1
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Nan Y, MacKerell AD. Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field. J Chem Theory Comput 2024; 20:3242-3257. [PMID: 38588064 PMCID: PMC11039353 DOI: 10.1021/acs.jctc.3c01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Molecular dynamics (MD) simulations are a commonly used method for investigating molecular behavior at the atomic level. Achieving reliable MD simulation results necessitates the use of an accurate force field. In the present work, we present a protocol to enhance the quality of group 1 monatomic ions (specifically Li+, Na+, K+, Rb+, and Cs+) with respect to their interactions with common polar model compounds in biomolecules in condensed phases in the context of the Drude polarizable force field. Instead of adjusting preexisting individual parameters for ions, model compounds, and water, we employ atom-pair specific Lennard-Jones (LJ) (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) terms to fine-tune the balance of ion-model compound, ion-water, and model compound-water interactions. This involved establishing a protocol for the optimization of NBFIX and NBTHOLE parameters targeting the difference between molecular mechanical (MM) and quantum mechanical (QM) potential energy scans (PES). It is shown that targeting PES involving complexes that include multiple model compounds and/or ions as trimers and tetramers yields parameters that produce condensed phase properties in agreement with experimental data. Validation of this protocol involved the reproduction of experimental thermodynamic benchmarks, including solvation free energies of ions in methanol and N-methylacetamide, osmotic pressures, ionic conductivities, and diffusion coefficients within the condensed phase. These results show the importance of including more complex ion-model compound complexes beyond dimers in the QM target data to account for many-body effects during parameter fitting. The presented parameters represent a significant refinement of the Drude polarizable force field, which will lead to improved accuracy for modeling ion-biomolecular interactions.
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Affiliation(s)
- Yiling Nan
- University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201 MD
| | - Alexander D. MacKerell
- University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201 MD
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2
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Stevens MJ, Rempe SLB. Insight into the K channel's selectivity from binding of K +, Na + and water to N-methylacetamide. Faraday Discuss 2024; 249:195-209. [PMID: 37846738 DOI: 10.1039/d3fd00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In potassium channels that conduct K+ selectively over Na+, which sites are occupied by K+ or water and the mechanism of selectivity are unresolved questions. The combination of the energetics and the constraints imposed by the protein structure yield the selective permeation and occupancy. To gain insight into the combination of structure and energetics, we performed density functional theory (DFT) calculations of multiple N-methyl acetamide (NMA) ligands binding to K+ and Na+, relative to hydrated K+ and Na+. NMA is an analogue of the amino acid backbone and provides the carbonyl binding to the ions that occurs in most binding sites of the K+ channel. Unconstrained optimal structures are obtained through geometry optimization calculations of the NMA ligand binding. The complexes formed by 8 NMA binding to the cations have the O atoms positioned in nearly identical locations as the O atoms in the selectivity filter. The transfer free energies between bulk water and K+ or Na+ bound to 8 NMA are almost identical, implying there is no selectivity by a single site. For water optimized with 8 NMA, binding is weak and O atoms are not positioned as in the K+ channel selectivity filter, suggesting that the ions are much more favored than water. Optimal structures of 8 NMA binding with two cations (K+ or Na+) are stable and have lower binding free energy than the optimal structures with just one cation. However, in the Na+ case, the optimal structure deforms and does not match the K+ channel; that is, two bound Na+ are destabilizing. In contrast, the two K+ structure is stabilized and the selectivity free energy favors K+. Overall, this study shows that binding site occupancy and the mechanism for K+ selectivity involves multiple K+ binding in multiple neighboring layers or sites of the K+ channel selectivity filter.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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3
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Kopec W, Thomson AS, de Groot BL, Rothberg BS. Interactions between selectivity filter and pore helix control filter gating in the MthK channel. J Gen Physiol 2023; 155:e202213166. [PMID: 37318452 PMCID: PMC10274084 DOI: 10.1085/jgp.202213166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 01/13/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
K+ channel activity can be limited by C-type inactivation, which is likely initiated in part by dissociation of K+ ions from the selectivity filter and modulated by the side chains that surround it. While crystallographic and computational studies have linked inactivation to a "collapsed" selectivity filter conformation in the KcsA channel, the structural basis for selectivity filter gating in other K+ channels is less clear. Here, we combined electrophysiological recordings with molecular dynamics simulations, to study selectivity filter gating in the model potassium channel MthK and its V55E mutant (analogous to KcsA E71) in the pore-helix. We found that MthK V55E has a lower open probability than the WT channel, due to decreased stability of the open state, as well as a lower unitary conductance. Simulations account for both of these variables on the atomistic scale, showing that ion permeation in V55E is altered by two distinct orientations of the E55 side chain. In the "vertical" orientation, in which E55 forms a hydrogen bond with D64 (as in KcsA WT channels), the filter displays reduced conductance compared to MthK WT. In contrast, in the "horizontal" orientation, K+ conductance is closer to that of MthK WT; although selectivity filter stability is lowered, resulting in more frequent inactivation. Surprisingly, inactivation in MthK WT and V55E is associated with a widening of the selectivity filter, unlike what is observed for KcsA and reminisces recent structures of inactivated channels, suggesting a conserved inactivation pathway across the potassium channel family.
