1
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Chen AY, Brooks BR, Damjanovic A. Ion channel selectivity through ion-modulated changes of selectivity filter p Ka values. Proc Natl Acad Sci U S A 2023; 120:e2220343120. [PMID: 37339196 PMCID: PMC10293820 DOI: 10.1073/pnas.2220343120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/26/2023] [Indexed: 06/22/2023] Open
Abstract
In bacterial voltage-gated sodium channels, the passage of ions through the pore is controlled by a selectivity filter (SF) composed of four glutamate residues. The mechanism of selectivity has been the subject of intense research, with suggested mechanisms based on steric effects, and ion-triggered conformational change. Here, we propose an alternative mechanism based on ion-triggered shifts in pKa values of SF glutamates. We study the NavMs channel for which the open channel structure is available. Our free-energy calculations based on molecular dynamics simulations suggest that pKa values of the four glutamates are higher in solution of K+ ions than in solution of Na+ ions. Higher pKa in the presence of K+ stems primarily from the higher population of dunked conformations of the protonated Glu sidechain, which exhibit a higher pKa shift. Since pKa values are close to the physiological pH, this results in predominant population of the fully deprotonated state of glutamates in Na+ solution, while protonated states are predominantly populated in K+ solution. Through molecular dynamics simulations we calculate that the deprotonated state is the most conductive, the singly protonated state is less conductive, and the doubly protonated state has significantly reduced conductance. Thus, we propose that a significant component of selectivity is achieved through ion-triggered shifts in the protonation state, which favors more conductive states for Na+ ions and less conductive states for K+ ions. This mechanism also suggests a strong pH dependence of selectivity, which has been experimentally observed in structurally similar NaChBac channels.
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Affiliation(s)
- Ada Y. Chen
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD21218
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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2
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Wang G, Xu L, Chen H, Liu Y, Pan P, Hou T. Recent advances in computational studies on voltage‐gated sodium channels: Drug design and mechanism studies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Gaoang Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou Jiangsu China
| | - Haiyi Chen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Yifei Liu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical Sciences, Zhejiang University Hangzhou Zhejiang China
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3
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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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4
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Alipour M, Motavaf M, Abdolmaleki P, Zali A, Ashrafi F, Safari S, Hajipour-Verdom B. Structural Analysis and Conformational Dynamics of Short Helical Hyperphosphorylated Segments of Tau Protein (Sequence 254–290) in Alzheimer’s Disease: A Molecular Dynamics Simulation Study. Front Mol Biosci 2022; 9:884705. [PMID: 36003083 PMCID: PMC9393928 DOI: 10.3389/fmolb.2022.884705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder whose early diagnosis leads to a chance for successful treatment and decreases the side effects. Hyperphosphorylation of tau proteins is a pathological hallmark of AD that causes it to lose its attachment ability to the microtubules. Alteration of tau structure due to its hyperphosphorylation is an exciting challenge regarding AD treatments. Here, we aimed to examine the structural alterations of short helical segments of tau protein with one to three phosphorylated sites by molecular dynamics simulation. Results indicated that the interaction of two similar segments with three phosphorylated sites (P-Ser262, 285, and 289) formed a compact and more stable structure than the one phosphorylated site complex (P-Ser262). Moreover, due to the high dynamics of the P-Ser262 complex, several structures were made with different conformational dynamics, but there was only one stable cluster of the P-Ser262, 285, and 289 complex during simulation. It seems that the P-Ser262, 285, and 289 complex plays an important role in the formation of paired helical filaments (PHFs) by forming a stable dimer. Generally, it is important to identify how structural features of segments in tau protein change when the phosphorylated sites increase from one to three sites and their effects on the formation of PHFs for drug design and diagnostic biomarkers.
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Affiliation(s)
- Mozhgan Alipour
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Motavaf
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alireza Zali
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Ashrafi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Safari
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Saeid Safari, ; Behnam Hajipour-Verdom,
| | - Behnam Hajipour-Verdom
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- *Correspondence: Saeid Safari, ; Behnam Hajipour-Verdom,
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5
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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6
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Ionic channels in nerve membranes, 50 years on. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:12-20. [PMID: 34856230 PMCID: PMC8977236 DOI: 10.1016/j.pbiomolbio.2021.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022]
Abstract
This retrospective traces the hypothesis of ion channels from an early statement in a 1970 essay in this journal (Hille, B., 1970, Prog. Biophys. Mol. Biol. 21, 1-32) to its realization today in biophysical, molecular, biochemical, and structural terms. The Na+ and K+ channels of the action potential have been isolated, reconstituted, cloned, mutated, and expressed. They are conformationally flexible, multi-pass glycosylated membrane proteins. Refined atomic structures of several conformational states are known. The discoveries over this half century history illustrate the growth of a field from initial ideas to a mature discipline of biology, physiology, and biomedical science.
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7
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Vallée C, Howlin B, Lewis R. Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis. Int J Mol Sci 2021; 22:ijms222010998. [PMID: 34681656 PMCID: PMC8536179 DOI: 10.3390/ijms222010998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022] Open
Abstract
The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.
