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Belmonte L, Moran O. On the interactions between nucleotide binding domains and membrane spanning domains in cystic fibrosis transmembrane regulator: A molecular dynamic study. Biochimie 2015; 111:19-29. [DOI: 10.1016/j.biochi.2015.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/21/2015] [Indexed: 12/20/2022]
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2
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Potassium ion channels and allergic asthma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 838:35-45. [PMID: 25315623 DOI: 10.1007/5584_2014_76] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
High-conductive calcium-sensitive potassium channels (BK+Ca) and ATP-sensitive potassium (K+ATP) channels play a significant role in the airway smooth muscle cell and goblet cell function, and cytokine production. The present study evaluated the therapeutic potential of BK+Ca and K+ATP openers, NS 1619 and pinacidil, respectively, in an experimental model of allergic inflammation. Airway allergic inflammation was induced with ovalbumine in guinea pigs during 21 days, which was followed by a 14-day treatment with BK+Ca and K+ATP openers. The outcome measures were airway smooth muscle cells reactivity in vivo and in vitro, cilia beating frequency and the level of exhaled NO (ENO), and the level of pro-inflammatory cytokines in the plasma and bronchoalveolar lavage fluid. The openers of both channels decreased airway smooth muscle cells reactivity, cilia beating frequency, and cytokine levels in the serum. Furthermore, NS1619 reduced ENO and inflammatory cells infiltration. The findings confirmed the presence of beneficial effects of BK+Ca and K+ATP openers on airway defence mechanisms. Although both openers dampened pro-inflammatory cytokines and mast cells infiltration, an evident anti-inflammatory effect was provided only by NS1619. Therefore, we conclude that particularly BK+Ca channels represent a promising new drug target in treatment of airway's allergic inflammation.
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3
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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4
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Nelson PH. A permeation theory for single-file ion channels: one- and two-step models. J Chem Phys 2011; 134:165102. [PMID: 21528981 DOI: 10.1063/1.3580562] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
How many steps are required to model permeation through ion channels? This question is investigated by comparing one- and two-step models of permeation with experiment and MD simulation for the first time. In recent MD simulations, the observed permeation mechanism was identified as resembling a Hodgkin and Keynes knock-on mechanism with one voltage-dependent rate-determining step [Jensen et al., PNAS 107, 5833 (2010)]. These previously published simulation data are fitted to a one-step knock-on model that successfully explains the highly non-Ohmic current-voltage curve observed in the simulation. However, these predictions (and the simulations upon which they are based) are not representative of real channel behavior, which is typically Ohmic at low voltages. A two-step association/dissociation (A/D) model is then compared with experiment for the first time. This two-parameter model is shown to be remarkably consistent with previously published permeation experiments through the MaxiK potassium channel over a wide range of concentrations and positive voltages. The A/D model also provides a first-order explanation of permeation through the Shaker potassium channel, but it does not explain the asymmetry observed experimentally. To address this, a new asymmetric variant of the A/D model is developed using the present theoretical framework. It includes a third parameter that represents the value of the "permeation coordinate" (fractional electric potential energy) corresponding to the triply occupied state n of the channel. This asymmetric A/D model is fitted to published permeation data through the Shaker potassium channel at physiological concentrations, and it successfully predicts qualitative changes in the negative current-voltage data (including a transition to super-Ohmic behavior) based solely on a fit to positive-voltage data (that appear linear). The A/D model appears to be qualitatively consistent with a large group of published MD simulations, but no quantitative comparison has yet been made. The A/D model makes a network of predictions for how the elementary steps and the channel occupancy vary with both concentration and voltage. In addition, the proposed theoretical framework suggests a new way of plotting the energetics of the simulated system using a one-dimensional permeation coordinate that uses electric potential energy as a metric for the net fractional progress through the permeation mechanism. This approach has the potential to provide a quantitative connection between atomistic simulations and permeation experiments for the first time.
