1
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Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B 2022; 126:8985-8999. [PMID: 36306164 DOI: 10.1021/acs.jpcb.2c05965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K+ and Cl- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K+, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.
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Affiliation(s)
- Michael A Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94035, United States.,SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California94043, United States
| | - Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94033, United States.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California94132, United States
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2
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Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. ENTROPY 2021; 23:e23050571. [PMID: 34066581 PMCID: PMC8148522 DOI: 10.3390/e23050571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions.
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Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
- Correspondence: ; Tel.: +1-650-604-5759
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3
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Ramos-Garcés MV, Li K, Lei Q, Bhattacharya D, Kole S, Zhang Q, Strzalka J, Angelopoulou PP, Sakellariou G, Kumar R, Arges CG. Understanding the ionic activity and conductivity value differences between random copolymer electrolytes and block copolymer electrolytes of the same chemistry. RSC Adv 2021; 11:15078-15084. [PMID: 35424026 PMCID: PMC8697982 DOI: 10.1039/d1ra02519h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 11/21/2022] Open
Abstract
Herein, a systematic study where the macromolecular architectures of poly(styrene-block-2-vinyl pyridine) block copolymer electrolytes (BCE) are varied and their activity coefficients and ionic conductivities are compared and rationalized versus a random copolymer electrolyte (RCE) of the same repeat unit chemistry. By performing quartz crystal microbalance, ion-sorption, and ionic conductivity measurements of the thin film copolymer electrolytes, it is found that the RCE has higher ionic activity coefficients. This observation is ascribed to the fact that the ionic groups in the RCE are more spaced out, reducing the overall chain charge density. However, the ionic conductivity of the BCE is 50% higher and 17% higher after the conductivity is normalized by their ion exchange capacity values on a volumetric basis. This is attributed to the presence of percolated pathways in the BCE. To complement the experimental findings, molecular dynamics (MD) simulations showed that the BCE has larger water cluster sizes, rotational dynamics, and diffusion coefficients, which are contributing factors to the higher ionic conductivity of the BCE variant. The findings herein motivate the design of new polymer electrolyte chemistries that exploit the advantages of both RCEs and BCEs.
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Affiliation(s)
- Mario V Ramos-Garcés
- Cain Department of Chemical Engineering, Louisiana State University Baton Rouge LA 70803 USA
| | - Ke Li
- Department of Chemistry, Louisiana State University Baton Rouge LA 70803 USA
| | - Qi Lei
- Cain Department of Chemical Engineering, Louisiana State University Baton Rouge LA 70803 USA
| | - Deepra Bhattacharya
- Cain Department of Chemical Engineering, Louisiana State University Baton Rouge LA 70803 USA
| | - Subarna Kole
- Cain Department of Chemical Engineering, Louisiana State University Baton Rouge LA 70803 USA
| | - Qingteng Zhang
- X-ray Science Division, Argonne National Laboratory Lemont IL 60439 USA
| | - Joseph Strzalka
- X-ray Science Division, Argonne National Laboratory Lemont IL 60439 USA
| | | | - Georgios Sakellariou
- Department of Chemistry, National and Kapodistrian University of Athens 15771 Athens Greece
| | - Revati Kumar
- Department of Chemistry, Louisiana State University Baton Rouge LA 70803 USA
| | - Christopher G Arges
- Cain Department of Chemical Engineering, Louisiana State University Baton Rouge LA 70803 USA
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4
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Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K +-ion across biological membranes. Nat Commun 2020; 11:469. [PMID: 31980608 PMCID: PMC6981123 DOI: 10.1038/s41467-019-13834-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.
