A Computational Study of the Closed and Open States of the Influenza A M2 Proton Channel
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| Publicat a: | Biophysical Journal vol. 89, no. 4 (Oct 2005), p. 2402-2411 |
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Biophysical Society
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| 100 | 1 | |a Wu, Yujie | |
| 245 | 1 | |a A Computational Study of the Closed and Open States of the Influenza A M2 Proton Channel | |
| 260 | |b Biophysical Society |c Oct 2005 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a In this study, four possible conformations of the His-37 and Trp-41 residues for the closed state of the influenza M2 ion channel were identified by a conformation scan based on a solid-state NMR restraint. In the four conformations, the His-37 residue can be of either the t-160 or t60 rotamer, whereas Trp-41 can be of either the t-105 or t90 rotamer. These conformations were further analyzed by density functional theory calculations and molecular dynamics simulations, and the data indicate that the His-37 residue most likely adopts the 160 rotamer and should be monoprotonated at the δ-nitrogen site, whereas Trp-41 adopts the t90 rotamer. This result is consistent with published experimental data and points to a simple gating mechanism: in the closed state, the His-37 and Trp-41 residues adopt the (t60, t90) conformation, which nearly occludes the pore, preventing nonproton ions from passing through due to the steric and desolvation effects. Moreover, the His-37 tetrad interrupts the otherwise continuous hydrogen-bonding network of the pore water by forcing the water molecules above and below it to adopt opposite orientations, thus adding to the blockage of proton shuttling. The channel can be easily opened by rotating the His-37^sub χ2^ angle from 60 to 0°. This open structure allows pore water to penetrate the constrictive region and to form a continuous water wire for protons to shuttle through, while being still narrow enough to exclude other ions. [PUBLICATION ABSTRACT] In this study, four possible conformations of the His-37 and Trp-41 residues for the closed state of the influenza M2 ion channel were identified by a conformation scan based on a solid-state NMR restraint. In the four conformations, the His-37 residue can be of either the t-160 or t60 rotamer, whereas Trp-41 can be of either the t-105 or t90 rotamer. These conformations were further analyzed by density functional theory calculations and molecular dynamics simulations, and the data indicate that the His-37 residue most likely adopts the t60 rotamer and should be monoprotonated at the delta-nitrogen site, whereas Trp-41 adopts the t90 rotamer. This result is consistent with published experimental data and points to a simple gating mechanism: in the closed state, the His-37 and Trp-41 residues adopt the (t60, t90) conformation, which nearly occludes the pore, preventing nonproton ions from passing through due to the steric and desolvation effects. Moreover, the His-37 tetrad interrupts the otherwise continuous hydrogen-bonding network of the pore water by forcing the water molecules above and below it to adopt opposite orientations, thus adding to the blockage of proton shuttling. The channel can be easily opened by rotating the His-37 chi2 angle from 60 to 0 degrees . This open structure allows pore water to penetrate the constrictive region and to form a continuous water wire for protons to shuttle through, while being still narrow enough to exclude other ions. | |
| 650 | 2 | 2 | |a Computer Simulation |
| 650 | 1 | 2 | |a Ion Channel Gating |
| 650 | 1 | 2 | |a Ion Channels |x chemistry |
| 650 | 2 | 2 | |a Models, Biological |
| 650 | 1 | 2 | |a Models, Chemical |
| 650 | 1 | 2 | |a Models, Molecular |
| 650 | 2 | 2 | |a Porosity |
| 650 | 2 | 2 | |a Protein Conformation |
| 650 | 1 | 2 | |a Proton Pumps |x chemistry |
| 650 | 2 | 2 | |a Structure-Activity Relationship |
| 650 | 1 | 2 | |a Viral Matrix Proteins |x chemistry |
| 653 | |a Influenza | ||
| 653 | |a Protons | ||
| 653 | |a Biophysics | ||
| 653 | |a Simulation | ||
| 653 | |a Molecules | ||
| 653 | |a Bacterial proteins | ||
| 653 | |a Residues | ||
| 653 | |a Pore water | ||
| 653 | |a Ions | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Voth, Gregory A | |
| 773 | 0 | |t Biophysical Journal |g vol. 89, no. 4 (Oct 2005), p. 2402-2411 | |
| 786 | 0 | |d ProQuest |t Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/215701810/abstract/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text + Graphics |u https://www.proquest.com/docview/215701810/fulltextwithgraphics/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/215701810/fulltextPDF/embedded/6A8EOT78XXH2IG52?source=fedsrch |