1
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Yang Y, Wang X, Dong H. Simulating chemical reactions promoted by self-assembled peptides with catalytic properties. Methods Enzymol 2024; 697:321-343. [PMID: 38816128 DOI: 10.1016/bs.mie.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Peptides that self-assemble exhibit distinct three-dimensional structures and attributes, positioning them as promising candidates for biocatalysts. Exploring their catalytic processes enhances our comprehension of the catalytic actions inherent to self-assembling peptides, laying a theoretical foundation for creating novel biocatalysts. The investigation into the intricate reaction mechanisms of these entities is rendered challenging due to the vast variability in peptide sequences, their aggregated formations, supportive elements, structures of active sites, types of catalytic reactions, and the interplay between these variables. This complexity hampers the elucidation of the linkage between sequence, structure, and catalytic efficiency in self-assembling peptide catalysts. This chapter delves into the latest progress in understanding the mechanisms behind peptide self-assembly, serving as a catalyst in hydrolysis and oxidation reactions, and employing computational analyses. It discusses the establishment of models, selection of computational strategies, and analysis of computational procedures, emphasizing the application of modeling techniques in probing the catalytic mechanisms of peptide self-assemblies. It also looks ahead to the potential future trajectories within this research domain. Despite facing numerous obstacles, a thorough investigation into the structural and catalytic mechanisms of peptide self-assemblies, combined with the ongoing advancement in computational simulations and experimental methodologies, is set to offer valuable theoretical insights for the development of new biocatalysts, thereby significantly advancing the biocatalysis field.
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Affiliation(s)
- Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Xiaoyu Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China; State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute for Brain Sciences, Nanjing University, Nanjing, P.R. China.
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2
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Kumar G, Sakharam KA. Tackling Influenza A virus by M2 ion channel blockers: Latest progress and limitations. Eur J Med Chem 2024; 267:116172. [PMID: 38330869 DOI: 10.1016/j.ejmech.2024.116172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Influenza outbreaks cause pandemics in millions of people. The treatment of influenza remains a challenge due to significant genetic polymorphism in the influenza virus. Also, developing vaccines to protect against seasonal and pandemic influenza infections is constantly impeded. Thus, antibiotics are the only first line of defense against antigenically distinct strains or new subtypes of influenza viruses. Among several anti-influenza targets, the M2 protein of the influenza virus performs several activities. M2 protein is an ion channel that permits proton conductance through the virion envelope and the deacidification of the Golgi apparatus. Both these functions are critical for viral replication. Thus, targeting the M2 protein of the influenza virus is an essential target. Rimantadine and amantadine are two well-known drugs that act on the M2 protein. However, these drugs acquired resistance to influenza and thus are not recommended to treat influenza infections. This review discusses an overview of anti-influenza therapy, M2 ion channel functions, and its working principle. It also discusses the M2 structure and its role, and the change in the structure leads to mutant variants of influenza A virus. We also shed light on the recently identified compounds acting against wild-type and mutated M2 proteins of influenza virus A. These scaffolds could be an alternative to M2 inhibitors and be developed as antibiotics for treating influenza infections.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
| | - Kakade Aditi Sakharam
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India
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3
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Asgharpour S, Chi LA, Spehr M, Carloni P, Alfonso-Prieto M. Fluoride Transport and Inhibition Across CLC Transporters. Handb Exp Pharmacol 2024; 283:81-100. [PMID: 36042142 DOI: 10.1007/164_2022_593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).
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Affiliation(s)
- Somayeh Asgharpour
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - L América Chi
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, Mexico
| | - Marc Spehr
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany.
- Department of Physics, RWTH Aachen University, Aachen, Germany.
- JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Lazaridis T. Molecular origins of asymmetric proton conduction in the influenza M2 channel. Biophys J 2023; 122:90-98. [PMID: 36403086 PMCID: PMC9822799 DOI: 10.1016/j.bpj.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
The M2 proton channel of influenza A is embedded into the viral envelope and allows acidification of the virion when the external pH is lowered. In contrast, no outward proton conductance is observed when the internal pH is lowered, although outward current is observed at positive voltage. Residues Trp41 and Asp44 are known to play a role in preventing pH-driven outward conductance, but the mechanism for this is unclear. We investigate this issue using classical molecular dynamics simulations with periodic proton hops. When all key His37 residues are neutral, inward proton movement is much more facile than outward movement if the His are allowed to shuttle the proton. The preference for inward movement increases further as the charge on the His37 increases. Analysis of the trajectories reveals three factors accounting for this asymmetry. First, in the outward direction, Asp44 traps the hydronium by strong electrostatic interactions. Secondly, Asp44 and Trp41 orient the hydronium with the protons pointing inward, hampering outward Grotthus hopping. As a result, the effective barrier is lower in the inward direction. Trp41 adds to the barrier by weakly H-bonding to potential H+ acceptors. Finally, for charged His, the H3O+ in the inner vestibule tends to get trapped at lipid-lined fenestrations of the cone-shaped channel. Simulations qualitatively reproduce the experimentally observed higher outward conductance of mutants. The ability of positive voltage, unlike proton gradient, to induce an outward current appears to arise from its ability to bias H3O+ and the waters around it toward more H-outward orientations.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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5
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Aledavood E, Selmi B, Estarellas C, Masetti M, Luque FJ. From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus. Front Mol Biosci 2022; 8:796229. [PMID: 35096969 PMCID: PMC8795881 DOI: 10.3389/fmolb.2021.796229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
With an estimated 1 billion people affected across the globe, influenza is one of the most serious health concerns worldwide. Therapeutic treatments have encompassed a number of key functional viral proteins, mainly focused on the M2 proton channel and neuraminidase. This review highlights the efforts spent in targeting the M2 proton channel, which mediates the proton transport toward the interior of the viral particle as a preliminary step leading to the release of the fusion peptide in hemagglutinin and the fusion of the viral and endosomal membranes. Besides the structural and mechanistic aspects of the M2 proton channel, attention is paid to the challenges posed by the development of efficient small molecule inhibitors and the evolution toward novel ligands and scaffolds motivated by the emergence of resistant strains.
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Affiliation(s)
- Elnaz Aledavood
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Beatrice Selmi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
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6
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Kolokouris D, Kalenderoglou IE, Kolocouris A. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. J Chem Inf Model 2021; 61:5550-5568. [PMID: 34714655 DOI: 10.1021/acs.jcim.1c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (Nδ or Νε), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having Nε Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
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Affiliation(s)
- Dimitrios Kolokouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Iris E Kalenderoglou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
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7
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Micikas R, Acharyya A, Gai F, Smith AB. A Scalable Synthesis of the Blue Fluorescent Amino Acid 4-Cyanotryptophan and the Fmoc Derivative: Utility Demonstrated with the Influenza M2 Peptide Tetramer. Org Lett 2021; 23:1247-1250. [DOI: 10.1021/acs.orglett.0c04055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Micikas
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
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8
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Development and application of reverse genetic technology for the influenza virus. Virus Genes 2021; 57:151-163. [PMID: 33528730 PMCID: PMC7851324 DOI: 10.1007/s11262-020-01822-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/28/2020] [Indexed: 12/28/2022]
Abstract
Influenza virus is a common virus in people's daily lives, and it has certain infectivity in humans and animals. Influenza viruses have the characteristics of a high mutation rate and wide distribution. Reverse genetic technology is primarily used to modify viruses at the DNA level through targeted modification of the virus cDNA. Genetically modified influenza viruses have a unique advantage when researching the transmission and pathogenicity of influenza. With the continuous development of oncolytic viruses in recent years, studies have found that influenza viruses also have certain oncolytic activity. Influenza viruses can specifically recognize tumor cells; activate cytotoxic T cells, NK cells, dendritic cells, etc.; and stimulate the body to produce an immune response, thereby killing tumor cells. This article will review the development and application of influenza virus reverse genetic technology.
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9
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M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. Proc Natl Acad Sci U S A 2020; 117:3583-3591. [PMID: 32015120 DOI: 10.1073/pnas.1913385117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The matrix-2 (M2) protein from influenza A virus is a tetrameric, integral transmembrane (TM) protein that plays a vital role in viral replication by proton flux into the virus. The His37 tetrad is a pH sensor in the center of the M2 TM helix that activates the channel in response to the low endosomal pH. M2 consists of different regions that are believed to be involved in membrane targeting, packaging, nucleocapsid binding, and proton transport. Although M2 has been the target of many experimental and theoretical studies that have led to significant insights into its structure and function under differing conditions, the main mechanism of proton transport, its conformational dynamics, and the role of the amphipathic helices (AHs) on proton conductance remain elusive. To this end, we have applied explicit solvent constant pH molecular dynamics using the multisite λ-dynamics approach (CpHMDMSλD) to investigate the buried ionizable residues comprehensively and to elucidate their effect on the conformational transition. Our model recapitulates the pH-dependent conformational transition of M2 from closed to open state when the AH domain is included in the M2 construct, revealing the role of the amphipathic helices on this transition and shedding light on the proton-transport mechanism. This work demonstrates the importance of including the amphipathic helices in future experimental and theoretical studies of ion channels. Finally, our work shows that explicit solvent CpHMDMSλD provides a realistic pH-dependent model for membrane proteins.