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5
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Ahumada JC, Alemán C, Soto-Delgado J, Torras J. Ion–Ion Repulsions and Charge-Shielding Effects Dominate the Permeation Mechanism through the OmpF Porin Channel. J Phys Chem B 2018; 123:86-94. [DOI: 10.1021/acs.jpcb.8b09549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Carlos Ahumada
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
- Departamento de Química, Universidad Técnica Federico Santa María, Casilla 110-V, 2390123 Valparaíso, Chile
| | - Carlos Alemán
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Quillota 980, 2531015 Viña del Mar, Chile
| | - Juan Torras
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
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6
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Lopes-Rodrigues M, Triguero J, Torras J, Perpète EA, Michaux C, Zanuy D, Alemán C. Influence of the surrounding environment in re-naturalized β-barrel membrane proteins. Biophys Chem 2018; 234:6-15. [DOI: 10.1016/j.bpc.2017.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 10/18/2022]
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7
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Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study. Biophys Chem 2018; 233:47-54. [DOI: 10.1016/j.bpc.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022]
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8
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Intrinsic, adaptive and acquired antimicrobial resistance in Gram-negative bacteria. Essays Biochem 2017; 61:49-59. [DOI: 10.1042/ebc20160063] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Gram-negative bacteria are responsible for a large proportion of antimicrobial-resistant infections in humans and animals. Among this class of bacteria are also some of the most successful environmental organisms. Part of this success is their adaptability to a variety of different niches, their intrinsic resistance to antimicrobial drugs and their ability to rapidly acquire resistance mechanisms. These mechanisms of resistance are not exclusive and the interplay of several mechanisms causes high levels of resistance. In this review, we explore the molecular mechanisms underlying resistance in Gram-negative organisms and how these different mechanisms enable them to survive many different stress conditions.
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9
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Bhamidimarri SP, Prajapati JD, van den Berg B, Winterhalter M, Kleinekathöfer U. Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example. Biophys J 2017; 110:600-611. [PMID: 26840725 DOI: 10.1016/j.bpj.2015.12.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022] Open
Abstract
To quantify the flow of small uncharged molecules into and across nanopores, one often uses ion currents. The respective ion-current fluctuations caused by the presence of the analyte make it possible to draw some conclusions about the direction and magnitude of the analyte flow. However, often this flow appears to be asymmetric with respect to the applied voltage. As a possible reason for this asymmetry, we identified the electroosmotic flow (EOF), which is the water transport associated with ions driven by the external transmembrane voltage. As an example, we quantify the contribution of the EOF through a nanopore by investigating the permeation of α-cyclodextrin through CymA, a cyclodextrin-specific channel from Klebsiella oxytoca. To understand the results from electrophysiology on a molecular level, all-atom molecular dynamics simulations are used to detail the effect of the EOF on substrate entry to and exit from a CymA channel in which the N-terminus has been deleted. The combined experimental and computational results strongly suggest that one needs to account for the significant contribution of the EOF when analyzing the penetration of cyclodextrins through the CymA pore. This example study at the same time points to the more general finding that the EOF needs to be considered in translocation studies of neutral molecules and, at least in many cases, should be able to help in discriminating between translocation and binding events.
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Affiliation(s)
| | | | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
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10
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Pohorille A, Wilson MA, Wei C. Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels. J Phys Chem B 2016; 121:3607-3619. [PMID: 27936743 DOI: 10.1021/acs.jpcb.6b09598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examine the validity and utility of the electrodiffusion (ED) equation, i.e., the generalized Nernst-Planck equation, to characterize, in combination with molecular dynamics, the electrophysiological behavior of simple ion channels. As models, we consider three systems-two naturally occurring channels formed by α-helical bundles of peptaibols, trichotoxin, and alamethicin, and a synthetic, hexameric channel, formed by a peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. Starting with equilibrium properties, such as the potential of mean force experienced by an ion traversing the channel and diffusivity, obtained from molecular dynamics simulations, the ED equation can be used to determine the full current-voltage dependence with modest or no additional effort. The potential of mean force can be obtained not only from equilibrium simulations, but also, with comparable accuracy, from nonequilibrium simulations at a single voltage. The main assumptions underlying the ED equation appear to hold well for the channels and voltages studied here. To expand the utility of the ED equation, we examine what are the necessary and sufficient conditions for Ohmic and nonrectifying behavior and relate deviations from this behavior to the shape of the ionic potential of mean force.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,SETI Institute , 189 N Bernardo Ave #200, Mountain View, California 94043, United States
| | - Chenyu Wei
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
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11
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Behmard E, Abdolmaleki P, Taghdir M. Molecular dynamics investigation on structural and transport properties of p7 ion channel. J Biomol Struct Dyn 2016; 35:2725-2735. [PMID: 27668345 DOI: 10.1080/07391102.2016.1230519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Esmaeil Behmard
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
| | - Parviz Abdolmaleki
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
| | - Majid Taghdir
- a Faculty of Biological Sciences, Department of Biophysics , Tarbiat Modares University , P.O. Box: 14115/175, Tehran , Iran
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12
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Tofail SAM, Bauer J. Electrically Polarized Biomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5470-5484. [PMID: 27122372 DOI: 10.1002/adma.201505403] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/31/2016] [Indexed: 06/05/2023]
Abstract
Electrically polarized biomaterials and their interactions with the surrounding biological environment is important for understanding the host response, growth and inhibition of biological species as well as the long-term fate and performance of the implants. Polarized materials possess electrical charges at the surface due to polar or electret properties. As these surfaces are at the frontier of biological reactions understanding biological interactions at the interface with polarized biomaterials requires a convergence of understanding multiple disciplines. This article discusses progress that has taken place in the fields of surface and interface science, materials science and biomedical device engineering to obtain a better perspective of such interactions.
