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Mukherjee S, Cassini TA, Hu N, Yang T, Li B, Shen W, Moth CW, Rinker DC, Sheehan JH, Cogan JD, Newman JH, Hamid R, Macdonald RL, Roden DM, Meiler J, Kuenze G, Phillips JA, Capra JA. Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants. HGG ADVANCES 2022; 3:100131. [PMID: 36035247 PMCID: PMC9399384 DOI: 10.1016/j.xhgg.2022.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Whole-exome sequencing (WES) in the clinic has identified several rare monogenic developmental and epileptic encephalopathies (DEE) caused by ion channel variants. However, WES often fails to provide actionable insight for rare diseases, such as DEEs, due to the challenges of interpreting variants of unknown significance (VUS). Here, we describe a "personalized structural biology" (PSB) approach that leverages recent innovations in the analysis of protein 3D structures to address this challenge. We illustrate this approach in an Undiagnosed Diseases Network (UDN) individual with DEE symptoms and a de novo VUS in KCNC2 (p.V469L), the Kv3.2 voltage-gated potassium channel. A nearby KCNC2 variant (p.V471L) was recently suggested to cause DEE-like phenotypes. Computational structural modeling suggests that both affect protein function. However, despite their proximity, the p.V469L variant is likely to sterically block the channel pore, while the p.V471L variant is likely to stabilize the open state. Biochemical and electrophysiological analyses demonstrate heterogeneous loss-of-function and gain-of-function effects, as well as differential response to 4-aminopyridine treatment. Molecular dynamics simulations illustrate that the pore of the p.V469L variant is more constricted, increasing the energetic barrier for K+ permeation, whereas the p.V471L variant stabilizes the open conformation. Our results implicate variants in KCNC2 as causative for DEE and guide the interpretation of a UDN individual. They further delineate the molecular basis for the heterogeneous clinical phenotypes resulting from two proximal pathogenic variants. This demonstrates how the PSB approach can provide an analytical framework for individualized hypothesis-driven interpretation of protein-coding VUS.
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Affiliation(s)
- Souhrid Mukherjee
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Thomas A. Cassini
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tao Yang
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bian Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christopher W. Moth
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - David C. Rinker
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan H. Sheehan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joy D. Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Undiagnosed Diseases Network
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John H. Newman
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Robert L. Macdonald
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
| | - John A. Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
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Bauer D, Wissmann J, Moroni A, Thiel G, Hamacher K. Weak Cation Selectivity in HCN Channels Results From K +-Mediated Release of Na + From Selectivity Filter Binding Sites. FUNCTION (OXFORD, ENGLAND) 2022; 3:zqac019. [PMID: 36156894 PMCID: PMC9492253 DOI: 10.1093/function/zqac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 01/07/2023]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels generate the pacemaker current which plays an important role in the timing of various biological processes like the heart beat. We used umbrella sampling to explore the potential of mean force for the conduction of potassium and sodium through the open HCN4 pore. Our data explain distinct functional features like low unitary conductance and weak selectivity as a result of high energetic barriers inside the selectivity filter of this channel. They exceed the 3-5 kJ/mol threshold which is presumed as maximal barrier for diffusion-limited conductance. Furthermore, simulations provide a thermodynamic explanation for the weak cation selectivity of HCN channels that contain only two ion binding sites in the selectivity filter (SF). We find that sodium ions bind more strongly to the SF than potassium and are easier released by binding of potassium than of another sodium. Hence ion transport and selectivity in HCN channels is not determined by the same mechanism as in potassium-selective channels; it rather relies on sodium as a weak blocker that can only be released by potassium.
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Affiliation(s)
- Daniel Bauer
- Department of Biology and Centre for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Jan Wissmann
- Department of Physics, TU Darmstadt, Schlossgartenstrasse 7, 64289 Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | | | - Kay Hamacher
- Department of Biology and Centre for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany,Department of Physics, TU Darmstadt, Schlossgartenstrasse 7, 64289 Darmstadt, Germany
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Tao E, Corry B. Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors. Biophys J 2022; 121:193-206. [PMID: 34958776 PMCID: PMC8790208 DOI: 10.1016/j.bpj.2021.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Voltage-gated sodium channels (Nav) underlie the electrical activity of nerve and muscle cells. Humans have nine different subtypes of these channels, which are the target of small-molecule inhibitors commonly used to treat a range of conditions. Structural studies have identified four lateral fenestrations within the Nav pore module that have been shown to influence Nav pore blocker access during resting-state inhibition. However, the structural differences among the nine subtypes are still unclear. In particular, the dimensions of the four individual fenestrations across the Nav subtypes and their differential accessibility to pore blockers is yet to be characterized. To address this, we applied classical molecular dynamics simulations to study the recently published structures of Nav1.1, Nav1.2, Nav1.4, Nav1.5, and Nav1.7. Although there is significant variability in the bottleneck sizes of the Nav fenestrations, the subtypes follow a common pattern, with wider DI-II and DIII-IV fenestrations, a more restricted DII-III fenestration, and the most restricted DI-IV fenestration. We further identify the key bottleneck residues in each fenestration and show that the motions of aromatic residue sidechains govern the bottleneck radii. Well-tempered metadynamics simulations of Nav1.4 and Nav1.5 in the presence of the pore blocker lidocaine also support the DI-II fenestration being the most likely access route for drugs. Our computational results provide a foundation for future in vitro experiments examining the route of drug access to sodium channels. Understanding the fenestrations and their accessibility to drugs is critical for future analyses of diseases mutations across different sodium channel subtypes, with the potential to inform pharmacological development of resting-state inhibitors and subtype-selective drug design.