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Affiliation(s)
- Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andrew S. Thomson
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Brad S. Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
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4
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Poier PP. Variational Formulation of the Bond Capacity Charge Polarization Model. J Chem Phys 2022; 156:104101. [DOI: 10.1063/5.0082680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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5
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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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6
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Smirnov PR. Structure of the Nearest Environment of
Na+, K+,
Rb+, and Cs+ Ions in
Oxygen-Containing Solvents. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220090169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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Inakollu VS, Geerke DP, Rowley CN, Yu H. Polarisable force fields: what do they add in biomolecular simulations? Curr Opin Struct Biol 2020; 61:182-190. [PMID: 32044671 DOI: 10.1016/j.sbi.2019.12.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which describe electrostatic interactions as the sum of Coulombic interactions between fixed atomic charges. Polarisation of these charge distributions is incorporated only in a mean-field manner. In the past decade, extensive efforts have been devoted to developing simple, efficient, and yet generally applicable polarisable force fields for biomolecular simulations. In this review, we summarise the latest developments in accounting for key biomolecular interactions with polarisable force fields and applications to address challenging biological questions. In the end, we provide an outlook for future development in polarisable force fields.
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Affiliation(s)
- Vs Sandeep Inakollu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia
| | - Daan P Geerke
- AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia.
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8
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Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019; 119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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9
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DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. J Physiol 2018; 597:679-698. [PMID: 30471114 DOI: 10.1113/jp277088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all-atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage-gated channels from the KV and NaV families, which have garnered many successes and engendered several long-standing controversies regarding the nature of their structure-function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Chemistry Department, American River College, Sacramento, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
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10
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Biernacki KA, Kaczkowska E, Bruździak P. Aqueous solutions of NMA, Na2HPO4, and NaH2PO4 as models for interaction studies in phosphate–protein systems. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Manin NG, Kolker AM. Thermodynamic properties of LiCl solutions in N-methylacetamide at 308.15–328.15 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417120184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Manin N, da Silva MC, Zdravkovic I, Eliseeva O, Dyshin A, Yaşar O, Salahub DR, Kolker AM, Kiselev MG, Noskov SY. LiCl solvation in N-methyl-acetamide (NMA) as a model for understanding Li(+) binding to an amide plane. Phys Chem Chem Phys 2016; 18:4191-200. [PMID: 26784370 DOI: 10.1039/c5cp04847h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The thermodynamics of ion solvation in non-aqueous solvents remains of great significance for understanding cellular transport and ion homeostasis for the design of novel ion-selective materials and applications in molecular pharmacology. Molecular simulations play pivotal roles in connecting experimental measurements to the microscopic structures of liquids. One of the most useful and versatile mimetic systems for understanding biological ion transport is N-methyl-acetamide (NMA). A plethora of theoretical studies for ion solvation in NMA have appeared recently, but further progress is limited by two factors. One is an apparent lack of experimental data on solubility and thermodynamics of solvation for a broad panel of 1 : 1 salts over an appropriate temperature and concentration range. The second concern is more substantial and has to do with the limitations hardwired in the additive (fixed charge) approximations used for most of the existing force-fields. In this submission, we report on the experimental evaluation of LiCl solvation in NMA over a broad range of concentrations and temperatures and compare the results with those of MD simulations with several additive and one polarizable force-field (Drude). By comparing our simulations and experimental results to density functional theory computations, we discuss the limiting factors in existing potential functions. To evaluate the possible implications of explicit and implicit polarizability treatments on ion permeation across biological channels, we performed potential of mean force (PMF) computations for Li(+) transport through a model narrow ion channel with additive and polarizable force-fields.