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Affiliation(s)
- Peter Hugo Nelson
- Department of Physics, Benedictine University, Lisle, Illinois 60532, USA.
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5
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Boukharta L, Keränen H, Stary-Weinzinger A, Wallin G, de Groot BL, Åqvist J. Computer Simulations of Structure–Activity Relationships for hERG Channel Blockers. Biochemistry 2011; 50:6146-56. [DOI: 10.1021/bi200173n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lars Boukharta
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Henrik Keränen
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Göran Wallin
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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6
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Hagiwara Y, Matsumura H, Tateno M. Functional roles of a structural element involving Na+-pi interactions in the catalytic site of T1 lipase revealed by molecular dynamics simulations. J Am Chem Soc 2010; 131:16697-705. [PMID: 19886661 DOI: 10.1021/ja903451b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between metal ions and pi systems (metal-pi interactions) are known to confer significant stabilization energy. However, in biological systems, few structures with metal-pi coordination have been determined; thus, its roles must still be elucidated. The cation-pi interactions are not correctly described by current molecular mechanics even when using a polarizable force field, and thus they require quantum mechanical calculations for accurate estimation. However, the huge computational costs of the latter methodologies prohibit long-time molecular dynamics (MD) simulations. Accordingly, we developed a novel scheme to obtain an effective potential for calculating the interaction energy with an accuracy comparable to that of advanced ab initio calculations at the CCSD(T) levels, and with computational costs comparable to those of conventional MM calculations. Then, to elucidate the functional roles of the Na(+)-phenylalanine (Phe) complex in the catalytic site of T1 lipase, we performed MD simulations in the presence/absence of the accurate Na(+)-pi interaction energy. A comparison of these MD simulations revealed that a significantly large enthalpy gain in Na(+)-Phe16 substantially stabilizes the catalytic site, whereas a water molecule could not be substituted for Na(+) for sufficient stabilization energy. Thus, the cation-pi interaction in the lipase establishes a remarkably stable core structure by combining a hydrophobic aromatic ring and hydrophilic residues, of which the latter form the catalytic triad, thereby contributing to large structural changes from the complex with ligands to the free form of the lipase. This is the first report to elucidate the detailed functional mechanisms of Na(+)-pi interactions.
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Affiliation(s)
- Yohsuke Hagiwara
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 189-0001, Japan
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7
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8
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Krishnan MN, Trombley P, Moczydlowski EG. Thermal stability of the K+ channel tetramer: cation interactions and the conserved threonine residue at the innermost site (S4) of the KcsA selectivity filter. Biochemistry 2008; 47:5354-67. [PMID: 18419132 DOI: 10.1021/bi702281p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The selectivity filter of most K+ channels contains a highly conserved Thr residue that uniquely forms the S4 binding site for K+ by dual coordination with the backbone carbonyl oxygen and side chain hydroxyl of the same residue. This study examines the effect of mutations of Thr75 in the S4 site of theKcsA K+ channel on the cation dependence of the thermal stability of the tetramer, a phenomenon that reflects the structural role of cations in the filter. Conservative mutations of Thr75 destabilize the tetramer and alter its temperature dependence. Replacement of Thr with Ala or Cys lowers the apparent affinity ofK+, Rb+, and Cs+ for tetramer stabilization by factors ranging from 4- to 14-fold. These same mutations lower the apparent affinity of Ba2+ by approximately 10(3)- or approximately 10(4)-fold for Ala and Cys substitution, respectively,consistent with the known preference of the S4 site for Ba2+. In contrast, substitution of Ala or Cys at T75 anomalously enhances the ability of Na+ to stabilize the tetramer, suggesting that the native Thr residue at S4 is important for ultrahigh K+/Na+ selectivity of K+ channel pores. Elevated temperature orCu2+ cation catalyzes formation of covalent dimers of the T75C mutant of KcsA via formation of disulfide bonds between Cys residues of adjacent subunits. Thiophilic cations such as Hg2+ and Ag+ specifically protect the T75C tetramer against heat-induced dimer formation, demonstrating the contribution of cation interactions to tetramer stability in a channel with a non-native S4 site engineered to bind foreign cations.