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10
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Saraei N, Hietsoi O, Frye BC, Gupta AJ, Mashuta MS, Gupta G, Buchanan RM, Grapperhaus CA. Water wire clusters in isostructural Cu(II) and Ni(II) complexes: Synthesis, characterization, and thermal analyses. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants. Biochemistry 2018; 57:5957-5968. [PMID: 30230310 DOI: 10.1021/acs.biochem.8b00722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influenza M2 proton channel is a major drug target, but unfortunately, the acquisition of resistance mutations greatly reduces the functional life span of a drug in influenza treatment. New M2 inhibitors that inhibit mutant M2 channels otherwise resistant to the early adamantine-based drugs have been reported, but it remains unclear whether and how easy resistance could arise to such inhibitors. We have combined a newly developed proton conduction assay with an established method for selection and screening, both Escherichia coli-based, to enable the study of M2 function and inhibition. Combining this platform with two groups of structurally different M2 inhibitors allowed us to isolate drug resistant M2 channels from a mutant library. Two groups of M2 variants emerged from this analysis. A first group appeared almost unaffected by the inhibitor, M_089 (N13I, I35L, and F47L) and M_272 (G16C and D44H), and the single-substitution variants derived from these (I35L, L43P, D44H, and L46P). Functionally, these resemble the known drug resistant M2 channels V27A, S31N, and swine flu. In addition, a second group of tested M2 variants were all still inhibited by drugs but to a lesser extent than wild type M2. Molecular dynamics simulations aided in distinguishing the two groups where drug binding to the wild type and the less resistant M2 group showed a stable positioning of the ligand in the canonical binding pose, as opposed to the drug resistant group in which the ligand rapidly dissociated from the complex during the simulations.
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Affiliation(s)
- Paul Santner
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - João Miguel da Silva Martins
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Caroline Kampmeyer
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Jonas S Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Amelie Stein
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Christian A Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark.,Center for Biopharmaceuticals, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Isaiah T Arkin
- Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Givat-Ram, Jerusalem 91904 , Israel
| | - Jakob R Winther
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
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The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations. SENSORS 2018; 18:s18093143. [PMID: 30231473 PMCID: PMC6163810 DOI: 10.3390/s18093143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGICs) to carry Na+ and K+ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently, the structure of a number of VGICs was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains (VSDs), each formed from four transmembrane (TM) segments, plus a pore domain through which ions move. Understanding the gating mechanism (how the channel opens and closes) requires structures. One TM segment (S4) has an arginine in every third position, with one such segment per domain. It is usually assumed that these arginines are all ionized, and in the resting state are held toward the intracellular side of the membrane by voltage across the membrane. They are assumed to move outward (extracellular direction) when released by depolarization of this voltage, producing a capacitive gating current and opening the channel. We suggest alternate interpretations of the evidence that led to these models. Measured gating current is the total charge displacement of all atoms in the VSD; we propose that the prime, but not sole, contributor is proton motion, not displacement of the charges on the arginines of S4. It is known that the VSD can conduct protons. Quantum calculations on the Kv1.2 potassium channel VSD show how; the key is the amphoteric nature of the arginine side chain, which allows it to transfer a proton. This appears to be the first time the arginine side chain has had its amphoteric character considered. We have calculated one such proton transfer in detail: this proton starts from a tyrosine that can ionize, transferring to the NE of the third arginine on S4; that arginine’s NH then transfers a proton to a glutamate. The backbone remains static. A mutation predicted to affect the proton transfer has been qualitatively confirmed experimentally, from the change in the gating current-voltage curve. The total charge displacement in going from a normal closed potential of −70 mV across the membrane to 0 mV (open), is calculated to be approximately consistent with measured values, although the error limits on the calculation require caution in interpretation.
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13
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Lillo VJ, Mansilla J, Saá JM. The role of proton shuttling mechanisms in solvent-free and catalyst-free acetalization reactions of imines. Org Biomol Chem 2018; 16:4527-4536. [DOI: 10.1039/c8ob01007b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalyst-free and solvent-free reactions of the type NuH + E → Nu–EH are NuH-catalyzed processes in which Grotthuss-like proton shuttling pays a key role.