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Affiliation(s)
- Elaine Tao
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, Australia.
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Musunuru P, Padhi S, Priyakumar UD. Ion Selectivity and Permeation Mechanism in a Cyclodextrin-Based Channel. J Phys Chem B 2021; 125:8028-8037. [PMID: 34283600 DOI: 10.1021/acs.jpcb.1c03212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic ion channels are a promising technology in the medical and materials sciences because of their ability to conduct ions. Channels based on cyclodextrin, a cyclic oligomer of glucose, are of particular interest because of their nontoxicity and biocompatibility. Using molecular dynamics-based free energy calculations, this study identifies cyclodextrin channel types that are best suited to serve as synthetic ion channels. Free energy profiles show that the connectivity in the channel determines whether the channel is cation-selective or anion-selective. Furthermore, the energy barrier for ion transport is governed by the number of glucose molecules making up the cyclodextrin units of the channel. A detailed mechanism is proposed for ion transport through these channels. Findings from this study will aid in designing cyclodextrin-based channels that could be either cation-selective or anion-selective, by modifying the linkages of the channel or the number of glucose molecules in the cyclodextrin rings.
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Affiliation(s)
- Pratyusha Musunuru
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Siladitya Padhi
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500 081, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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Lee J, Kang M, Kim S, Chang I. Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity. PLoS Comput Biol 2020; 16:e1007405. [PMID: 32315300 PMCID: PMC7173763 DOI: 10.1371/journal.pcbi.1007405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/13/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding the gating mechanism of ion channel proteins is key to understanding the regulation of cell signaling through these channels. Channel opening and closing are regulated by diverse environmental factors that include temperature, electrical voltage across the channel, and proton concentration. Low permeability in voltage-gated potassium ion channels (Kv) is intimately correlated with the prolonged action potential duration observed in many acidosis diseases. The Kv channels consist of voltage-sensing domains (S1-S4 helices) and central pore domains (S5-S6 helices) that include a selectivity filter and water-filled cavity. The voltage-sensing domain is responsible for the voltage-gating of Kv channels. While the low permeability of Kv channels to potassium ion is highly correlated with the cellular proton concentration, it is unclear how an intracellular acidic condition drives their closure, which may indicate an additional pH-dependent gating mechanism of the Kv family. Here, we show that two residues E327 and H418 in the proximity of the water cavity of Kv1.2 play crucial roles as a pH switch. In addition, we present a structural and molecular concept of the pH-dependent gating of Kv1.2 in atomic detail, showing that the protonation of E327 and H418 disrupts the electrostatic balance around the S6 helices, which leads to a straightening transition in the shape of their axes and causes dewetting of the water-filled cavity and closure of the channel. Our work offers a conceptual advancement to the regulation of the pH-dependent gating of various voltage-gated ion channels and their related biological functions.
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Affiliation(s)
- Juhwan Lee
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Department of Emerging Material Sciences, DGIST, Daegu, Korea
- Core Protein Resources Center, DGIST, Daegu, Korea
| | - Mooseok Kang
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, Korea
| | - Sangyeol Kim
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
- * E-mail: (SK); (IC)
| | - Iksoo Chang
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Core Protein Resources Center, DGIST, Daegu, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
- * E-mail: (SK); (IC)
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6
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Tikhonov DB, Zhorov BS. Intersegment contacts determine geometry of the open and closed states in P-loop channels. J Biomol Struct Dyn 2019; 38:1012-1027. [DOI: 10.1080/07391102.2019.1592026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Denis B. Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Boris S. Zhorov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russian Federation
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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7
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Atomistic modeling and molecular dynamics analysis of human Ca V1.2 channel using external electric field and ion pulling simulations. Biochim Biophys Acta Gen Subj 2019; 1863:1116-1126. [PMID: 30978379 DOI: 10.1016/j.bbagen.2019.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human CaV1.2 (hCav1.2), a calcium selective voltage-gated channel, plays important roles in normal cardiac and neuronal functions. Calcium influx and gating mechanisms leading to the activation of hCaV1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCaV1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCaV1.2 model and studying calcium influx using computational approaches. METHODS We employed homology modeling and molecular dynamics (MD) to build the structure of hCaV1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCaV1.2. RESULTS We report a comprehensive three-dimensional model of a closed state hCaV1.2 refined under physiological membrane-bound conditions using MD simulations. Our SMD simulations on the model revealed four important barriers for ion permeation: this includes three calcium binding sites formed by the EEEE- and TTTT- rings within the selectivity filter region and a large barrier rendered by the hydrophobic internal gate. Our results also revealed that the first hydration shell of calcium remained intact throughout the simulations, thus playing an important role in ion permeation in hCaV1.2. CONCLUSIONS Our results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCaV1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation.