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Affiliation(s)
- Cédric Vallée
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Brendan Howlin
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rebecca Lewis
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
- Correspondence:
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8
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Direct proof of soft knock-on mechanism of ion permeation in a voltage gated sodium channel. Int J Biol Macromol 2021; 188:369-374. [PMID: 34371044 DOI: 10.1016/j.ijbiomac.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022]
Abstract
Sodium channels selectively conduct Na+ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na+ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na+ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug.
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9
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Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology and Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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10
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11
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Chen AY, Brooks BR, Damjanovic A. Determinants of conductance of a bacterial voltage-gated sodium channel. Biophys J 2021; 120:3050-3069. [PMID: 34214541 DOI: 10.1016/j.bpj.2021.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/22/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022] Open
Abstract
Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel NavMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Nav channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na+ in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.
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Affiliation(s)
- Ada Y Chen
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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12
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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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13
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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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14
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Pohorille A, Wilson MA. Computational Electrophysiology from a Single Molecular Dynamics Simulation and the Electrodiffusion Model. J Phys Chem B 2021; 125:3132-3144. [DOI: 10.1021/acs.jpcb.0c10737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California 94035, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, United States
| | - Michael A. Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California 94035, United States
- SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California 94043, United States
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15
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Preisler SS, Wiuf AD, Friis M, Kjaergaard L, Hurd M, Becares ER, Nurup CN, Bjoerkskov FB, Szathmáry Z, Gourdon PE, Calloe K, Klaerke DA, Gotfryd K, Pedersen PA. Saccharomyces cerevisiae as a superior host for overproduction of prokaryotic integral membrane proteins. Curr Res Struct Biol 2021; 3:51-71. [PMID: 34235486 PMCID: PMC8244417 DOI: 10.1016/j.crstbi.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/02/2023] Open
Abstract
Integral membrane proteins (IMPs) constitute ~30% of all proteins encoded by the genome of any organism and Escherichia coli remains the first-choice host for recombinant production of prokaryotic IMPs. However, the expression levels of prokaryotic IMPs delivered by this bacterium are often low and overproduced targets often accumulate in inclusion bodies. The targets are therefore often discarded to avoid an additional and inconvenient refolding step in the purification protocol. Here we compared expression of five prokaryotic (bacterial and archaeal) IMP families in E. coli and Saccharomyces cerevisiae. We demonstrate that our S. cerevisiae-based production platform is superior in expression of four investigated IMPs, overall being able to deliver high quantities of active target proteins. Surprisingly, in case of the family of zinc transporters (Zrt/Irt-like proteins, ZIPs), S. cerevisiae rescued protein expression that was undetectable in E. coli. We also demonstrate the effect of localization of the fusion tag on expression yield and sample quality in detergent micelles. Lastly, we present a road map to achieve the most efficient expression of prokaryotic IMPs in our yeast platform. Our findings demonstrate the great potential of S. cerevisiae as host for high-throughput recombinant overproduction of bacterial and archaeal IMPs for downstream biophysical characterization. S. cerevisiae is superior to E. coli in expressing correctly folded and active IMPs. S. cerevisiae completely rescues the expression of the family of zinc transporters. Localization of the fusion tag affects expression yields and protein quality. We provide a roadmap to efficient expression of prokaryotic IMPs in S. cerevisiae.
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Affiliation(s)
- Sarah Spruce Preisler
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Anders Drabaek Wiuf
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Marc Friis
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Lasse Kjaergaard
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Molly Hurd
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Eva Ramos Becares
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Casper Normann Nurup
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | | | - Zsófia Szathmáry
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Pontus Emanuel Gourdon
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Kirstine Calloe
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Dan A Klaerke
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Kamil Gotfryd
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
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16
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Fuel Cell Using Squid Axon Electrolyte and Its Proton Conductivity. J Funct Biomater 2020; 11:jfb11040086. [PMID: 33287321 PMCID: PMC7768438 DOI: 10.3390/jfb11040086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Fuel cells using biomaterials have the potential for environmentally friendly clean energy and have attracted a lot of interest. Moreover, biomaterials are expected to develop into in vivo electrical devices such as pacemakers with no side effects. Ion channels, which are membrane proteins, are known to have a fast ion transport capacity. Therefore, by using ion channels, the realization of fuel cell electrolytes with high-proton conductivity can be expected. In this study, we have fabricated a fuel cell using an ion channel electrolyte for the first time and investigated the electrical properties of the ion channel electrolyte. It was found that the fuel cell using the ion channel membrane shows a power density of 0.78 W/cm2 in the humidified condition. On the other hand, the power density of the fuel cell blocking the ion channel with the channel blocker drastically decreased. These results indicate that the fuel cell using the ion channel electrolyte operates through the existence of the ion channel and that the ion channel membrane can be used as the electrolyte of the fuel cell in humidified conditions. Furthermore, the proton conductivity of the ion channel electrolyte drastically increases above 85% relative humidity (RH) and becomes 2 × 10-2 S/m at 96% RH. This result indicates that the ion channel becomes active above 96%RH. In addition, it was deduced from the impedance analysis that the high proton conductivity of the ion channel electrolyte above 96% RH is caused by the activation of ion channels, which are closely related to the fractionalization of water molecule clusters. From these results, it was found that a fuel cell using the squid axon becomes a new fuel cell using the function of the ion channel above 96% RH.