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Affiliation(s)
- Victor J. Lillo
- Departamento de Química
- Universidad de las islas Baleares
- 07122 Palma de Mallorca
- Spain
| | - Javier Mansilla
- Departamento de Química
- Universidad de las islas Baleares
- 07122 Palma de Mallorca
- Spain
| | - José M. Saá
- Departamento de Química
- Universidad de las islas Baleares
- 07122 Palma de Mallorca
- Spain
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14
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Abstract
An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry & Physics, Graduate Center, City University of New York , 365 Fifth Ave, New York, New York 10016, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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15
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Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid activation mechanism of the influenza A M2 proton channel. Proc Natl Acad Sci U S A 2016; 113:E6955-E6964. [PMID: 27791184 PMCID: PMC5111692 DOI: 10.1073/pnas.1615471113] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel responsible for the acidification of the influenza virus interior, an important step in the viral lifecycle. Four histidine residues (His37) in the center of the channel act as a pH sensor and proton selectivity filter. Despite intense study, the pH-dependent activation mechanism of the AM2 channel has to date not been completely understood at a molecular level. Herein we have used multiscale computer simulations to characterize (with explicit proton transport free energy profiles and their associated calculated conductances) the activation mechanism of AM2. All proton transfer steps involved in proton diffusion through the channel, including the protonation/deprotonation of His37, are explicitly considered using classical, quantum, and reactive molecular dynamics methods. The asymmetry of the proton transport free energy profile under high-pH conditions qualitatively explains the rectification behavior of AM2 (i.e., why the inward proton flux is allowed when the pH is low in viral exterior and high in viral interior, but outward proton flux is prohibited when the pH gradient is reversed). Also, in agreement with electrophysiological results, our simulations indicate that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain; the four transmembrane helices flanking the channel lumen alone seem to determine the proton conduction mechanism.
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Affiliation(s)
- Ruibin Liang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Jessica M J Swanson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of San Francisco, San Francisco, CA 94158
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
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Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F. Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel. Phys Chem Chem Phys 2016; 18:28939-28950. [PMID: 27725984 PMCID: PMC5157935 DOI: 10.1039/c6cp03426h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The M2 proton channel of the influenza A virus has been the subject of extensive studies because of its critical role in viral replication. As such, we now know a great deal about its mechanism of action, especially how it selects and conducts protons in an asymmetric fashion. The conductance of this channel is tuned to conduct protons at a relatively low biologically useful rate, which allows acidification of the viral interior of a virus entrapped within an endosome, but not so great as to cause toxicity to the infected host cell prior to packaging of the virus. The dynamic, structural and chemical features that give rise to this tuning are not fully understood. Herein, we use a tryptophan (Trp) analog, 5-cyanotryptophan, and various methods, including linear and nonlinear infrared spectroscopies, static and time-resolved fluorescence techniques, and molecular dynamics simulations, to site-specifically interrogate the structure and hydration dynamics of the Trp41 gate in the transmembrane domain of the M2 proton channel. Our results suggest that the Trp41 sidechain adopts the t90 rotamer, the χ2 dihedral angle of which undergoes an increase of approximately 35° upon changing the pH from 7.4 to 5.0. Furthermore, we find that Trp41 is situated in an environment lacking bulk-like water, and somewhat surprisingly, the water density and dynamics do not show a measurable difference between the high (7.4) and low (5.0) pH states. Since previous studies have shown that upon channel opening water flows into the cavity above the histidine tetrad (His37), the present finding thus provides evidence indicating that the lack of sufficient water molecules near Trp41 needed to establish a continuous hydrogen bonding network poses an additional energetic bottleneck for proton conduction.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. and Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. and Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Padhi S, Priyakumar UD. Urea-Aromatic Stacking and Concerted Urea Transport: Conserved Mechanisms in Urea Transporters Revealed by Molecular Dynamics. J Chem Theory Comput 2016; 12:5190-5200. [PMID: 27576044 DOI: 10.1021/acs.jctc.6b00602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Urea transporters are membrane proteins that selectively allow urea molecules to pass through. It is not clear how these transporters allow rapid conduction of urea, a polar molecule, in spite of the presence of a hydrophobic constriction lined by aromatic rings. The current study elucidates the mechanism that is responsible for this rapid conduction by performing free energy calculations on the transporter dvUT with a cumulative sampling time of about 1.3 μs. A parallel arrangement of aromatic rings in the pore enables stacking of urea with these rings, which, in turn, lowers the energy barrier for urea transport. Such interaction of the rings with urea is proposed to be a conserved mechanism across all urea-conducting proteins. The free energy landscape for the permeation of multiple urea molecules reveals an interplay between interurea interaction and the solvation state of the urea molecules. This is for the first time that multiple molecule permeation through any small molecule transporter has been modeled.
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Affiliation(s)
- Siladitya Padhi
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032, India
| | - U Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032, India
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