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8
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Li S, Wu B, Han W. Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins. J Phys Chem B 2019; 123:2254-2269. [DOI: 10.1021/acs.jpcb.8b11244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shu Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bohua Wu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. J Physiol 2018; 597:679-698. [PMID: 30471114 DOI: 10.1113/jp277088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all-atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage-gated channels from the KV and NaV families, which have garnered many successes and engendered several long-standing controversies regarding the nature of their structure-function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Chemistry Department, American River College, Sacramento, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
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The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations. SENSORS 2018; 18:s18093143. [PMID: 30231473 PMCID: PMC6163810 DOI: 10.3390/s18093143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGICs) to carry Na+ and K+ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently, the structure of a number of VGICs was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains (VSDs), each formed from four transmembrane (TM) segments, plus a pore domain through which ions move. Understanding the gating mechanism (how the channel opens and closes) requires structures. One TM segment (S4) has an arginine in every third position, with one such segment per domain. It is usually assumed that these arginines are all ionized, and in the resting state are held toward the intracellular side of the membrane by voltage across the membrane. They are assumed to move outward (extracellular direction) when released by depolarization of this voltage, producing a capacitive gating current and opening the channel. We suggest alternate interpretations of the evidence that led to these models. Measured gating current is the total charge displacement of all atoms in the VSD; we propose that the prime, but not sole, contributor is proton motion, not displacement of the charges on the arginines of S4. It is known that the VSD can conduct protons. Quantum calculations on the Kv1.2 potassium channel VSD show how; the key is the amphoteric nature of the arginine side chain, which allows it to transfer a proton. This appears to be the first time the arginine side chain has had its amphoteric character considered. We have calculated one such proton transfer in detail: this proton starts from a tyrosine that can ionize, transferring to the NE of the third arginine on S4; that arginine’s NH then transfers a proton to a glutamate. The backbone remains static. A mutation predicted to affect the proton transfer has been qualitatively confirmed experimentally, from the change in the gating current-voltage curve. The total charge displacement in going from a normal closed potential of −70 mV across the membrane to 0 mV (open), is calculated to be approximately consistent with measured values, although the error limits on the calculation require caution in interpretation.
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11
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Rashid MH, Kuyucak S. Computational Study of the Loss-of-Function Mutations in the Kv1.5 Channel Associated with Atrial Fibrillation. ACS OMEGA 2018; 3:8882-8890. [PMID: 31459020 PMCID: PMC6645308 DOI: 10.1021/acsomega.8b01094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/31/2018] [Indexed: 06/10/2023]
Abstract
Atrial fibrillation (AF) is a heart disease caused by defective ion channels in the atria, which affect the action potential (AP) duration and disturb normal heart rhythm. Rapid firing of APs in neighboring atrial cells is a common mechanism of AF, and therefore, therapeutic approaches have focused on extending the AP duration by inhibiting the K+ channels involved in repolarization. Of these, Kv1.5 that carries the I Kur current is a promising target because it is expressed mainly in atria and not in ventricles. In genetic studies of AF patients, both loss-of-function and gain-of-function mutations in Kv1.5 have been identified, indicating that either decreased or increased I Kur currents could trigger AF. Blocking of already downregulated Kv1.5 channels could cause AF to become chronic. Thus, a molecular-level understanding of how the loss-of-function mutations in Kv1.5 affect I Kur would be useful for developing new therapeutics. Here, we perform molecular dynamics simulations to study the effect of three loss-of-function mutations in the pore domain of Kv1.5 on ion permeation. Comparison of the pore structures and ion free energies in the wild-type and mutant Kv1.5 channels indicates that conformational changes in the selectivity filter could hinder ion permeation in the mutant channels.
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Affiliation(s)
- Md Harunur Rashid
- Department of Chemistry,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia
| | - Serdar Kuyucak
- School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia
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12
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Wawrzkiewicz-Jałowiecka A, Grzywna ZJ. The role of entropic potential in voltage activation and K + transport through Kv 1.2 channels. J Chem Phys 2018; 148:115103. [PMID: 29566502 DOI: 10.1063/1.5011298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze the entropic effects of inner pore geometry changes of Kv 1.2 channel during membrane depolarization and their implications for the rate of transmembrane transport of potassium ions. We base this on the idea that spatial confinements within the channel pore give rise to entropic barriers which can both effectively affect the stability of open macroconformation and influence channel's ability to conduct the potassium ions through the membrane. First, we calculate the differences in entropy between voltage-activated and resting states of the channel. As a template, we take a set of structures of channel pore in an open state at different membrane potentials generated in our previous research. The obtained results indicate that tendency to occupy open states at membrane depolarization is entropy facilitated. Second, we describe the differences in rates of K+ transport through the channel pore at different voltages based on the results of appropriate random walk simulations in entropic and electric potentials. The simulated single channel currents (I) suggest that the geometry changes during membrane depolarization are an important factor contributing to the observed flow of potassium ions through the channel. Nevertheless, the charge distribution within the channel pore (especially at the extracellular entrance) seems most prominent for the observed I/Imax relation at a qualitative level at analyzed voltages.
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Affiliation(s)
- Agata Wawrzkiewicz-Jałowiecka
- Faculty of Chemistry, Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland
| | - Zbigniew J Grzywna
- Faculty of Chemistry, Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland
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13
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Jalily Hasani H, Ganesan A, Ahmed M, Barakat KH. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PLoS One 2018; 13:e0191905. [PMID: 29444113 PMCID: PMC5812580 DOI: 10.1371/journal.pone.0191905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/12/2018] [Indexed: 12/23/2022] Open
Abstract
The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel that lead to cardiotoxic effects.