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Affiliation(s)
- Manoj N Krishnan
- Department of Biology, Box 5805, Clarkson UniVersity, Potsdam, New York 13699, USA
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9
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De Fabritiis G, Coveney PV, Villà-Freixa J. Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics. Proteins 2008; 73:185-94. [DOI: 10.1002/prot.22036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Abstract
We present here a fast method for the exploration of channels in proteins based on molecular dynamics simulations of probe particles in a discrete grid space defined by an ensemble of protein conformations obtained either experimentally or by out-of-the-grid atomistic molecular dynamics simulations. The method is able to provide millisecond-long trajectories with a small computational effort, requires no human intervention in defining possible exit pathways and can detect both major and minor channels, giving a correct balance to the relative flux between them. The Grid-Molecular-Dynamics approach is then a suitable method for massive exploration of channels in proteins, even of those with unknown functional annotation.
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Affiliation(s)
- Oliver Carrillo
- Molecular Modelling and Bioinformatics, Institut de Recerca Biomèdica, Parc Científic de Barcelona and Nacional Institut of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, Spain
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11
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Andér M, Luzhkov VB, Åqvist J. Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model. Biophys J 2007; 94:820-31. [PMID: 17905851 PMCID: PMC2186239 DOI: 10.1529/biophysj.107.112045] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The binding of blockers to the human voltage-gated Kv1.5 potassium ion channel is investigated using a three-step procedure consisting of homology modeling, automated docking, and binding free energy calculations from molecular dynamics simulations, in combination with the linear interaction energy method. A reliable homology model of Kv1.5 is constructed using the recently published crystal structure of the Kv1.2 channel as a template. This model is expected to be significantly more accurate than earlier ones based on less similar templates. Using the three-dimensional homology model, a series of blockers with known affinities are docked into the cavity of the ion channel and their free energies of binding are calculated. The predicted binding free energies are in very good agreement with experimental data and the binding is predicted to be mainly achieved through nonpolar interactions, whereas the relatively small differences in the polar contribution determine the specificity. Apart from confirming the importance of residues V505, I508, V512, and V516 for ligand binding in the cavity, the results also show that A509 and P513 contribute significantly to the nonpolar binding interactions. Furthermore, we find that pharmacophore models based only on optimized free ligand conformations may not necessarily capture the geometric features of ligands bound to the channel cavity. The calculations herein give a detailed structural and energetic picture of blocker binding to Kv1.5 and this model should thus be useful for further ligand design efforts.
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Affiliation(s)
| | | | - Johan Åqvist
- Address reprint requests to Johan Åqvist, Tel.: 46-18-471-4109; Fax: 46-18-53-69-71.
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12
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Thomas M, Jayatilaka D, Corry B. The predominant role of coordination number in potassium channel selectivity. Biophys J 2007; 93:2635-43. [PMID: 17573427 PMCID: PMC1989715 DOI: 10.1529/biophysj.107.108167] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potassium channels are exquisitely selective, allowing K+ to pass across cell membranes while blocking other ion types. Here we demonstrate that the number of carbonyl oxygen atoms that surround permeating ions is the most important factor in determining ion selectivity rather than the size of the pore or the strength of the coordinating dipoles. Although the electrostatic properties of the coordinating ligands can lead to Na+ or K+ selectivity at some values of the dipole moment, no significant selectivity arises at the specific value of the dipole moment for carbonyl groups found in potassium channels when the ligands have complete freedom. Rather, we show that the main contribution to selectivity arises from slight constraints on the conformational freedom of the channel protein that limit the number of carbonyl oxygen atoms to a value better suited to K+ than Na+, despite the pore being flexible. This mechanism provides an example of a general framework for explaining ion discrimination in a range of natural and synthetic macromolecules in which selectivity is controlled by the number of coordinating ligands in addition to their dipole moment.