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Affiliation(s)
- Nikolai Manin
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Mauricio C da Silva
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Igor Zdravkovic
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
| | - Olga Eliseeva
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Alexey Dyshin
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Orhan Yaşar
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
| | - Dennis R Salahub
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Arkadiy M Kolker
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Michael G Kiselev
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
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13
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Kita A, Jimbo M, Sakai R, Morimoto Y, Miki K. Crystal structure of a symbiosis-related lectin from octocoral. Glycobiology 2015; 25:1016-23. [DOI: 10.1093/glycob/cwv033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 05/15/2015] [Indexed: 11/14/2022] Open
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14
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Li H, Ngo V, Da Silva MC, Salahub DR, Callahan K, Roux B, Noskov SY. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field. J Phys Chem B 2015; 119:9401-16. [PMID: 25578354 PMCID: PMC4516320 DOI: 10.1021/jp510560k] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Small metal ions play critical roles
in numerous biological processes.
Of particular interest is how metalloenzymes are allosterically regulated
by the binding of specific ions. Understanding how ion binding affects
these biological processes requires atomic models that accurately
treat the microscopic interactions with the protein ligands. Theoretical
approaches at different levels of sophistication can contribute to
a deeper understanding of these systems, although computational models
must strike a balance between accuracy and efficiency in order to
enable long molecular dynamics simulations. In this study, we present
a systematic effort to optimize the parameters of a polarizable force
field based on classical Drude oscillators to accurately represent
the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid
residues for a set of 30 biologically important proteins. By combining
ab initio calculations and experimental thermodynamic data, we derive
a polarizable force field that is consistent with a wide range of
properties, including the geometries and interaction energies of gas-phase
ion/protein-like model compound clusters, and the experimental solvation
free-energies of the cations in liquids. The resulting models display
significant improvements relative to the fixed-atomic-charge additive
CHARMM C36 force field, particularly in their ability to reproduce
the many-body electrostatic nonadditivity effects estimated from ab
initio calculations. The analysis clarifies the fundamental limitations
of the pairwise additivity assumption inherent in classical fixed-charge
force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable
to computationally efficient large-scale MD simulations, set a firm
foundation and offer a powerful avenue to study the roles of the ions
in soluble and membrane transport proteins.
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Affiliation(s)
- Hui Li
- †Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | | | | | | | - Karen Callahan
- †Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- †Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
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15
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Zhang R, Li J, Wu WJ. Relative Chemical Shifts for Obtaining Accurate Chemical Shifts of Hydrogen Atoms in CH Groups. CHINESE J CHEM PHYS 2014. [DOI: 10.1063/1674-0068/27/02/240-242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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16
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Yang Z, Lin H, Gui T, Zhou RF, Chen XS. Infrared spectroscopy of N-methylacetamide in water from high-level QM/MM calculations. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2013.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Beck JP, Gaigeot MP, Lisy JM. Anharmonic vibrations of N-H in Cl(-)(N-methylacetamide)1(H2O)(0-2)Ar2 cluster ions. Combined IRPD experiments and BOMD simulations. Phys Chem Chem Phys 2013; 15:16736-45. [PMID: 23986352 DOI: 10.1039/c3cp52418c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Infrared Predissociation (IRPD) spectra of Cl(-)(NMA)1(H2O)0-2Ar2 combined with Born-Oppenheimer Molecular Dynamics (BOMD) IR spectra have been acquired, providing the structure and dynamics of these systems. We show that the chloride ion is bound to the hydrogen of the amide N-H group, forming a strong ionic hydrogen bond, weakening the N-H stretch, and shifting it to lower frequency. The presence of water molecules enhances the ionic hydrogen bond by binding to the amide carbonyl oxygen of NMA and shifts the N-H stretch further to lower frequency. The BOMD IR spectra can recapture all, but about 100 cm(-1), of the 600 to 700 cm(-1) shifts due to the strong N-H stretch anharmonicities observed in experiments. This residual error was found to be due to the lack of zero point energy in the classical treatment of motion in the BOMD method.
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Affiliation(s)
- Jordan P Beck
- Concordia University Wisconsin, 12800 N. Lakeshore Drive, Mequon, Wisconsin 53097, USA
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18
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Lev B, Roux B, Noskov SY. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations. J Chem Theory Comput 2013; 9:4165-75. [PMID: 26592407 DOI: 10.1021/ct400296w] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying structural properties of the ion-solvent system.