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Affiliation(s)
- Syed A M Tofail
- Department of Physics and Energy, and Materials and Surface Science Institute, University of Limerick, Ireland
| | - Joanna Bauer
- Department of Biomedical Engineering, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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13
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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14
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García-Giménez E, Alcaraz A, Aguilella-Arzo M, Aguilella VM. Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations. J Phys Chem B 2015; 119:8475-9. [PMID: 26091047 DOI: 10.1021/acs.jpcb.5b03547] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.
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Affiliation(s)
- Elena García-Giménez
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Antonio Alcaraz
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Marcel Aguilella-Arzo
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Vicente M Aguilella
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
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15
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Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level. PLoS Comput Biol 2015; 11:e1004255. [PMID: 25955156 PMCID: PMC4425685 DOI: 10.1371/journal.pcbi.1004255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane. They feature a constriction zone, contributed by the plunging of extracellular loop 3 (L3) into the channel lumen. Porins are generally in the open state, but undergo gating in response to external voltages. To date the underlying mechanism is unclear. Here we report results from molecular dynamics simulations on the two porins of Providenica stuartii, Omp-Pst1 and Omp-Pst2, which display distinct voltage sensitivities. Voltage gating was observed in Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 and Omp-Pst2 structures and trajectories suggests that their sensitivity to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall, as we observed that it is the strength of this network that governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel furthermore suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis. Porins are the main conduits for hydrophilic nutrients and ions uptake into the periplasm of Gram-negative bacteria. Their translocation permeability is determined by the amino-acid distribution on their extracellular loop L3. Bacterial porin channels have long been known to undergo step-wise gating, under the application of a transmembrane potential. Yet the exact molecular mechanism by which gating is achieved and the exact relevance of this evolved characteristic remain elusive. In the present study, we report on electrophysiology experiments and molecular dynamics simulations on the two general-diffusion porins of Providencia stuartii, Omp-Pst1 and Omp-Pst2. Our results show that gating in Omp-Pst2 occurs as the result of L3 displacement, which follows from the binding of cations in acidic niches between L3 and the barrel wall and effects in exposing the side chain of a highly conserved aromatic residue at the tip of L3 in the channel lumen. That Omp-Pst2 displays asymmetric voltage sensitivity and that the likelihood of gating is increased when cations transit from the extracellular to the intracellular side suggests voltage-gating underlies a regulatory role in bacterial homeostasis. Rational antibiotic-design strategies based on the maximization of antibiotic penetration and accumulation at their target sites, should take this role into account.
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16
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Calero C, Martí J, Guàrdia E. 1H Nuclear Spin Relaxation of Liquid Water from Molecular Dynamics Simulations. J Phys Chem B 2015; 119:1966-73. [DOI: 10.1021/jp510013q] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Calero
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya-Barcelona Tech, B5-209 Campus Nord., 08034 Barcelona, Spain
- Center
for Polymer Studies and Department of Physics, Boston University, 590
Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - J. Martí
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya-Barcelona Tech, B5-209 Campus Nord., 08034 Barcelona, Spain
| | - E. Guàrdia
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya-Barcelona Tech, B5-209 Campus Nord., 08034 Barcelona, Spain
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17
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Alcaraz A, Queralt-Martín M, Verdiá-Báguena C, Aguilella VM, Mafé S. Entropy-enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF. NANOSCALE 2014; 6:15210-15215. [PMID: 25375963 DOI: 10.1039/c4nr03811h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy-entropy compensation for different salts and concentrations.