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Affiliation(s)
- Michael Thomas
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Crawley WA 6009, Australia
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13
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Bucher D, Guidoni L, Rothlisberger U. The protonation state of the Glu-71/Asp-80 residues in the KcsA potassium channel: a first-principles QM/MM molecular dynamics study. Biophys J 2007; 93:2315-24. [PMID: 17526559 PMCID: PMC1965436 DOI: 10.1529/biophysj.106.102509] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although a few x-ray structures of the KcsA K(+) channel have been crystallized several issues concerning the mechanisms of the ionic permeation and the protonation state of the selectivity filter ionizable side chains are still open. Using a first-principles quantum mechanical/molecular mechanical simulation approach, we have investigated the protonation state of Glu-71 and Asp-80, two important residues located in the vicinity of the selectivity filter. Results from the dynamics show that a proton is shared between the two residues, with a slight preference for Glu-71. The proton is found to exchange on the picosecond timescale, an interesting phenomenon that cannot be observed in classical molecular dynamics. Simulations of different ionic loading states of the filter show that the probability for the proton transfer is correlated with the filter occupancy. In addition, the Glu-71/Asp-80 pair is able to modulate the potential energy profile experienced by a K(+) ion as it translates along the pore axis. These theoretical predictions, along with recent experimental results, suggest that changes of the filter structure could be associated with a shift in the Glu-Asp protonation state, which in turn would influence the ion translocation.
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Affiliation(s)
- Denis Bucher
- Federal Institute of Technology EPFL, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
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14
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Abstract
K+ ions seemingly permeate K-channels rapidly because channel binding sites mimic coordination of K+ ions in water. Highly selective ion discrimination should occur when binding sites form rigid cavities that match K+, but not the smaller Na+, ion size or when binding sites are composed of specific chemical groups. Although conceptually attractive, these views cannot account for critical observations: 1), K+ hydration structures differ markedly from channel binding sites; 2), channel thermal fluctuations can obscure sub-Angström differences in ion sizes; and 3), chemically identical binding sites can exhibit diverse ion selectivities. Our quantum mechanical studies lead to a novel paradigm that reconciles these observations. We find that K-channels utilize a "phase-activated" mechanism where the local environment around the binding sites is tuned to sustain high coordination numbers (>6) around K+ ions, which otherwise are rarely observed in liquid water. When combined with the field strength of carbonyl ligands, such high coordinations create the electrical scenario necessary for rapid and selective K+ partitioning. Specific perturbations to the local binding site environment with respect to strongly selective K-channels result in altered K+/Na+ selectivities.
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Affiliation(s)
- Sameer Varma
- Computational Bioscience Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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15
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Boiteux C, Kraszewski S, Ramseyer C, Girardet C. Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. J Mol Model 2007; 13:699-713. [PMID: 17415597 DOI: 10.1007/s00894-007-0202-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 03/08/2007] [Accepted: 03/19/2007] [Indexed: 12/29/2022]
Abstract
KcsA potassium channel belongs to a wide family of allosteric proteins that switch between closed and open states conformations in response to a stimulus, and act as a regulator of cation activity in living cells. The gating mechanism and cation selectivity of such channels have been extensively studied in the literature, with a revival emphasis these latter years, due to the publication of the crystallized structure of KcsA. Despite the increasing number of research and review papers on these topics, quantitative interpretation of these processes at the atomic scale is far from achieved. On the basis of available experimental and theoretical data, and by including our recent results, we review the progresses in this field of activity and discuss the weaknesses that should be corrected. In this spirit, we partition the channel into the filter, cavity, extra and intracellular media, in order to analyze separately the specificity of each region. Special emphasis is brought to the study of an open state for the channel and to the different properties generated by the opening. The influence of water as a structural and dynamical component of the channel properties in closed and open states, as well as in the sequential motions of the cations, is analyzed using molecular dynamics simulations and ab initio calculations. The polarization and charge transfer effects on the ions' dynamics and kinetics are discussed in terms of partial charge models.