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Affiliation(s)
- Horia Jalily Hasani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Aravindhan Ganesan
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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14
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Högel P, Götz A, Kuhne F, Ebert M, Stelzer W, Rand KD, Scharnagl C, Langosch D. Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix. Biochemistry 2018; 57:1326-1337. [DOI: 10.1021/acs.biochem.7b01197] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Philipp Högel
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Alexander Götz
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Felix Kuhne
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Maximilian Ebert
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Walter Stelzer
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christina Scharnagl
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
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15
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Padhi S, Reddy LK, Priyakumar UD. pH-mediated gating and formate transport mechanism in the Escherichia coli formate channel. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1353691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Siladitya Padhi
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Lekkala Karthik Reddy
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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16
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Starek G, Freites JA, Bernèche S, Tobias DJ. Gating energetics of a voltage-dependent K + channel pore domain. J Comput Chem 2017; 38:1472-1478. [PMID: 28211063 DOI: 10.1002/jcc.24742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/14/2023]
Abstract
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities. We found that the extent of hydration of the interior of the pore domain could influence the free energy landscape for pore opening/closing. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Greg Starek
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland.,Department of Chemistry, University of California, Irvine, California, 92697-2025
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, California, 92697-2025
| | - Simon Bernèche
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, California, 92697-2025
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17
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Fowler PW, Sansom MSP, Reithmeier RAF. Effect of the Southeast Asian Ovalocytosis Deletion on the Conformational Dynamics of Signal-Anchor Transmembrane Segment 1 of Red Cell Anion Exchanger 1 (AE1, Band 3, or SLC4A1). Biochemistry 2017; 56:712-722. [PMID: 28068080 PMCID: PMC5299548 DOI: 10.1021/acs.biochem.6b00966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The first transmembrane (TM1) helix in the red cell anion exchanger (AE1, Band 3, or SLC4A1) acts as an internal signal anchor that binds the signal recognition particle and directs the nascent polypeptide chain to the endoplasmic reticulum (ER) membrane where it moves from the translocon laterally into the lipid bilayer. The sequence N-terminal to TM1 forms an amphipathic helix that lies at the membrane interface and is connected to TM1 by a bend at Pro403. Southeast Asian ovalocytosis (SAO) is a red cell abnormality caused by a nine-amino acid deletion (Ala400-Ala408) at the N-terminus of TM1. Here we demonstrate, by extensive (∼4.5 μs) molecular dynamics simulations of TM1 in a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membrane, that the isolated TM1 peptide is highly dynamic and samples the structure of TM1 seen in the crystal structure of the membrane domain of AE1. The SAO deletion not only removes the proline-induced bend but also causes a "pulling in" of the part of the amphipathic helix into the hydrophobic phase of the bilayer, as well as the C-terminal of the peptide. The dynamics of the SAO peptide very infrequently resembles the structure of TM1 in AE1, demonstrating the disruptive effect the SAO deletion has on AE1 folding. These results provide a precise molecular view of the disposition and dynamics of wild-type and SAO TM1 in a lipid bilayer, an important early biosynthetic intermediate in the insertion of AE1 into the ER membrane, and extend earlier results of cell-free translation experiments.
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Affiliation(s)
- Philip W Fowler
- 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
| | - Reinhart A F Reithmeier
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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18
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Pearlstein RA, Dickson CJ, Hornak V. Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:177-194. [PMID: 27836643 DOI: 10.1016/j.bbamem.2016.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/28/2016] [Accepted: 11/06/2016] [Indexed: 01/27/2023]
Abstract
The membrane dipole potential (Ψd) constitutes one of three electrical potentials generated by cell membranes. Ψd arises from the unfavorable parallel alignment of phospholipid and water dipoles, and varies in magnitude both longitudinally and laterally across the bilayer according to membrane composition and phospholipid packing density. In this work, we propose that dynamic counter-balancing between Ψd and the transmembrane potential (ΔΨm) governs the conformational state transitions of voltage-gated ion channels. Ψd consists of 1) static outer, and dynamic inner leaflet components (Ψd(extra) and Ψd(intra), respectively); and 2) a transmembrane component (ΔΨd(inner-outer)), ariing from differences in intra- and extracellular leaflet composition. Ψd(intra), which transitions between high and low energy states (Ψd(intra, high) and Ψd(intra, low)) as a function of channel conformation, is transduced by the pore domain. ΔΨd(inner-outer) is transduced by the voltage-sensing (VS) domain in summation with ΔΨm. Potentiation of voltage-gated ion channels is of interest for the treatment of cardiac, neuronal, and other disorders arising from inherited/acquired ion channel dysfunction. Potentiators are widely believed to alter the rates and voltage-dependencies of channel gating transitions by binding to pockets in the membrane-facing and other regions of ion channel targets. Here, we propose that potentiators alter Ψd(intra) and/or Ψd(extra), thereby increasing or decreasing the energy barriers governing channel gating transitions. We used quantum mechanical and molecular dynamics (MD) simulations to predict the overall Ψd-modulating effects of a series of published positive hERG potentiators partitioned into model DOPC bilayers. Our findings suggest a strong correlation between the magnitude of Ψd-lowering and positive hERG potentiation across the series.
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Affiliation(s)
- Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA.
| | - Callum J Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
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19
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TRPV1: A Target for Rational Drug Design. Pharmaceuticals (Basel) 2016; 9:ph9030052. [PMID: 27563913 PMCID: PMC5039505 DOI: 10.3390/ph9030052] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/12/2016] [Accepted: 08/18/2016] [Indexed: 12/18/2022] Open
Abstract
Transient Receptor Potential Vanilloid 1 (TRPV1) is a non-selective, Ca2+ permeable cation channel activated by noxious heat, and chemical ligands, such as capsaicin and resiniferatoxin (RTX). Many compounds have been developed that either activate or inhibit TRPV1, but none of them are in routine clinical practice. This review will discuss the rationale for antagonists and agonists of TRPV1 for pain relief and other conditions, and strategies to develop new, better drugs to target this ion channel, using the newly available high-resolution structures.