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Affiliation(s)
- Antonio Alcaraz
- Department of Physics, Laboratory of Molecular Biophysics, University Jaume I, E-12080 Castellón, Spain.
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18
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Wilson MA, Nguyen TH, Pohorille A. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance. J Chem Phys 2014; 141:22D519. [DOI: 10.1063/1.4900879] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, California 94035, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, USA
| | - Thuy Hien Nguyen
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, California 94035, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, USA
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Zhou S. Effects of discreteness of surface charges on the effective electrostatic interactions. J Chem Phys 2014; 140:234704. [PMID: 24952557 DOI: 10.1063/1.4881601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Shiqi Zhou
- School of Physics and Electronics, Central South University, Changsha, Hunan 410083, China
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20
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Lu J, Modi N, Kleinekathöfer U. Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering. J Phys Chem B 2013; 117:15966-75. [DOI: 10.1021/jp408495v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Lu
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Niraj Modi
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- School of Engineering and
Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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21
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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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22
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Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity. Biochem Res Int 2012; 2012:245786. [PMID: 23008773 PMCID: PMC3449104 DOI: 10.1155/2012/245786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/17/2022] Open
Abstract
Electrophysiological characterization of large protein channels, usually displaying multi-ionic transport and weak ion selectivity, is commonly performed at physiological conditions (moderate gradients of KCl solutions at decimolar concentrations buffered at neutral pH). We extend here the characterization of the OmpF porin, a wide channel of the outer membrane of E. coli, by studying the effect of salts of divalent cations on the transport properties of the channel. The regulation of divalent cations concentration is essential in cell metabolism and understanding their effects is of key importance, not only in the channels specifically designed to control their passage but also in other multiionic channels. In particular, in porin channels like OmpF, divalent cations modulate the efficiency of molecules having antimicrobial activity. Taking advantage of the fact that the OmpF channel atomic structure has been resolved both in water and in MgCl2 aqueous solutions, we analyze the single channel conductance and the channel selectivity inversion aiming to separate the role of the electrolyte itself, and the counterion accumulation induced by the protein channel charges and other factors (binding, steric effects, etc.) that being of minor importance in salts of monovalent cations become crucial in the case of divalent cations.
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23
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Gan Z, Xing X, Xu Z. Effects of image charges, interfacial charge discreteness, and surface roughness on the zeta potential of spherical electric double layers. J Chem Phys 2012; 137:034708. [DOI: 10.1063/1.4736570] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wilson MA, Wei C, Bjelkmar P, Wallace BA, Pohorille A. Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance. Biophys J 2011; 100:2394-402. [PMID: 21575573 DOI: 10.1016/j.bpj.2011.03.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
Abstract
Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K⁺ and Cl⁻ with their first solvation shells intact. The free energy barrier encountered by K⁺ is only 2.2 kcal/mol whereas Cl⁻ encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.
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Affiliation(s)
- Michael A Wilson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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25
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Calero C, Faraudo J, Aguilella-Arzo M. First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:021908. [PMID: 21405864 DOI: 10.1103/physreve.83.021908] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Indexed: 05/30/2023]
Abstract
We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force F(eff) can be obtained after appropriate subdivision of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
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Affiliation(s)
- Carles Calero
- Institut de Ciència dels Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain.
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26
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Aguilella VM, Queralt-Martín M, Aguilella-Arzo M, Alcaraz A. Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity. Integr Biol (Camb) 2010; 3:159-72. [PMID: 21132209 DOI: 10.1039/c0ib00048e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion channels are hollow proteins that have evolved to exhibit discrimination between charged solutes. This property, known as ion selectivity is critical for several biological functions. By using the bacterial porin OmpF as a model system of wide protein channels, we demonstrate that significant insights can be gained when selectivity measurements are combined with electrodiffusion continuum models and simulations based on the atomic structure. A correct interpretation of the mechanisms ruling the many sources of channel discrimination is a first, indispensable step for the understanding of the controlled movement of ions into or out of cells characteristic of many physiological processes. We conclude that the scattered information gathered from several independent approaches should be appropriately merged to provide a unified and coherent picture of the channel selectivity.
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Affiliation(s)
- Vicente M Aguilella
- Dept. Physics, Lab. Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain.
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