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Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein. J CHEM-NY 2015. [DOI: 10.1155/2015/908204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges ofab initiocalculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation ofR=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angleχ1and small variations ofχ2of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.
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DiFrancesco ML, Hansen UP, Thiel G, Moroni A, Schroeder I. Effect of cytosolic pH on inward currents reveals structural characteristics of the proton transport cycle in the influenza A protein M2 in cell-free membrane patches of Xenopus oocytes. PLoS One 2014; 9:e107406. [PMID: 25211283 PMCID: PMC4174909 DOI: 10.1371/journal.pone.0107406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/17/2014] [Indexed: 01/01/2023] Open
Abstract
Transport activity through the mutant D44A of the M2 proton channel from influenza virus A was measured in excised inside-out macro-patches of Xenopus laevis oocytes at cytosolic pH values of 5.5, 7.5 and 8.2. The current-voltage relationships reveal some peculiarities: 1. "Transinhibition", i.e., instead of an increase of unidirectional outward current with increasing cytosolic H(+) concentration, a decrease of unidirectional inward current was found. 2. Strong inward rectification. 3. Exponential rise of current with negative potentials. In order to interpret these findings in molecular terms, different kinetic models have been tested. The transinhibition basically results from a strong binding of H(+) to a site in the pore, presumably His37. This assumption alone already provides inward rectification and exponential rise of the IV curves. However, it results in poor global fits of the IV curves, i.e., good fits were only obtained for cytosolic pH of 8.2, but not for 7.5. Assuming an additional transport step as e.g. caused by a constriction zone at Val27 resulted in a negligible improvement. In contrast, good global fits for cytosolic pH of 7.5 and 8.2 were immediately obtained with a cyclic model. A "recycling step" implies that the protein undergoes conformational changes (assigned to Trp41 and Val27) during transport which have to be reset before the next proton can be transported. The global fit failed at the low currents at pHcyt = 5.5, as expected from the interference of putative transport of other ions besides H(+). Alternatively, a regulatory effect of acidic cytosolic pH may be assumed which strongly modifies the rate constants of the transport cycle.
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Affiliation(s)
| | - Ulf-Peter Hansen
- Department of Structural Biology, University of Kiel, Kiel, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technical University of Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences and CNR-IBF, University of Milan, Milan, Italy
| | - Indra Schroeder
- Plant Membrane Biophysics, Technical University of Darmstadt, Darmstadt, Germany
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Wei C, Pohorille A. Activation and proton transport mechanism in influenza A M2 channel. Biophys J 2014; 105:2036-45. [PMID: 24209848 DOI: 10.1016/j.bpj.2013.08.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/09/2013] [Accepted: 08/08/2013] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics trajectories 2 μs in length have been generated for the pH-activated, tetrameric M2 proton channel of the influenza A virus in all protonation states of the pH sensor located at the His(37) tetrad. All simulated structures are in very good agreement with high-resolution structures. Changes in the channel caused by progressive protonation of His(37) provide insight into the mechanism of proton transport. The channel is closed at both His(37) and Trp(41) sites in the singly and doubly protonated states, but it opens at Trp(41) upon further protonation. Anions access the charged His(37) and by doing so stabilize the protonated states of the channel. The narrow opening at the His(37) site, further blocked by anions, is inconsistent with the water-wire mechanism of proton transport. Instead, conformational interconversions of His(37) correlated with hydrogen bonding to water molecules indicate that these residues shuttle protons in high-protonation states. Hydrogen bonds between charged and uncharged histidines are rare. The valve at Val(27) remains on average quite narrow in all protonation states but fluctuates sufficiently to support water and proton transport. A proton transport mechanism in which the channel, depending on pH, opens at either the histidine or valine gate is only partially supported by the simulations.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California.
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Alhadeff R, Assa D, Astrahan P, Krugliak M, Arkin IT. Computational and experimental analysis of drug binding to the Influenza M2 channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1068-73. [PMID: 24016551 DOI: 10.1016/j.bbamem.2013.07.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/22/2013] [Accepted: 07/25/2013] [Indexed: 01/23/2023]
Abstract
The Influenza Matrix 2 (M2) protein is the target of Amantadine and Rimantadine which block its H(+) channel activity. However, the potential of these aminoadamantyls to serve as anti-flu agents is marred by the rapid resistance that the virus develops against them. Herein, using a cell based assay that we developed, we identify two new aminoadamantyl derivatives that show increased activity against otherwise resistant M2 variants. In order to understand the distinguishing binding patterns of the different blockers, we computed the potential of mean force of the drug binding process. The results reveal that the new derivatives are less mobile and bind to a larger pocket in the channel. Finally, such analyses may prove useful in designing new, more effective M2 blockers as a means of curbing influenza. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking.
