of IBV NA-specific B cells with broad protective potential, a feature that warrants further study for universal influenza vaccine development.IMPORTANCE Influenza virus infections continue to cause substantial morbidity and mortality despite the availability of seasonal vaccines. The extensive genetic variability in seasonal and potentially pandemic influenza strains necessitates new vaccine strategies that can induce universal protection by focusing the immune response on generating protective antibodies against conserved targets such as regions within the influenza neuraminidase protein. We have demonstrated that seasonal immunization stimulates neuraminidase-specific antibodies in humans that are broad and potent in their protection from influenza B virus when tested in mice. These antibodies further persist in the bone marrow, where they are expressed by long-lived antibody-producing cells, referred to here as plasma cells. The significance in our research is the demonstration that seasonal influenza immunization can induce a subset of neuraminidase-specific B cells with broad protective potential, a process that if further studied and enhanced could aid in the development of a universal influenza vaccine.
Collapse
Affiliation(s)
| | - Aitor Nogales
- Department of Microbiology & Immunology, University of Rochester, Rochester, New York, USA
| | - Madhubanti Basu
- Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - Christopher F Fucile
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jane L Liesveld
- Division of Hematology/Oncology/James P. Wilmot Cancer Institute, University of Rochester, Rochester, New York, USA
| | - Michael C Keefer
- Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - Alexander F Rosenberg
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Luis Martinez-Sobrido
- Department of Microbiology & Immunology, University of Rochester, Rochester, New York, USA
| | - James J Kobie
- Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| |
Collapse
|
40
|
Mandala VS, Liao SY, Gelenter MD, Hong M. The Transmembrane Conformation of the Influenza B Virus M2 Protein in Lipid Bilayers. Sci Rep 2019; 9:3725. [PMID: 30842530 PMCID: PMC6403292 DOI: 10.1038/s41598-019-40217-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Influenza A and B viruses cause seasonal flu epidemics. The M2 protein of influenza B (BM2) is a membrane-embedded tetrameric proton channel that is essential for the viral lifecycle. BM2 is a functional analog of AM2 but shares only 24% sequence identity for the transmembrane (TM) domain. The structure and function of AM2, which is targeted by two antiviral drugs, have been well characterized. In comparison, much less is known about the structure of BM2 and no drug is so far available to inhibit this protein. Here we use solid-state NMR spectroscopy to investigate the conformation of BM2(1-51) in phospholipid bilayers at high pH, which corresponds to the closed state of the channel. Using 2D and 3D correlation NMR experiments, we resolved and assigned the 13C and 15N chemical shifts of 29 residues of the TM domain, which yielded backbone (φ, ψ) torsion angles. Residues 6-28 form a well-ordered α-helix, whereas residues 1-5 and 29-35 display chemical shifts that are indicative of random coil or β-sheet conformations. The length of the BM2-TM helix resembles that of AM2-TM, despite their markedly different amino acid sequences. In comparison, large 15N chemical shift differences are observed between bilayer-bound BM2 and micelle-bound BM2, indicating that the TM helix conformation and the backbone hydrogen bonding in lipid bilayers differ from the micelle-bound conformation. Moreover, HN chemical shifts of micelle-bound BM2 lack the periodic trend expected for coiled coil helices, which disagree with the presence of a coiled coil structure in micelles. These results establish the basis for determining the full three-dimensional structure of the tetrameric BM2 to elucidate its proton-conduction mechanism.
Collapse
Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
| |
Collapse
|
41
|
Zhang Y, Zhang H, Zheng Q. A unique activation-promotion mechanism of the influenza B M2 proton channel uncovered by multiscale simulations. Phys Chem Chem Phys 2019; 21:2984-2991. [PMID: 30672572 DOI: 10.1039/c9cp00130a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The influenza B M2 protein (BM2) forms an acid-activated proton channel that is important for the virus's lifecycle. Despite extensive research efforts, the detailed activation mechanism of the BM2 proton channel is often elusive. Herein a pH-regulated mechanism of the BM2TM domain has been systematically characterized using multiscale computer simulations, including classical molecular dynamics, constant pH molecular dynamics (CpHMD) and quantum mechanics/molecular mechanics (QM/MM) approaches. Our simulations reveal a pH-dependent conformational switch from the C-terminal closed to the C-terminal open conformers, and provide the free energy of conformational activation coupled to the titration of the His19 tetrad. Importantly, our results confirm the coupling titration between the His19 tetrad and His27 tetrad, and identify that the full-cationic state (His2744+) dominates at the low pH (the His19 tetrad at +2, +3 and +4 charge states). Our QM/MM simulations indicate that the second titratable histidine, His27, could further promote the BM2 acid activation and speed up proton dissociation from the HxxxW motif, thus facilitating proton conduction by BM2. Taken together, a unique "activation-promotion mechanism" about the BM2 proton channel is proposed, and these results may be helpful for the understanding of other similar proton channels and the development of BM2 inhibitors.
