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Rahman RA, Zaman B, Khan MR, Islam MS, Rashid MH. Computational Studies Show How the H463R Mutation Turns hKv1.5 into an Inactivation State. J Phys Chem B 2024; 128:429-439. [PMID: 38179652 DOI: 10.1021/acs.jpcb.3c05634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The KCNA5 gene provides the code for the α-subunit of the potassium channel Kv1.5. The genetic variant H463R in the Kv1.5 channel has been reported to cause a functional loss in atrial fibrillation (AF) patients. Understanding the mutations at a molecular level is key to developing improved therapeutics concerning cardiac hKv1.5 and hKv1.4 channels. Molecular dynamics and umbrella sampling free energy simulations are an effective tool to understand the mutation's effect on ion conduction, which we have employed and found that the hKv1.5[H463R] mutation imposes an energy barrier on the ion conduction pathway compared to the wild-type channel's ion free energy and pore structure. These results imply that the arginine mutation associated with the AF disease in particular modulates the inactivation process of hKv1.5. Kv1.4, encoded by the KCNA4 gene, is also present in the heart. Therefore, we considered simulation studies of the equivalent H507R mutation in the hKv1.4 channel and found that the mutation slightly reduces the ion conduction barrier in the ion conduction pathway, making it insignificant.
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Affiliation(s)
- Ramisha A Rahman
- Department of Mathematics & Physics, North South University, Plot # 15, Dhaka 1229, Bangladesh
| | - Bushra Zaman
- Department of Mathematics & Physics, North South University, Plot # 15, Dhaka 1229, Bangladesh
| | - Mohammad Radid Khan
- Department of Mathematics & Physics, North South University, Plot # 15, Dhaka 1229, Bangladesh
| | - Md Shariful Islam
- Department of Mathematics & Physics, North South University, Plot # 15, Dhaka 1229, Bangladesh
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Md Harunur Rashid
- Department of Mathematics & Physics, North South University, Plot # 15, Dhaka 1229, Bangladesh
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Zhao X, Ding W, Wang H, Wang Y, Liu Y, Li Y, Liu C. Permeability enhancement of Kv1.2 potassium channel by a terahertz electromagnetic field. J Chem Phys 2023; 159:045101. [PMID: 37486058 DOI: 10.1063/5.0143648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
As biomolecules vibrate and rotate in the terahertz band, the biological effects of terahertz electromagnetic fields have drawn considerable attention from the physiological and medical communities. Ion channels are the basis of biological electrical signals, so studying the effect of terahertz electromagnetic fields on ion channels is significant. In this paper, the effect of a terahertz electromagnetic field with three different frequencies, 6, 15, and 25 THz, on the Kv1.2 potassium ion channel was investigated by molecular dynamics simulations. The results show that an electromagnetic field with a 15 THz frequency can significantly enhance the permeability of the Kv1.2 potassium ion channel, which is 1.7 times higher than without an applied electric field. By analyzing the behavior of water molecules, it is found that the electromagnetic field with the 15 THz frequency shortens the duration of frozen and relaxation processes when potassium ions pass through the channel, increases the proportion of the direct knock-on mode, and, thus, enhances the permeability of the Kv1.2 potassium ion channel.
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Affiliation(s)
- Xiaofei Zhao
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wen Ding
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hongguang Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yize Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yanjiang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yongdong Li
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Chunliang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
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Wang Y, Wang H, Ding W, Zhao X, Li Y, Liu C. Regulation of Ion Permeation of the KcsA Channel by Applied Midinfrared Field. Int J Mol Sci 2022; 24:ijms24010556. [PMID: 36613998 PMCID: PMC9820211 DOI: 10.3390/ijms24010556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
Ion transport molecules are involved in many physiological and pathological processes and are considered potential targets for cancer treatment. In the large family of ion transport molecules, potassium (K) ion channels, as surface-expressed proteins, show the highest variability and most frequent expression changes in many tumor types. The key to exploring the permeation of K+ through potassium channels lies in the conserved sequence TVGYG, which is common in the selectivity filter (SF) region of all potassium channels. We found that the K+ flux significantly increased with the help of a specific frequency terahertz electromagnetic wave (51.87 THz) in the KcsA channel using a molecular dynamics combined model through the combined simulation of the constant electric field method and ion imbalance method. This frequency has the strongest absorption peak in the infrared spectrum of -C=O groups in the SF region. With the applied electric field of 51.87 THz, the Y78 residue at the S1 site of the SF has a smaller vibration amplitude and a more stable structure, which enables the K+ to bind closely with the carbonyl oxygen atoms in the SF and realize ion conduction in a more efficient direct Coulomb knock-on.