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20
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Shelar A, Bansal M. Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2804-2817. [PMID: 27521749 DOI: 10.1016/j.bbamem.2016.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/07/2016] [Indexed: 12/11/2022]
Abstract
Transmembrane (TM) helices in integral membrane proteins are primarily α-helical in structure. Here we analyze 1134 TM helices in 90 high resolution membrane proteins and find that apart from the widely prevalent α-helices, TM regions also contain stretches of 310 (3 to 8 residues) and π-helices (5 to 19 residues) with distinct sequence signatures. The various helix perturbations in TM regions comprise of helices with kinked geometry, as well as those with an interspersed 310/π-helical fragment and show high occurrence in a few membrane proteins. Proline is frequently present at sites of these perturbations, but it is neither a necessary nor a sufficient requirement. Helix perturbations are also conserved within a family of membrane proteins despite low sequence identity in the perturbed region. Furthermore, a perturbation influences the geometry of the TM helix, mediates inter-helical interactions within and across protein chains and avoids hydrophobic mismatch of the helix termini with the bilayer. An analysis of π-helices in the TM regions of the heme copper oxidase superfamily shows that interspersed π-helices can vary in length from 6 to 19 amino acids or be entirely absent, depending upon the protein function. The results presented here would be helpful for prediction of 310 and π-helices in TM regions and can assist the computational design of membrane proteins.
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Affiliation(s)
- Ashish Shelar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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21
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Wawrzkiewicz-Jałowiecka A, Borys P, Grzywna ZJ. On Application Of Langevin Dynamics In Logarithmic Potential To Model Ion Channel Gate Activity. Cell Mol Biol Lett 2016; 20:663-84. [PMID: 26317442 DOI: 10.1515/cmble-2015-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 08/07/2015] [Indexed: 11/15/2022] Open
Abstract
We model the activity of an ion channel gate by Langevin dynamics in a logarithmic potential. This approach enables one to describe the power-law dwell-time distributions of the considered system, and the long-term correlations between the durations of the subsequent channel states, or fractal scaling of statistical characteristics of the gate's movement with time. Activity of an ion channel gate is described as an overdamped motion of the reaction coordinate in a confining logarithmic potential, which ensures great flexibility of the model. Depending on the chosen parameters, it allows one to reproduce many types of gate dynamics within the family of non-Markovian, anomalous conformational diffusion processes. In this study we apply the constructed model to largeconductance voltage and Ca2+-activated potassium channels (BKCa). The interpretation of model assumptions and parameters is provided in terms of this biological system. Our results show good agreement with the experimental data.
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22
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Grafting voltage and pharmacological sensitivity in potassium channels. Cell Res 2016; 26:935-45. [PMID: 27174053 DOI: 10.1038/cr.2016.57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/04/2016] [Accepted: 03/29/2016] [Indexed: 11/08/2022] Open
Abstract
A classical voltage-gated ion channel consists of four voltage-sensing domains (VSDs). However, the roles of each VSD in the channels remain elusive. We developed a GVTDT (Graft VSD To Dimeric TASK3 channels that lack endogenous VSDs) strategy to produce voltage-gated channels with a reduced number of VSDs. TASK3 channels exhibit a high host tolerance to VSDs of various voltage-gated ion channels without interfering with the intrinsic properties of the TASK3 selectivity filter. The constructed channels, exemplified by the channels grafted with one or two VSDs from Kv7.1 channels, exhibit classical voltage sensitivity, including voltage-dependent opening and closing. Furthermore, the grafted Kv7.1 VSD transfers the potentiation activity of benzbromarone, an activator that acts on the VSDs of the donor channels, to the constructed channels. Our study indicates that one VSD is sufficient to voltage-dependently gate the pore and provides new insight into the roles of VSDs.
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23
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Brown PMGE, Aurousseau MRP, Musgaard M, Biggin PC, Bowie D. Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. J Physiol 2016; 594:1821-40. [PMID: 26682513 PMCID: PMC4818602 DOI: 10.1113/jp271690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 12/07/2015] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Kainate receptor heteromerization and auxiliary subunits, Neto1 and Neto2, attenuate polyamine ion-channel block by facilitating blocker permeation. Relief of polyamine block in GluK2/GluK5 heteromers results from a key proline residue that produces architectural changes in the channel pore α-helical region. Auxiliary subunits exert an additive effect to heteromerization, and thus relief of polyamine block is due to a different mechanism. Our findings have broad implications for work on polyamine block of other cation-selective ion channels. ABSTRACT Channel block and permeation by cytoplasmic polyamines is a common feature of many cation-selective ion channels. Although the channel block mechanism has been studied extensively, polyamine permeation has been considered less significant as it occurs at extreme positive membrane potentials. Here, we show that kainate receptor (KAR) heteromerization and association with auxiliary proteins, Neto1 and Neto2, attenuate polyamine block by enhancing blocker permeation. Consequently, polyamine permeation and unblock occur at more negative and physiologically relevant membrane potentials. In GluK2/GluK5 heteromers, enhanced permeation is due to a single proline residue in GluK5 that alters the dynamics of the α-helical region of the selectivity filter. The effect of auxiliary proteins is additive, and therefore the structural basis of polyamine permeation and unblock is through a different mechanism. As native receptors are thought to assemble as heteromers in complex with auxiliary proteins, our data identify an unappreciated impact of polyamine permeation in shaping the signalling properties of neuronal KARs and point to a structural mechanism that may be shared amongst other cation-selective ion channels.