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Affiliation(s)
- Raphael Alhadeff
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Dror Assa
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Peleg Astrahan
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Miriam Krugliak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel.
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Manor J, Feldblum ES, Zanni MT, Arkin IT. Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy. J Phys Chem Lett 2012; 3:939-944. [PMID: 22563521 PMCID: PMC3341589 DOI: 10.1021/jz300150v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The polarity pattern of a macromolecule is of utmost importance to its structure and function. For example, one of the main driving forces for protein folding is the burial of hydrophobic residues. Yet polarity remains a difficult property to measure experimentally, due in part to its non-uniformity in the protein interior. Herein, we show that FTIR linewidth analysis of noninvasive 1-(13)C=(18)O labels can be used to obtain a reliable measure of the local polarity, even in a highly multi-phasic system, such as a membrane protein. We show that in the Influenza M2 H(+) channel, residues that line the pore are located in an environment that is as polar as fully solvated residues, while residues that face the lipid acyl chains are located in an apolar environment. Taken together, FTIR linewidth analysis is a powerful, yet chemically non-perturbing approach to examine one of the most important properties in proteins - polarity.
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Affiliation(s)
- Joshua Manor
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| | - Esther S. Feldblum
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396, USA
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry. The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
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Leonov H, Astrahan P, Krugliak M, Arkin IT. How Do Aminoadamantanes Block the Influenza M2 Channel, and How Does Resistance Develop? J Am Chem Soc 2011; 133:9903-11. [DOI: 10.1021/ja202288m] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hadas Leonov
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Peleg Astrahan
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Miriam Krugliak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
| | - Isaiah T. Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel
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Qin G, Yu K, Shi T, Luo C, Li G, Zhu W, Jiang H. How does influenza virus a escape from amantadine? J Phys Chem B 2010; 114:8487-93. [PMID: 20521806 DOI: 10.1021/jp911588y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antiflu drugs such as amantadine (AMT) were reported to be insensitive to influenza A virus gradually after their marketing. Mutation experiments indicate that the trans-membrane domain of M2 protein plays an essential role in AMT resistance, especially the S31N mutation. To investigate the details of structure and mechanism, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations have been carried out on both the wild-type protein and its S31N mutant. Our MD simulations reveal AMT can occupy different binding positions in the pore of M2 channel, and the binding modes have also been verified and analyzed by QM/MM calculations. More importantly, we find the formation of a water wire modulated by the binding position of AMT to be essential for the function of M2 protein, and, the block of water wire can inhibit channel function in the WT system. Failure of channel blocking would cause AMT drug resistance in the S31N mutant. These results support one of the conflicting views about M2-drug binding sites: AMT binds to the pore of M2 channel. Our findings help clarify the resistant mechanism of AMT to M2 protein and should facilitate the discovery of new drugs for treating influenza A virus.
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Affiliation(s)
- Guangrong Qin
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Phongphanphanee S, Rungrotmongkol T, Yoshida N, Hannongbua S, Hirata F. Proton Transport through the Influenza A M2 Channel: Three-Dimensional Reference Interaction Site Model Study. J Am Chem Soc 2010; 132:9782-8. [DOI: 10.1021/ja1027293] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Saree Phongphanphanee
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan, Center of Innovative Nanotechnology and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Thanyada Rungrotmongkol
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan, Center of Innovative Nanotechnology and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Norio Yoshida
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan, Center of Innovative Nanotechnology and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Supot Hannongbua
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan, Center of Innovative Nanotechnology and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Fumio Hirata
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan, Center of Innovative Nanotechnology and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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Kozakov D, Chuang GY, Beglov D, Vajda S. Where does amantadine bind to the influenza virus M2 proton channel? Trends Biochem Sci 2010; 35:471-5. [PMID: 20382026 DOI: 10.1016/j.tibs.2010.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 03/03/2010] [Accepted: 03/10/2010] [Indexed: 01/25/2023]
Abstract
Structures of the influenza A virus M2 proton channel in the open conformation have been determined by X-ray crystallography, and in the closed conformation by NMR. Whereas the X-ray structure shows a single inhibitor molecule in the middle of the channel, four inhibitor molecules bind the channel's outer surface in the NMR structure. In both structures, the strongest hot spots (i.e., regions that contribute substantially to the free energy of binding any potential ligand) lie inside the pore, and other hot spots are found at exterior locations. By considering all available models, we propose the primary drug binding site is inside the pore, but that exterior binding occurs under appropriate conditions.
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Affiliation(s)
- Dima Kozakov
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
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Chapter 7 Influenza A M2. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1554-4516(09)10007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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