Collapse
Affiliation(s)
- Yulai Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People's Republic of China.
| | | | | |
Collapse
|
42
|
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.
Collapse
Affiliation(s)
- Yu Cao
- Institute of Precision Medicine, The Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | |
Collapse
|
43
|
Kesinger E, Liu J, Jensen A, Chia CP, Demers A, Moriyama H. Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. PLoS One 2018; 13:e0199227. [PMID: 29927982 PMCID: PMC6013169 DOI: 10.1371/journal.pone.0199227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/04/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A new type of influenza virus, known as type D, has recently been identified in cattle and pigs. Influenza D virus infection in cattle is typically asymptomatic; however, its infection in swine can result in clinical disease. Swine can also be infected with all other types of influenza viruses, namely A, B, and C. Consequently, swine can serve as a "mixing vessel" for highly pathogenic influenza viruses, including those with zoonotic potential. Currently, the only antiviral drug available targets influenza M2 protein ion channel is not completely effective. Thus, it is necessary to develop an M2 ion channel blocker capable of suppressing the induction of resistance to the genetic shift. To provide a basis for developing novel ion channel-blocking compounds, we investigated the properties of influenza D virus M2 protein (DM2) as a drug target. RESULTS To test the ion channel activity of DM2, the DNA corresponding to DM2 with cMyc-tag conjugated to its carboxyl end was cloned into the shuttle vector pNCB1. The mRNA of the DM2-cMyc gene was synthesized and injected into Xenopus oocytes. The translation products of DM2-cMyc mRNA were confirmed by immunofluorescence and mass spectrometry analyses. The DM2-cMyc mRNA-injected oocytes were subjected to the two-electrode voltage-clamp (TEVC) method, and the induced inward current was observed. The midpoint (Vmid) values in Boltzmann modeling for oocytes injected with DM2-cMyc RNA or a buffer were -152 and -200 mV, respectively. Assuming the same expression level in the Xenopus oocytes, DM2 without tag and influenza C virus M2 protein (CM2) were subjected to the TEVC method. DM2 exhibited ion channel activity under the condition that CM2 ion channel activity was reproduced. The gating voltages represented by Vmid for CM2 and DM2 were -141 and -146 mV, respectively. The reversal potentials observed in ND96 for CM2 and DM2 were -21 and -22 mV, respectively. Compared with intact DM2, DM2 variants with mutation in the YxxxK motif, namely Y72A and K76A DM2, showed lower Vmid values while showing no change in reversal potential. CONCLUSION The M2 protein from newly isolated influenza D virus showed ion channel activity similar to that of CM2. The gating voltage was shown to be affected by the YxxxK motif and by the hydrophobicity and bulkiness of the carboxyl end of the molecule.
Collapse
Affiliation(s)
- Evan Kesinger
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jianing Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Aaron Jensen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Catherine P. Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Andrew Demers
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
| |
Collapse
|
44
|
Shcherbakov AA, Hong M. Rapid measurement of long-range distances in proteins by multidimensional 13C- 19F REDOR NMR under fast magic-angle spinning. JOURNAL OF BIOMOLECULAR NMR 2018; 71:31-43. [PMID: 29785460 PMCID: PMC6314655 DOI: 10.1007/s10858-018-0187-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/16/2018] [Indexed: 05/24/2023]
Abstract
The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13C-15N distances, which are usually measured using the rotational-echo double-resonance (REDOR) technique. However, these measurements are restricted to distances of up to ~ 5 Å due to the low gyromagnetic ratios of 15N and 13C. Here we present a robust 2D 13C-19F REDOR experiment to measure multiple distances to ~ 10 Å. The technique targets proteins that contain a small number of recombinantly or synthetically incorporated fluorines. The 13C-19F REDOR sequence is combined with 2D 13C-13C correlation to resolve multiple distances in highly 13C-labeled proteins. We show that, at the high magnetic fields which are important for obtaining well resolved 13C spectra, the deleterious effect of the large 19F chemical shift anisotropy for REDOR is ameliorated by fast magic-angle spinning and is further taken into account in numerical simulations. We demonstrate this 2D 13C-13C resolved 13C-19F REDOR technique on 13C, 15N-labeled GB1. A 5-19F-Trp tagged GB1 sample shows the extraction of distances to a single fluorine atom, while a 3-19F-Tyr labeled GB1 sample allows us to evaluate the effects of multi-spin coupling and statistical 19F labeling on distance measurement. Finally, we apply this 2D REDOR experiment to membrane-bound influenza B M2 transmembrane peptide, and show that the distance between the proton-selective histidine residue and the gating tryptophan residue differs from the distances in the solution NMR structure of detergent-bound BM2. This 2D 13C-19F REDOR technique should facilitate SSNMR-based protein structure determination by increasing the measurable distances to the ~ 10 Å range.