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Affiliation(s)
- Bogdan Lev
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, The University of Calgary , 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States of America
| | - Sergei Yu Noskov
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, The University of Calgary , 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
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19
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Huang L, Roux B. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA. J Chem Theory Comput 2013; 9. [PMID: 24223528 DOI: 10.1021/ct4003477] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.
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Affiliation(s)
- Lei Huang
- Department of Biochemistry and Molecular Biology University of Chicago 929 East 57th Street, Chicago, IL 60637
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Pattanayak SK, Chowdhuri S. Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Lu X, Cui Q. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins. J Phys Chem B 2013; 117:2005-18. [PMID: 23347181 DOI: 10.1021/jp309877z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Free energy simulations using a finite sphere boundary condition rather than a periodic boundary condition (PBC) are attractive in the study of very large biomolecular systems. To understand the quantitative impact of various approximations in such simulations, we compare charging free energies in both solution and protein systems calculated in a linear response framework with the Generalized Solvent Boundary Potential (GSBP) and PBC simulations. For simple ions in solution, we find good agreements between GSBP and PBC charging free energies, once the relevant correction terms are taken into consideration. For PBC simulations with the particle-mesh-Ewald for long-range electrostatics, the contribution (ΔG(P-M)) due to the use of a particle rather than molecule based summation scheme in real space is found to be significant, as pointed out by Hünenberger and co-workers. For GSBP, when the inner region is close to be charge neutral, the key correction is the overpolarization of water molecules at the inner/outer dielectric boundary; the magnitude of the correction (ΔG(s-pol)), however, is relatively small. For charging (oxidation) free energy in proteins, the situation is more complex, although good agreement between GSBP and PBC can still be obtained when care is exercised. The smooth dielectric boundary approximation inherent to GSBP tends to make significant errors when the inner region is featured with a high net charge. However, the error can be corrected with Poisson-Boltzmann calculations using snapshots from GSBP simulations in a straightforward and robust manner. Because of the more complex charge and solvent distributions, the magnitudes of ΔG(P-M) and ΔG(s-pol) in protein simulations appear to be different from those derived for solution simulations, leading to uncertainty in directly comparing absolute charging free energies from PBC and GSBP simulations for protein systems. The relative charging/oxidation free energies, however, are robust. With the linear response approximation, for the specific protein system (CueR) studied, the effect of freezing the protein structure in the outer region is found to be small, unless a very small (8 Å) inner region is used; even in the latter case, the result is substantially improved when the nearby metal binding loop is allowed to respond to metal oxidation. The implications of these results to the applicability of GSBP to complex biomolecules and in ab initio QM/MM simulations are discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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Yu W, Lopes PEM, Roux B, MacKerell AD. Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys 2013; 138:034508. [PMID: 23343286 PMCID: PMC3562330 DOI: 10.1063/1.4774577] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/21/2012] [Indexed: 01/23/2023] Open
Abstract
A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.
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Affiliation(s)
- Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
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Thomas M, Jayatilaka D, Corry B. How does overcoordination create ion selectivity? Biophys Chem 2012; 172:37-42. [PMID: 23337473 DOI: 10.1016/j.bpc.2012.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/20/2012] [Accepted: 11/23/2012] [Indexed: 11/28/2022]
Abstract
Some biological molecules can distinguish between ions of similar nature, which may be achieved by enforcing specific coordination numbers on ions in the binding site. It is suggested that when this number is favourable for one ion type, but too large for another, this creates ion selectivity through the proposed mechanism of 'overcoordination'. Much debate has occurred about the role overcoordination plays, and suggestions made as to how molecules can enforce particular coordination numbers, but there has not been an examination of the microscopic underpinning of ion selectivity by overcoordination. Here we use molecular-dynamics to systematically investigate how the number of ligands affects the ion-ligand and ligand-ligand interaction energies, and thus the thermodynamic ion selectivity, of a combination of model systems: three ions (Li(+)/Na(+)/K(+)) with three different ligands (water/formaldehyde/formamide). We find that the ligand-ligand repulsion controls the changes in geometry of each system with changing ligand number. Ion selectivity by overcoordination is achieved as smaller ions exhibit anomalous geometrical changes with the addition of extra ligands, whilst larger ions do not.