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Affiliation(s)
- Patricia M G E Brown
- Integrated Program in Neurosciences, McGill University, Montréal, Québec, Canada, H3G 0B1
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada, H3G 0B1
| | - Mark R P Aurousseau
- Graduate Program in Pharmacology, McGill University, Montréal, Québec, Canada, H3G 0B1
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada, H3G 0B1
| | - Maria Musgaard
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada, H3G 0B1
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24
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Taghian T, Narmoneva DA, Kogan AB. Modulation of cell function by electric field: a high-resolution analysis. J R Soc Interface 2016; 12:rsif.2015.0153. [PMID: 25994294 DOI: 10.1098/rsif.2015.0153] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Regulation of cell function by a non-thermal, physiological-level electromagnetic field has potential for vascular tissue healing therapies and advancing hybrid bioelectronic technology. We have recently demonstrated that a physiological electric field (EF) applied wirelessly can regulate intracellular signalling and cell function in a frequency-dependent manner. However, the mechanism for such regulation is not well understood. Here, we present a systematic numerical study of a cell-field interaction following cell exposure to the external EF. We use a realistic experimental environment that also recapitulates the absence of a direct electric contact between the field-sourcing electrodes and the cells or the culture medium. We identify characteristic regimes and present their classification with respect to frequency, location, and the electrical properties of the model components. The results show a striking difference in the frequency dependence of EF penetration and cell response between cells suspended in an electrolyte and cells attached to a substrate. The EF structure in the cell is strongly inhomogeneous and is sensitive to the physical properties of the cell and its environment. These findings provide insight into the mechanisms for frequency-dependent cell responses to EF that regulate cell function, which may have important implications for EF-based therapies and biotechnology development.
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Affiliation(s)
- T Taghian
- Department of Physics, University of Cincinnati, 345 Clifton Court, RM 400 Geo/Physics Building, Cincinnati, OH 45221-0011, USA
| | - D A Narmoneva
- Department of Biomedical, Chemical, and Environmental Engineering, University of Cincinnati, 2901 Woodside Dr., ML 0012, Cincinnati, OH 45221, USA
| | - A B Kogan
- Department of Physics, University of Cincinnati, 345 Clifton Court, RM 400 Geo/Physics Building, Cincinnati, OH 45221-0011, USA
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25
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Sun H, Chen P, Li D, Li Y, Hou T. Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1. J Chem Theory Comput 2016; 12:851-60. [DOI: 10.1021/acs.jctc.5b00973] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
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26
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Posson DJ, Rusinova R, Andersen OS, Nimigean CM. Calcium ions open a selectivity filter gate during activation of the MthK potassium channel. Nat Commun 2015; 6:8342. [PMID: 26395539 PMCID: PMC4580985 DOI: 10.1038/ncomms9342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/11/2015] [Indexed: 12/25/2022] Open
Abstract
Ion channel opening and closing are fundamental to cellular signalling and homeostasis. Gates that control K+ channel activity were found both at an intracellular pore constriction and within the selectivity filter near the extracellular side but the specific location of the gate that opens Ca2+-activated K+ channels has remained elusive. Using the Methanobacterium thermoautotrophicum homologue (MthK) and a stopped-flow fluorometric assay for fast channel activation, we show that intracellular quaternary ammonium blockers bind to closed MthK channels. Since the blockers are known to bind inside a central channel cavity, past the intracellular entryway, the gate must be within the selectivity filter. Furthermore, the blockers access the closed channel slower than the open channel, suggesting that the intracellular entryway narrows upon pore closure, without preventing access of either the blockers or the smaller K+. Thus, Ca2+-dependent gating in MthK occurs at the selectivity filter with coupled movement of the intracellular helices. Ion channels open and close to allow the regulated passage of ions through the membrane. Here the authors use selective ion channel blockers to analyse this regulation in a potassium channel and show that the gate is in the selectivity filter, past the entrance to the channel.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Radda Rusinova
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA.,Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA
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27
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Zíma V, Witschas K, Hynkova A, Zímová L, Barvík I, Vlachova V. Structural modeling and patch-clamp analysis of pain-related mutation TRPA1-N855S reveal inter-subunit salt bridges stabilizing the channel open state. Neuropharmacology 2015; 93:294-307. [DOI: 10.1016/j.neuropharm.2015.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/14/2015] [Accepted: 02/16/2015] [Indexed: 11/28/2022]
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28
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Dai J, Wollmuth LP, Zhou HX. Mechanism-Based Mathematical Model for Gating of Ionotropic Glutamate Receptors. J Phys Chem B 2015; 119:10934-40. [PMID: 25793415 DOI: 10.1021/acs.jpcb.5b00521] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a mathematical model for ionotropic glutamate receptors (iGluR's) that is built on mechanistic understanding and yields a number of thermodynamic and kinetic properties of channel gating. iGluR's are ligand-gated ion channels responsible for the vast majority of fast excitatory neurotransmission in the central nervous system. The effects of agonist-induced closure of the ligand-binding domain (LBD) are transmitted to the transmembrane channel (TMC) via interdomain linkers. Our model demonstrates that, relative to full agonists, partial agonists may reduce either the degree of LBD closure or the curvature of the LBD free energy basin, leading to less stabilization of the channel open state and hence lower channel open probability. A rigorous relation is derived between the channel closed-to-open free energy difference and the tension within the linker. Finally, by treating LBD closure and TMC opening as diffusive motions, we obtain gating trajectories that resemble stochastic current traces from single-channel recordings and calculate the rate constants for transitions between the channel open and closed states. Our model can be implemented by molecular dynamics simulations to realistically depict iGluR gating and may guide functional experiments in gaining deeper insight into this essential family of channel proteins.