Collapse
Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
| |
Collapse
|
45
|
Baumruck AC, Tietze D, Steinacker LK, Tietze AA. Chemical synthesis of membrane proteins: a model study on the influenza virus B proton channel. Chem Sci 2018; 9:2365-2375. [PMID: 29719709 PMCID: PMC5897842 DOI: 10.1039/c8sc00004b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 01/21/2018] [Indexed: 12/16/2022] Open
Abstract
NCL results in the quantitative yield of a membrane protein, where a thioester peptide is formed from an oxo-ester with an in situ cleavable solubilizing tag.
In the present study we have developed and optimized a robust strategy for the synthesis of highly hydrophobic peptides, especially membrane proteins, exemplarily using the influenza B M2 proton channel (BM2(1–51)). This strategy is based on the native chemical ligation of two fragments, where the thioester fragment is formed from an oxo-ester peptide, which is synthesized using Fmoc-SPPS, and features an in situ cleavable solubilizing tag (ADO, ADO2 or ADO-Lys5). The nearly quantitative production of the ligation product was followed by an optimized work up protocol, resulting in almost quantitative desulfurization and Acm-group cleavage. Circular dichroism analysis in a POPC lipid membrane revealed that the synthetic BM2(1–51) construct adopts a helical structure similar to that of the previously characterized BM2(1–33).
Collapse
Affiliation(s)
- A C Baumruck
- Darmstadt University of Technology , Clemens-Schöpf Institute of Organic Chemistry and Biochemistry , Alarich-Weiss Str. 4 , 64287 Darmstadt , Germany .
| | - D Tietze
- Darmstadt University of Technology , Eduard-Zintl-Institute of Inorganic and Physical Chemistry , Alarich-Weiss-Str. 4 , 64287 Darmstadt , Germany
| | - L K Steinacker
- Darmstadt University of Technology , Clemens-Schöpf Institute of Organic Chemistry and Biochemistry , Alarich-Weiss Str. 4 , 64287 Darmstadt , Germany .
| | - A A Tietze
- Darmstadt University of Technology , Clemens-Schöpf Institute of Organic Chemistry and Biochemistry , Alarich-Weiss Str. 4 , 64287 Darmstadt , Germany .
| |
Collapse
|
46
|
Agrahari AK, Kumar A, R S, Zayed H, C GPD. Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-tooth disease: A computational study. J Theor Biol 2018; 437:305-317. [PMID: 29111421 DOI: 10.1016/j.jtbi.2017.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
Abstract
X-linked Charcot-Marie-Tooth type 1 X (CMTX1) disease is a subtype of Charcot-Marie-Tooth (CMT), which is mainly caused by mutations in the GJB1 gene. It is also known as connexin 32 (Cx32) that leads to Schwann cell abnormalities and peripheral neuropathy. CMTX1 is considered as the second most common form of CMT disease. The aim of this study is to computationally predict the potential impact of different single amino acid substitutions at position 75 of Cx32, from arginine (R) to proline (P), glutamine (Q) and tryptophan (W). This position is known to be highly conserved among the family of connexin. To understand the structural and functional changes due to these single amino acid substitutions, we employed a homology-modeling technique to build the three-dimensional structure models for the native and mutant proteins. The protein structures were further embedded into a POPC lipid bilayer, inserted into a water box, and subjected to molecular dynamics simulation for 50 ns. Our results show that the mutants R75P, R75Q and R75W display variable structural conformation and dynamic behavior compared to the native protein. Our data proves useful in predicting the potential pathogenicity of the mutant proteins and is expected to serve as a platform for drug discovery for patients with CMT.
Collapse
Affiliation(s)
| | - Amit Kumar
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy; Biosciences Sector, Center for advanced study research and development in Sardinia (CRS4), Loc. Piscina Manna, 09010 Pula, Italy
| | - Siva R
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
| | - George Priya Doss C
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
| |
Collapse
|
47
|
Ma C, Wang J. Functional studies reveal the similarities and differences between AM2 and BM2 proton channels from influenza viruses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:272-280. [PMID: 29106970 DOI: 10.1016/j.bbamem.2017.10.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/30/2022]
Abstract
AM2 and BM2 proton channels are attractive antiviral drug targets due to their essential roles during influenza virus replication. Although both AM2 and BM2 are proton-selective ion channels, they share little sequence similarity except for the HXXXW sequence, which suggests that their proton conductance properties might differ. To test this hypothesis, we applied two-electrode voltage clamp electrophysiological assays to study the specific conductance, leakage current, channel activation, and inhibition of AM2 and BM2 proton channels. It was found that BM2 channel has a higher specific conductance than AM2 channel at pH5.5. Unlike AM2 channel, whose proton conductance is asymmetric (from viral exterior to interior), BM2 channel is capable of conducting proton in both directions. Moreover, BM2 requires a more acidic pH for channel activation than AM2, as revealed by its lower pKa values. Finally, both AM2 and BM2 can be inhibited by Cu(II) and Cu(I). Overall, the results from this side-by-side comparison of AM2 and BM2 channels reveal the structure-function relationships of these two viroporins, and such information might be important for the designing of novel ion channels.