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Affiliation(s)
- Michael Thomas
- Research School of Biology, The Australian National University, Canberra, Australia
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Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4787-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Pattanayak SK, Chowdhuri S. A molecular dynamics simulations study on the behavior of liquid N-methylacetamide in presence of NaCl: Structure, dynamics and H-bond properties. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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PATTANAYAK SUBRATKUMAR, CHOWDHURI SNEHASIS. SIZE DEPENDENCE OF SOLVATION STRUCTURE AND DYNAMICS OF IONS IN LIQUID N-METHYLACETAMIDE: A MOLECULAR DYNAMICS SIMULATION STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500241] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The solvation structure and dynamics of alkali metal (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions in liquid N -methylacetamide (NMA) are calculated at two different temperatures T = 313 K and 453 K, by using classical molecular dynamics simulations. We have also considered [Formula: see text] and some larger cations such as I +, Me 4 N +, and Et4N+ in this study to investigate the size dependence solvation structure and dynamics of ions in liquid NMA. With the increase of ion size, the self-diffusion coefficients of cations are found to increase and the maximum is observed at Me4N+ , whereas for halide ions the increase of diffusion coefficient with ion size continues up to I- and no maximum is observed. However, the relative increase of the diffusion coefficients of larger ion compared to those of Li+ and F+ are found to be significantly higher at low temperature. Results are very good in agreement with experimental observation.
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Affiliation(s)
| | - SNEHASIS CHOWDHURI
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751013, India
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Yu H, Ratheal I, Artigas P, Roux B. Molecular Mechanisms of K+ Selectivity in Na/K Pump. Aust J Chem 2012. [DOI: 10.1071/ch12026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The sodium–potassium (Na/K) pump plays an essential role in maintaining cell volume and secondary active transport of other solutes by establishing the Na+ and K+ concentration gradients across the plasma membrane of animal cells. The recently determined crystal structures of the Na/K pump to atomic resolution provide a new impetus to investigate molecular determinants governing the binding of Na+ and K+ ions and conformational transitions during the functional cycle. The pump cycle is generally described by the alternating access mechanism, in which the pump toggles between different conformational states, where ions can bind from either the intracellular or the extracellular side. However, important issues concerning the selectivity of the Na/K pump remain to be addressed. In particular, two out of the three binding sites are shared between Na+ and K+ and it is not clear how the protein is able to select K+ over Na+ when it is in the outwardly facing phosphorylated conformation (E2P), and Na+ over K+ when it is in the inwardly facing conformation (E1). In this review article, we will first briefly review the recent advancement in understanding the microscopic mechanism of K+ selectivity in the Na/K pump at the E2·Pi state and then outline the remaining challenges to be addressed about ion selectivity.
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Ioannou F, Archontis G, Leontidis E. Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics. J Phys Chem B 2011; 115:13389-400. [PMID: 21978277 DOI: 10.1021/jp207068m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space is achieved by the replica exchange method. In agreement with other works, we observe preferential sodium interactions with the peptide carbonyl groups, which are enhanced in the NaI solutions due to the increased affinity of the less hydrophilic iodide anion for the peptide methyl side-chains and terminal blocking groups. These interactions have been associated with a decrease in the helicities of more complex peptides. In our simulations, both salts have a small effect on the dipeptide, but consistently stabilize the intramolecular hydrogen-bonding interactions and "α-helical" conformations of the tetrapeptide. This behavior, and an analysis of the intermolecular interaction energies show that ion-peptide interactions, or changes in the peptide hydration due to salts, are not sufficient determining factors of the peptide conformational preferences. Additional simulations suggest that the observed stabilizing effect is not due to the employed force-field, and that it is maintained in short peptides but is reversed in longer peptides. Thus, the peptide conformational preferences are determined by an interplay of energetic and entropic factors, arising from the peptide sequence and length and the composition of the solution.
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Varma S, Rogers DM, Pratt LR, Rempe SB. Perspectives on: ion selectivity: design principles for K+ selectivity in membrane transport. ACTA ACUST UNITED AC 2011; 137:479-88. [PMID: 21624944 PMCID: PMC3105521 DOI: 10.1085/jgp.201010579] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sameer Varma
- Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, USA
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Roux B, Bernèche S, Egwolf B, Lev B, Noskov SY, Rowley CN, Yu H. Ion selectivity in channels and transporters. ACTA ACUST UNITED AC 2011; 137:415-26. [PMID: 21518830 PMCID: PMC3082929 DOI: 10.1085/jgp.201010577] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, University of Chicago, Chicago, IL 60637, USA. roux@uchicago.edu
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