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Affiliation(s)
- Jian Dai
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Lonnie P Wollmuth
- Department of Neurobiology and Behavior and Center for Nervous System Disorders, Stony Brook University , Stony Brook, New York 11794, United States
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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29
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Lörinczi É, Gómez-Posada JC, de la Peña P, Tomczak AP, Fernández-Trillo J, Leipscher U, Stühmer W, Barros F, Pardo LA. Voltage-dependent gating of KCNH potassium channels lacking a covalent link between voltage-sensing and pore domains. Nat Commun 2015; 6:6672. [PMID: 25818916 PMCID: PMC4389246 DOI: 10.1038/ncomms7672] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 02/18/2015] [Indexed: 12/25/2022] Open
Abstract
Voltage-gated channels open paths for ion permeation upon changes in membrane potential, but how voltage changes are coupled to gating is not entirely understood. Two modules can be recognized in voltage-gated potassium channels, one responsible for voltage sensing (transmembrane segments S1 to S4), the other for permeation (S5 and S6). It is generally assumed that the conversion of a conformational change in the voltage sensor into channel gating occurs through the intracellular S4–S5 linker that provides physical continuity between the two regions. Using the pathophysiologically relevant KCNH family, we show that truncated proteins interrupted at, or lacking the S4–S5 linker produce voltage-gated channels in a heterologous model that recapitulate both the voltage-sensing and permeation properties of the complete protein. These observations indicate that voltage sensing by the S4 segment is transduced to the channel gate in the absence of physical continuity between the modules. The pore of voltage-gated ion channels opens in response to membrane depolarization sensed by a separate voltage-sensing domain. Here, Lörinczi et al. show that, contrary to assumptions, no physical linker is required to transmit changes from the voltage-sensing to the permeation domain of KCNH channels.
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Affiliation(s)
- Éva Lörinczi
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Juan Camilo Gómez-Posada
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Pilar de la Peña
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006 Oviedo, Spain
| | - Adam P Tomczak
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Jorge Fernández-Trillo
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Ulrike Leipscher
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Walter Stühmer
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073 Göttingen, Germany
| | - Francisco Barros
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, Campus de El Cristo, 33006 Oviedo, Spain
| | - Luis A Pardo
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
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30
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De Simone A, Mote KR, Veglia G. Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations. Biophys J 2015; 106:2566-76. [PMID: 24940774 DOI: 10.1016/j.bpj.2014.03.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023] Open
Abstract
Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes.
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Affiliation(s)
- Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Kaustubh R Mote
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota; Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota.
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31
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Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, Forrest LR, Newstead S. Gating topology of the proton-coupled oligopeptide symporters. Structure 2015; 23:290-301. [PMID: 25651061 PMCID: PMC4321885 DOI: 10.1016/j.str.2014.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/10/2023]
Abstract
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | | | - Sebastian Radestock
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia M Dijkman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Jane Kwok
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lucy R Forrest
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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32
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Reduced curvature of ligand-binding domain free-energy surface underlies partial agonism at NMDA receptors. Structure 2014; 23:228-236. [PMID: 25543253 DOI: 10.1016/j.str.2014.11.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/04/2014] [Accepted: 11/14/2014] [Indexed: 01/17/2023]
Abstract
NMDA receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. Partial agonists elicit submaximal channel activation, but crystal structures of the ligand-binding domains (LBDs) bound with partial and full agonists show little difference. To uncover the molecular mechanism for partial agonism, here we computed the free-energy surfaces of the GluN1 (an obligatory subunit of NMDA receptors) LBD bound with a variety of ligands. The free-energy minima are similarly positioned for full and partial agonists, but the curvatures are significantly reduced in the latter case, indicating higher probabilities for sampling conformations with a not fully closed domain cleft. The free-energy surfaces for antagonists have both shifted minima and further reduced curvatures. Reduced curvature of free-energy surface appears to explain well the partial agonism at NMDA receptors and may present a unique paradigm in producing graded responses for receptors in general.