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Affiliation(s)
- Céline Boiteux
- Laboratoire de Physique Moléculaire UMR CNRS 6624, Université de Franche-Comté, La Bouloie, 25030, Besançon Cedex, France
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16
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Liu B, Westhead DR, Boyett MR, Warwicker J. Modelling the pH-dependent properties of Kv1 potassium channels. J Mol Biol 2007; 368:328-35. [PMID: 17359997 DOI: 10.1016/j.jmb.2007.02.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 02/09/2007] [Accepted: 02/12/2007] [Indexed: 11/24/2022]
Abstract
It is known that the pH dependence of conductance for the rat potassium channel Kv1.4 is susbstantially reduced upon mutation of either H508 or K532. These residues lie in the extracellular mouth of the channel pore. We have used continuum electrostatics to investigate their interactions with K(+) sites in the pore. The predicted scale of interactions between H508/K532 and potassium sites is sufficient to significantly alter potassium occupancy and thus channel function. We interpret the effect of K532 mutation as indicating that the pH-dependent effect requires not only an ionisable group with a suitable pK(a) value (i.e. histidine), but also that other charged groups set the potential profile at a threshold level. This hypothesis is examined in the context of pH dependence for other members of the Kv1 family, and may represent a general tool with which to study potassium channels.
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Affiliation(s)
- Binbin Liu
- Cardiovascular Research Group, School of Medicine, University of Manchester, Core Technology Facility, 46 Grafton Street, Manchester M13 9NT, UK
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17
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Bucher D, Raugei S, Guidoni L, Dal Peraro M, Rothlisberger U, Carloni P, Klein ML. Polarization effects and charge transfer in the KcsA potassium channel. Biophys Chem 2006; 124:292-301. [PMID: 16737771 DOI: 10.1016/j.bpc.2006.04.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 04/18/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
The electronic structure of the selectivity filter of KcsA K(+) channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].
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Affiliation(s)
- Denis Bucher
- Ecole Polytechnique Fédérale de Lausanne EPFL, Institute of Chemical Sciences and Engineering, CH-1015 Lausanne, Switzerland
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Sumikama T, Saito S, Ohmine I. Mechanism of Ion Permeation in a Model Channel: Free Energy Surface and Dynamics of K+Ion Transport in an Anion-Doped Carbon Nanotube. J Phys Chem B 2006; 110:20671-7. [PMID: 17034258 DOI: 10.1021/jp062547r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the ion permeation is investigated for an anion-doped carbon nanotube, as a model of the K+ channel, by analyzing the free energy surface and the dynamics of the ion permeation through the model channel. It is found that the main rate-determining step is how an ion enters the channel. The entrance of the ion is mostly blocked by a water molecule located at this entrance. Only about 10% of K+ ions which reach the mouth of the channel can really enter the channel. The rejection rate sensitively depends on the location of this water molecule, which is easily controlled by the charge of the carbon nanotube; for example, the maximum permeation is obtained when the anion charge is at a certain value, -5.4e in the present model. At this charge, the facile translocation of the ion inside the channel is also induced due to the number of fluctuations of the ions inside the channel. Therefore, the so-called "Newton's balls", a toy model, combined with a simple ion diffusion model for explaining the fast ion permeation should be modified. The present analysis thus suggests that there exists an optimum combination of the length and the charge of the carbon nanotube for the most efficient ion permeation.
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Affiliation(s)
- Takashi Sumikama
- Department of Chemistry, Faculty of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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19
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Warshel A, Sharma PK, Kato M, Parson WW. Modeling electrostatic effects in proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1647-76. [PMID: 17049320 DOI: 10.1016/j.bbapap.2006.08.007] [Citation(s) in RCA: 424] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 08/17/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
Electrostatic energies provide what is perhaps the most effective tool for structure-function correlation of biological molecules. This review considers the current state of simulations of electrostatic energies in macromolecules as well as the early developments of this field. We focus on the relationship between microscopic and macroscopic models, considering the convergence problems of the microscopic models and the fact that the dielectric 'constants' in semimacroscopic models depend on the definition and the specific treatment. The advances and the challenges in the field are illustrated considering a wide range of functional properties including pK(a)'s, redox potentials, ion and proton channels, enzyme catalysis, ligand binding and protein stability. We conclude by pointing out that, despite the current problems and the significant misunderstandings in the field, there is an overall progress that should lead eventually to quantitative descriptions of electrostatic effects in proteins and thus to quantitative descriptions of the function of proteins.