Collapse
Affiliation(s)
- Chunlong Ma
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, United States
| | - Jun Wang
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, United States; Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, United States.
| |
Collapse
|
48
|
Williams JK, Shcherbakov AA, Wang J, Hong M. Protonation equilibria and pore-opening structure of the dual-histidine influenza B virus M2 transmembrane proton channel from solid-state NMR. J Biol Chem 2017; 292:17876-17884. [PMID: 28893910 DOI: 10.1074/jbc.m117.813998] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Indexed: 12/14/2022] Open
Abstract
The influenza A and B viruses are the primary cause of seasonal flu epidemics. Common to both viruses is the M2 protein, a homotetrameric transmembrane proton channel that acidifies the virion after endocytosis. Although influenza A M2 (AM2) and B M2 (BM2) are functional analogs, they have little sequence homology, except for a conserved HXXXW motif, which is responsible for proton selectivity and channel gating. Importantly, BM2 contains a second titratable histidine, His-27, in the tetrameric transmembrane domain that forms a reverse WXXXH motif with the gating tryptophan. To understand how His-27 affects the proton conduction property of BM2, we have used solid-state NMR to characterize the pH-dependent structure and dynamics of His-27. In cholesterol-containing lipid membranes mimicking the virus envelope, 15N NMR spectra show that the His-27 tetrad protonates with higher pKa values than His-19, indicating that the solvent-accessible His-27 facilitates proton conduction of the channel by increasing the proton dissociation rates of His-19. AM2 is inhibited by the amantadine class of antiviral drugs, whereas BM2 has no known inhibitors. We measured the N-terminal interhelical separation of the BM2 channel using fluorinated Phe-5. The interhelical 19F-19F distances show a bimodal distribution of a short distance of 7 Å and a long distance of 15-20 Å, indicating that the phenylene rings do not block small-molecule entry into the channel pore. These results give insights into the lack of amantadine inhibition of BM2 and reveal structural diversities in this family of viral proton channels.
Collapse
Affiliation(s)
- Jonathan K Williams
- From the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | - Alexander A Shcherbakov
- From the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
| | - Mei Hong
- From the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| |
Collapse
|
49
|
Hu Y, Sneyd H, Dekant R, Wang J. Influenza A Virus Nucleoprotein: A Highly Conserved Multi-Functional Viral Protein as a Hot Antiviral Drug Target. Curr Top Med Chem 2017; 17:2271-2285. [PMID: 28240183 DOI: 10.2174/1568026617666170224122508] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 01/25/2023]
Abstract
Prevention and treatment of influenza virus infection is an ongoing unmet medical need. Each year, thousands of deaths and millions of hospitalizations are attributed to influenza virus infection, which poses a tremendous health and economic burden to the society. Aside from the annual influenza season, influenza viruses also lead to occasional influenza pandemics as a result of emerging or re-emerging influenza strains. Influenza viruses are RNA viruses that exist in quasispecies, meaning that they have a very diverse genetic background. Such a feature creates a grand challenge in devising therapeutic intervention strategies to inhibit influenza virus replication, as a single agent might not be able to inhibit all influenza virus strains. Both classes of currently approved anti-influenza drugs have limitations: the M2 channel blockers amantadine and rimantadine are no longer recommended for use in the U.S. due to predominant drug resistance, and resistance to the neuraminidase inhibitor oseltamivir is continuously on the rise. In pursuing the next generation of antiviral drugs with broad-spectrum activity and higher genetic barrier of drug resistance, the influenza virus nucleoprotein (NP) stands out as a high-profile drug target. This review summarizes recent developments in designing inhibitors targeting influenza NP and their mechanisms of action.
Collapse
Affiliation(s)
- Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Hannah Sneyd
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Raphael Dekant
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| |
Collapse
|
50
|
Applications of NMR to membrane proteins. Arch Biochem Biophys 2017; 628:92-101. [PMID: 28529197 DOI: 10.1016/j.abb.2017.05.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/14/2023]
Abstract
Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction. Recent advances in NMR instrumentation, spectroscopic methods, computational methods, and sample preparations are driving exciting new efforts in membrane protein structural biology.
Collapse
|