Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel
The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Wate...
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| Published in | PloS one Vol. 12; no. 10; p. e0186789 |
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| Main Author | |
| Format | Journal Article |
| Language | English |
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Public Library of Science
19.10.2017
Public Library of Science (PLoS) |
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| Abstract | The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation. |
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| AbstractList | The selectivity filter of the KcsA K+ channel has two typical conformations—the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation. The selectivity filter of the KcsA K + channel has two typical conformations—the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K + channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation. The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation.The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation. |
| Author | Wu, Di |
| AuthorAffiliation | Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China Zhejiang University Life Science Institute, CHINA |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29049423$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_3389_fmolb_2022_880660 crossref_primary_10_1103_PhysRevE_100_022406 |
| Cites_doi | 10.1073/pnas.0911270107 10.1038/nsmb.1968 10.1126/science.1133415 10.1038/nsmb1069 10.1038/35102009 10.1002/anie.201606594 10.1038/nsmb1311 10.1002/jcc.20084 10.1016/S0006-3495(02)75439-8 10.1021/jp0007843 10.1073/pnas.1014186108 10.1038/nsmb1309 10.1016/j.bpj.2011.01.073 10.1038/nature09153 10.1021/ja0118340 10.1021/jp973084f 10.1085/jgp.200709844 10.1021/bi00360a021 10.1038/nature12395 10.1002/anie.201509170 10.1002/jcc.20289 10.1016/j.jmb.2010.06.031 10.1038/nature02943 10.1002/jcc.20065 10.1093/proeng/gzg001 10.1038/nature09136 10.1002/pro.5560030808 10.1016/0969-2126(93)90011-5 10.1038/35102067 10.1016/S0006-3495(02)75520-3 10.1016/0263-7855(96)00018-5 10.1021/ja411450y 10.1085/jgp.200709843 10.1073/pnas.1308699110 |
| ContentType | Journal Article |
| Copyright | 2017 Di Wu. This is an open access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2017 Di Wu 2017 Di Wu |
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| Snippet | The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from... The selectivity filter of the KcsA K+ channel has two typical conformations—the conductive and the collapsed conformations, respectively. The transition from... The selectivity filter of the KcsA K + channel has two typical conformations—the conductive and the collapsed conformations, respectively. The transition from... |
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| SubjectTerms | Bacterial Proteins - chemistry Biology and Life Sciences Chains Conformation Deactivation Dynamic stability Environmental factors Hydrogen Inactivation Molecular dynamics Molecular Dynamics Simulation Nuclear Magnetic Resonance, Biomolecular Physical Sciences Potassium channels Potassium Channels - chemistry Protein Conformation Protein Stability Proteins Research and Analysis Methods Selectivity Simulation Spectrum analysis Studies Water - chemistry Water purification |
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| Title | Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel |
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