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Affiliation(s)
- Arieh Warshel
- University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
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20
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Hellgren M, Sandberg L, Edholm O. A comparison between two prokaryotic potassium channels (KirBac1.1 and KcsA) in a molecular dynamics (MD) simulation study. Biophys Chem 2005; 120:1-9. [PMID: 16253415 DOI: 10.1016/j.bpc.2005.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/03/2005] [Accepted: 10/03/2005] [Indexed: 10/25/2022]
Abstract
The two potassium ion channels KirBac1.1 and KcsA are compared in a Molecular Dynamics (MD) simulation study. The location and motion of the potassium ions observed in the simulations are compared to those in the X-ray structures and previous simulations. In our simulations several of the crystallography resolved ion sites in KirBac1.1 are occupied by ions. In addition to this, two in KirBac1.1 unresolved sites where occupied by ions at sites that are in close correspondence to sites found in KcsA. There is every reason to believe that the conserved alignment of the selectivity filter in the potassium ion channel family corresponds to a very similar mechanism for ion transport across the filter. The gate residues, Phe146 in KirBac1.1 and Ala111 in KcsA acted in the simulations as effective barriers which never were passed by ions nor water molecules.
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Affiliation(s)
- Mikko Hellgren
- Theoretical Biological Physics, Department of Physics, Royal Institute of Technology, AlbaNova University Centre, SE-106 91 Stockholm, Sweden
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Kato M, Warshel A. Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels. J Phys Chem B 2005; 109:19516-22. [PMID: 16853521 PMCID: PMC2531223 DOI: 10.1021/jp053208l] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microscopic calculations of free energy profiles for ion transport through biological ion channels present a very serious challenge to modern simulation approaches. The main problem is due to the major convergence problems associated with the heterogeneous landscape of the electrostatic environment in ion channels and with the need to evaluate the profile associated with the transfer of the ion from bulk water to the channel environment. This problem is compounded by the lack of reliable and relevant benchmarks that can discriminate between alternative approaches. The present study is aimed at reducing the above problems by defining benchmarks that are directly relevant to ion channels and can also give converging results. This is done by constructing a series of models of a truncated gramicidin channel with different numbers of water molecules and by comparing the profiles for going around the channel and through the channel. These discriminating models are then used to validate and compare the adiabatic charging free energy perturbation (FEP) approach combined with an umbrella sampling approach (Warshel, A. J. Phys. Chem. 1982, 86, 2218) and the potential of mean force (PMF) approach used frequently in studies of ion channels. It is found that both approaches work quite well until one moves to the case of the fully solvated channel. In this limit, the PMF approach may give different results for the overall work of going through the channel and around the channel, while the FEP approach gives physically consistent results. The present benchmark also indicates that the weighted histogram analysis method (WHAM) approach does not offer a significant advantage over earlier approaches at least as much as studies of ion channels are concerned. Finally, it is concluded that the FEP approach may be more useful in evaluating the overall barrier for moving ions from water to ion channels and that in some cases it might be beneficial to use the FEP approach for selective points along the channel and then to connect these points by PMF calculations.
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Affiliation(s)
- Mitsunori Kato
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
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Warshel A. Inverting the selectivity of aquaporin 6: gating versus direct electrostatic interaction. Proc Natl Acad Sci U S A 2005; 102:1813-4. [PMID: 15684047 PMCID: PMC548591 DOI: 10.1073/pnas.0409788102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
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