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Chen YN, Liu YZ, Sun Q. The Molecular Mechanism of Ion Selectivity in Nanopores. Molecules 2024; 29:853. [PMID: 38398605 PMCID: PMC10891634 DOI: 10.3390/molecules29040853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Ion channels exhibit strong selectivity for specific ions over others under electrochemical potentials, such as KcsA for K+ over Na+. Based on the thermodynamic analysis, this study is focused on exploring the mechanism of ion selectivity in nanopores. It is well known that ions must lose part of their hydration layer to enter the channel. Therefore, the ion selectivity of a channel is due to the rearrangement of water molecules when entering the nanopore, which may be related to the hydrophobic interactions between ions and channels. In our recent works on hydrophobic interactions, with reference to the critical radius of solute (Rc), it was divided into initial and hydrophobic solvation processes. Additionally, the different dissolved behaviors of solutes in water are expected in various processes, such as dispersed and accumulated distributions in water. Correspondingly, as the ion approaches the nanopore, there seems to exist the "repulsive" or "attractive" forces between them. In the initial process (
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Affiliation(s)
| | | | - Qiang Sun
- Key Laboratory of Orogenic Belts and Crustal Evolution, The School of Earth and Space Sciences, Ministry of Education, Peking University, Beijing 100871, China; (Y.-N.C.); (Y.-Z.L.)
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2
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Ryan M, Gao L, Valiyaveetil FI, Zanni MT, Kananenka AA. Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy. J Am Chem Soc 2023; 145:18529-18537. [PMID: 37578394 PMCID: PMC10450685 DOI: 10.1021/jacs.3c05339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Indexed: 08/15/2023]
Abstract
The potassium ion (K+) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single 13C-18O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K+ transport mechanisms: soft-knock and hard-knock. According to the former, water molecules alternate between K+ ions in the selectivity filter while the latter assumes that K+ ions occupy the adjacent sites. Molecular dynamics simulations and computational spectroscopy are employed to interpret experimental 2D IR spectra. We find that in the closed conductive state of the KcsA channel, K+ ions do not occupy adjacent binding sites. The experimental data is consistent with simulated 2D IR spectra of soft-knock ion configurations. In contrast, the simulated spectra for the hard-knock ion configurations do not reproduce the experimental results. 2D IR spectra of the hard-knock mechanism have lower frequencies, homogeneous 2D lineshapes, and multiple peaks. In contrast, ion configurations of the soft-knock model produce 2D IR spectra with a single peak at a higher frequency and inhomogeneous lineshape. We conclude that under equilibrium conditions, in the absence of transmembrane voltage, both water and K+ ions occupy the selectivity filter of the KcsA channel in the closed conductive state. The ion configuration is central to the mechanism of ion transport through potassium channels.
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Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
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3
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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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Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021; 153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
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Affiliation(s)
- E Duboué-Dijon
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - M Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Delcroix
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - H Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
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Strong SE, Hestand NJ, Kananenka AA, Zanni MT, Skinner JL. IR Spectroscopy Can Reveal the Mechanism of K + Transport in Ion Channels. Biophys J 2019; 118:254-261. [PMID: 31812356 DOI: 10.1016/j.bpj.2019.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023] Open
Abstract
Ion channels like KcsA enable ions to move across cell membranes at near diffusion-limited rates and with very high selectivity. Various mechanisms have been proposed to explain this phenomenon. Broadly, there is disagreement among the proposed mechanisms about whether ions occupy adjacent sites in the channel during the transport process. Here, using a mixed quantum-classical approach to calculate theoretical infrared spectra, we propose a set of infrared spectroscopy experiments that can discriminate between mechanisms with and without adjacent ions. These experiments differ from previous ones in that they independently probe specific ion binding sites within the selectivity filter. When ions occupy adjacent sites in the selectivity filter, the predicted spectra are significantly redshifted relative to when ions do not occupy adjacent sites. Comparisons between theoretical and experimental peak frequencies will therefore discriminate the mechanisms.
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Affiliation(s)
- Steven E Strong
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Nicholas J Hestand
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Natural and Applied Sciences, Evangel University, Springfield, Missouri
| | - Alexei A Kananenka
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - J L Skinner
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.
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Kratochvil HT, Carr JK, Matulef K, Annen AW, Li H, Maj M, Ostmeyer J, Serrano AL, Raghuraman H, Moran SD, Skinner JL, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science 2016; 353:1040-1044. [PMID: 27701114 PMCID: PMC5544905 DOI: 10.1126/science.aag1447] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/03/2016] [Indexed: 11/02/2022]
Abstract
Potassium channels are responsible for the selective permeation of K+ ions across cell membranes. K+ ions permeate in single file through the selectivity filter, a narrow pore lined by backbone carbonyls that compose four K+ binding sites. Here, we report on the two-dimensional infrared (2D IR) spectra of a semisynthetic KcsA channel with site-specific heavy (13C18O) isotope labels in the selectivity filter. The ultrafast time resolution of 2D IR spectroscopy provides an instantaneous snapshot of the multi-ion configurations and structural distributions that occur spontaneously in the filter. Two elongated features are resolved, revealing the statistical weighting of two structural conformations. The spectra are reproduced by molecular dynamics simulations of structures with water separating two K+ ions in the binding sites, ruling out configurations with ions occupying adjacent sites.
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Affiliation(s)
- Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua K Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Alvin W Annen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Hui Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Arnaldo L Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Raghuraman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sean D Moran
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J L Skinner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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7
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Soniat M, Rick SW. The effects of charge transfer on the aqueous solvation of ions. J Chem Phys 2012; 137:044511. [DOI: 10.1063/1.4736851] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Grigoryan G, Moore DT, DeGrado WF. Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors. Annu Rev Biochem 2011; 80:211-37. [PMID: 21548783 DOI: 10.1146/annurev-biochem-091008-152423] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Signal transduction across biological membranes is central to life. This process generally happens through communication between different domains and hierarchical coupling of information. Here, we review structural and thermodynamic principles behind transmembrane (TM) signal transduction and discuss common themes. Communication between signaling domains can be understood in terms of thermodynamic and kinetic principles, and complex signaling patterns can arise from simple wiring of thermodynamically coupled domains. We relate this to functions of several signal transduction systems: the M2 proton channel from influenza A virus, potassium channels, integrin receptors, and bacterial kinases. We also discuss key features in the structural rearrangements responsible for signal transduction in these systems.
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Affiliation(s)
- Gevorg Grigoryan
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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