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Georgiev DD. Quantum information theoretic approach to the mind–brain problem. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 158:16-32. [DOI: 10.1016/j.pbiomolbio.2020.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/25/2022]
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Fernández-Ballester G, Fernández-Carvajal A, Ferrer-Montiel A. Targeting thermoTRP ion channels: in silico preclinical approaches and opportunities. Expert Opin Ther Targets 2020; 24:1079-1097. [PMID: 32972264 DOI: 10.1080/14728222.2020.1820987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION A myriad of cellular pathophysiological responses are mediated by polymodal ion channels that respond to chemical and physical stimuli such as thermoTRP channels. Intriguingly, these channels are pivotal therapeutic targets with limited clinical pharmacology. In silico methods offer an unprecedented opportunity for discovering new lead compounds targeting thermoTRP channels with improved pharmacological activity and therapeutic index. AREAS COVERED This article reviews the progress on thermoTRP channel pharmacology because of (i) advances in solving their atomic structure using cryo-electron microscopy and, (ii) progress on computational techniques including homology modeling, molecular docking, virtual screening, molecular dynamics, ADME/Tox and artificial intelligence. Together, they have increased the number of lead compounds with clinical potential to treat a variety of pathologies. We used original and review articles from Pubmed (1997-2020), as well as the clinicaltrials.gov database, containing the terms thermoTRP, artificial intelligence, docking, and molecular dynamics. EXPERT OPINION The atomic structure of thermoTRP channels along with computational methods constitute a realistic first line strategy for designing drug candidates with improved pharmacology and clinical translation. In silico approaches can also help predict potential side-effects that can limit clinical development of drug candidates. Together, they should provide drug candidates with upgraded therapeutic properties.
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Affiliation(s)
- Gregorio Fernández-Ballester
- Professor Gregorio Fernández-Ballester. Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández , Alicante, Spain
| | - Asia Fernández-Carvajal
- Professor Gregorio Fernández-Ballester. Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández , Alicante, Spain
| | - Antonio Ferrer-Montiel
- Professor Gregorio Fernández-Ballester. Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández , Alicante, Spain
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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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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21
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Damjanovic A, Chen AY, Rosenberg RL, Roe DR, Wu X, Brooks BR. Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions. Proteins 2019; 88:527-539. [DOI: 10.1002/prot.25831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/03/2019] [Accepted: 09/17/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Ana Damjanovic
- Department of BiophysicsJohns Hopkins University Baltimore Maryland
| | - Ada Y. Chen
- Department of PhysicsJohns Hopkins University Baltimore Maryland
| | | | - Daniel R. Roe
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood InstituteNational Institutes of Health Bethesda Maryland
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Wang Y, Finol-Urdaneta RK, Ngo VA, French RJ, Noskov SY. Bases of Bacterial Sodium Channel Selectivity Among Organic Cations. Sci Rep 2019; 9:15260. [PMID: 31649292 PMCID: PMC6813354 DOI: 10.1038/s41598-019-51605-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Hille’s (1971) seminal study of organic cation selectivity of eukaryotic voltage-gated sodium channels showed a sharp size cut-off for ion permeation, such that no ion possessing a methyl group was permeant. Using the prokaryotic channel, NaChBac, we found some similarity and two peculiar differences in the selectivity profiles for small polyatomic cations. First, we identified a diverse group of minimally permeant cations for wildtype NaChBac, ranging in sizes from ammonium to guanidinium and tetramethylammonium; and second, for both ammonium and hydrazinium, the charge-conserving selectivity filter mutation (E191D) yielded substantial increases in relative permeability (PX/PNa). The relative permeabilities varied inversely with relative Kd calculated from 1D Potential of Mean Force profiles (PMFs) for the single cations traversing the channel. Several of the cations bound more strongly than Na+, and hence appear to act as blockers, as well as charge carriers. Consistent with experimental observations, the E191D mutation had little impact on Na+ binding to the selectivity filter, but disrupted the binding of ammonium and hydrazinium, consequently facilitating ion permeation across the NaChBac-like filter. We concluded that for prokaryotic sodium channels, a fine balance among filter size, binding affinity, occupancy, and flexibility seems to contribute to observed functional differences.
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Affiliation(s)
- Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rocio K Finol-Urdaneta
- Department of Physiology and Pharmacology, and the Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
| | - Van Anh Ngo
- Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada.,Center for Nonlinear Studies, Los Alamos National Lab, Los Alamos, NM, 87544, USA
| | - Robert J French
- Department of Physiology and Pharmacology, and the Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and the Department of Biological Sciences, University of Calgary, Calgary, Canada.
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