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Affiliation(s)
- Yize Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Hongguang Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- Correspondence: ; Tel.: +86-18191765263
| | - Wen Ding
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaofei Zhao
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yongdong Li
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunliang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
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Bauer D, Wissmann J, Moroni A, Thiel G, Hamacher K. Weak Cation Selectivity in HCN Channels Results From K +-Mediated Release of Na + From Selectivity Filter Binding Sites. FUNCTION (OXFORD, ENGLAND) 2022; 3:zqac019. [PMID: 36156894 PMCID: PMC9492253 DOI: 10.1093/function/zqac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 01/07/2023]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels generate the pacemaker current which plays an important role in the timing of various biological processes like the heart beat. We used umbrella sampling to explore the potential of mean force for the conduction of potassium and sodium through the open HCN4 pore. Our data explain distinct functional features like low unitary conductance and weak selectivity as a result of high energetic barriers inside the selectivity filter of this channel. They exceed the 3-5 kJ/mol threshold which is presumed as maximal barrier for diffusion-limited conductance. Furthermore, simulations provide a thermodynamic explanation for the weak cation selectivity of HCN channels that contain only two ion binding sites in the selectivity filter (SF). We find that sodium ions bind more strongly to the SF than potassium and are easier released by binding of potassium than of another sodium. Hence ion transport and selectivity in HCN channels is not determined by the same mechanism as in potassium-selective channels; it rather relies on sodium as a weak blocker that can only be released by potassium.
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Affiliation(s)
- Daniel Bauer
- Department of Biology and Centre for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Jan Wissmann
- Department of Physics, TU Darmstadt, Schlossgartenstrasse 7, 64289 Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | | | - Kay Hamacher
- Department of Biology and Centre for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany,Department of Physics, TU Darmstadt, Schlossgartenstrasse 7, 64289 Darmstadt, Germany
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Ohmine I, Saito S. Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Iwao Ohmine
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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Conductance selectivity of Na + across the K + channel via Na + trapped in a tortuous trajectory. Proc Natl Acad Sci U S A 2021; 118:2017168118. [PMID: 33741736 DOI: 10.1073/pnas.2017168118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ion selectivity of the potassium channel is crucial for regulating electrical activity in living cells; however, the mechanism underlying the potassium channel selectivity that favors large K+ over small Na+ remains unclear. Generally, Na+ is not completely excluded from permeation through potassium channels. Herein, the distinct nature of Na+ conduction through the prototypical KcsA potassium channel was examined. Single-channel current recordings revealed that, at a high Na+ concentration (200 mM), the channel was blocked by Na+, and this blocking was relieved at high membrane potentials, suggesting the passage of Na+ across the channel. At a 2,000 mM Na+ concentration, single-channel Na+ conductance was measured as one-eightieth of the K+ conductance, indicating that the selectivity filter allows substantial conduit of Na+ Molecular dynamics simulations revealed unprecedented atomic trajectories of Na+ permeation. In the selectivity filter having a series of carbonyl oxygen rings, a smaller Na+ was distributed off-center in eight carbonyl oxygen-coordinated sites as well as on-center in four carbonyl oxygen-coordinated sites. This amphipathic nature of Na+ coordination yielded a continuous but tortuous path along the filter. Trapping of Na+ in many deep free energy wells in the filter caused slow elution. Conversely, K+ is conducted via a straight path, and as the number of occupied K+ ions increased to three, the concerted conduction was accelerated dramatically, generating the conductance selectivity ratio of up to 80. The selectivity filter allows accommodation of different ion species, but the ion coordination and interactions between ions render contrast conduction rates, constituting the potassium channel conductance selectivity.
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Gibby WAT, Barabash ML, Guardiani C, Luchinsky DG, McClintock PVE. Physics of Selective Conduction and Point Mutation in Biological Ion Channels. PHYSICAL REVIEW LETTERS 2021; 126:218102. [PMID: 34114848 DOI: 10.1103/physrevlett.126.218102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
We introduce a statistical and linear response theory of selective conduction in biological ion channels with multiple binding sites and possible point mutation. We derive an effective grand-canonical ensemble and generalized Einstein relations for the selectivity filter, assuming strongly coordinated ionic motion, and allowing for ionic Coulomb blockade. The theory agrees well with data from the KcsA K^{+} channel and a mutant. We show that the Eisenman relations for thermodynamic selectivity follow from the condition for fast conduction and find that maximum conduction requires the binding sites to be nearly identical.
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Affiliation(s)
- W A T Gibby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - M L Barabash
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - C Guardiani
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Department of Mechanical and Aerospace Engineering, Sapienza University, Rome 00184, Italy
| | - D G Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- KBR Inc., Ames Research Center, Moffett Field, Mountain View, California 94035, USA
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
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Mironenko A, Zachariae U, de Groot BL, Kopec W. The Persistent Question of Potassium Channel Permeation Mechanisms. J Mol Biol 2021; 433:167002. [PMID: 33891905 DOI: 10.1016/j.jmb.2021.167002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/09/2023]
Abstract
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K+ ions by the channel. However, the molecular mechanism of K+ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K+ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.
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Affiliation(s)
- Andrei Mironenko
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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Cosseddu SM, Choe EJ, Khovanov IA. Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel. ENTROPY (BASEL, SWITZERLAND) 2021; 23:E72. [PMID: 33418985 PMCID: PMC7825352 DOI: 10.3390/e23010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/02/2021] [Indexed: 12/26/2022]
Abstract
The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network's residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.
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Affiliation(s)
| | | | - Igor A. Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (S.M.C.); (E.J.C.)
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