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33
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Hsu HJ, Lin MH, Schindler C, Fischer WB. Structure based computational assessment of channel properties of assembled ORF-8a from SARS-CoV. Proteins 2014; 83:300-8. [PMID: 25394339 PMCID: PMC7167713 DOI: 10.1002/prot.24721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 10/30/2014] [Accepted: 10/30/2014] [Indexed: 01/21/2023]
Abstract
ORF 8a is a short 39 amino acid bitopic membrane protein encoded by severe acute respiratory syndrome causing corona virus (SARS‐CoV). It has been identified to increase permeability of the lipid membrane for cations. Permeability is suggested to occur due to the assembly of helical bundles. Computational models of a pentameric assembly of 8a peptides are generated using the first 22 amino acids, which include the transmembrane domain. Low energy structures reveal a hydrophilic pore mantled by residues Thr‐8, and −18, Ser‐11, Cys‐13, and Arg‐22. Potential of mean force (PMF) profiles for mono (Na+, K+, Cl−) and divalent (Ca2+) ions along the pore are calculated. The data support experimental findings of a weak cation selectivity of the channel. Calculations on 8a are compared to data derived for a pentameric bundle consisting of the M2 helices of the bacterial pentameric ligand gated ion channel GLIC (3EHZ). PMF curves of both, bundles 8a and M2, show sigmoidal shaped profiles. In comparison to the data for the M2‐GLIC model, data of the 8a bundle show lower amplitude of the PMF values between maximum and minimum and less discrimination amongst ions. Proteins 2015; 83:300–308. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Hao-Jen Hsu
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, 112, Taiwan; Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, 112, Taiwan
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34
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Wilman HR, Ebejer JP, Shi J, Deane CM, Knapp B. Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J Chem Inf Model 2014; 54:2585-93. [DOI: 10.1021/ci500403a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Henry R. Wilman
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Jean-Paul Ebejer
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Jiye Shi
- UCB Celltech, a branch of UCB Pharma S. A., 208 Bath Road, Slough SL1 3WE, U.K
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
| | - Bernhard Knapp
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K
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35
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Martinez-Morales E, Snyders DJ, Labro AJ. Mutations in the S6 gate isolate a late step in the activation pathway and reduce 4-AP sensitivity in shaker K(v) channel. Biophys J 2014; 106:134-44. [PMID: 24411245 DOI: 10.1016/j.bpj.2013.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/28/2013] [Accepted: 11/12/2013] [Indexed: 01/12/2023] Open
Abstract
Kv channels detect changes in the membrane potential via their voltage-sensing domains (VSDs) that control the status of the S6 bundle crossing (BC) gate. The movement of the VSDs results in a transfer of the S4 gating charges across the cell membrane but only the last 10-20% of the total gating charge movement is associated with BC gate opening, which involves cooperative transition(s) in the subunits. Substituting the proline residue P475 in the S6 of the Shaker channel by a glycine or alanine causes a considerable shift in the voltage-dependence of the cooperative transition(s) of BC gate opening, effectively isolating the late gating charge component from the other gating charge that originates from earlier VSD movements. Interestingly, both mutations also abolished Shaker's sensitivity to 4-aminopyridine, which is a pharmacological tool to isolate the late gating charge component. The alanine substitution (that would promote a α-helical configuration compared to proline) resulted in the largest separation of both gating charge components; therefore, BC gate flexibility appears to be important for enabling the late cooperative step of channel opening.
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Affiliation(s)
- Evelyn Martinez-Morales
- Laboratory for Molecular Biophysics, Physiology and Pharmacology, University of Antwerp, Antwerp, Belgium
| | - Dirk J Snyders
- Laboratory for Molecular Biophysics, Physiology and Pharmacology, University of Antwerp, Antwerp, Belgium
| | - Alain J Labro
- Laboratory for Molecular Biophysics, Physiology and Pharmacology, University of Antwerp, Antwerp, Belgium.
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36
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KCNC3(R420H), a K(+) channel mutation causative in spinocerebellar ataxia 13 displays aberrant intracellular trafficking. Neurobiol Dis 2014; 71:270-9. [PMID: 25152487 DOI: 10.1016/j.nbd.2014.08.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/29/2014] [Accepted: 08/13/2014] [Indexed: 12/23/2022] Open
Abstract
Spinocerebellar ataxia 13 (SCA13) is an autosomal dominant disease resulting from mutations in KCNC3 (Kv3.3), a voltage-gated potassium channel. The KCNC3(R420H) mutation was first identified as causative for SCA13 in a four-generation Filipino kindred with over 20 affected individuals. Electrophysiological analyses in oocytes previously showed that this mutation did not lead to a functional channel and displayed a dominant negative phenotype. In an effort to identify the molecular basis of this allelic form of SCA13, we first determined that human KCNC3(WT) and KCNC3(R420H) display disparate post-translational modifications, and the mutant protein has reduced complex glycan adducts. Immunohistochemical analyses demonstrated that KCNC3(R420H) was not properly trafficking to the plasma membrane and surface biotinylation demonstrated that KCNC3(R420H) exhibited only 24% as much surface expression as KCNC3(WT). KCNC3(R420H) trafficked through the ER but was retained in the Golgi. KCNC3(R420H) expression results in altered Golgi and cellular morphology. Electron microscopy of KCNC3(R420H) localization further supports retention in the Golgi. These results are specific to the KCNC3(R420H) allele and provide new insight into the molecular basis of disease manifestation in SCA13.
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37
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General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels. Nat Commun 2014; 5:4641. [PMID: 25105557 PMCID: PMC4133698 DOI: 10.1038/ncomms5641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/09/2014] [Indexed: 12/20/2022] Open
Abstract
The pore-lining helix (PLH) bundles are central to the function of all ion channels,
as their conformational rearrangements dictate channel gating. Here we explore all
plausible oligomeric arrangements of the PLH bundles within homomeric ion channels
by building models using generic restraints. In particular, the distance between two
neighbouring PLHs was bounded both below and above in order to avoid steric clash
and allow proper packing. The resulting models provide a theoretical representation
of the accessible space for oligomeric arrangements. While the represented space is
confined, it encompasses nearly all the ion channel PLH bundles for which the
structures are currently known. For a multitude of channels, gating models suggested
by paths within the confined accessible space are in qualitative agreement with
those established in previous structural and computational studies. Rearrangements of the pore-lining helix (PLH) bundles of ion channels
are central to their gating mechanisms. Here, Dai et al. use a modelling approach
to define the general rules that govern the arrangements and gating motions of the PLHs
in homomeric ion channels.
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38
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Sun H, Li Y, Tian S, Wang J, Hou T. P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape. PLoS Comput Biol 2014; 10:e1003729. [PMID: 25033171 PMCID: PMC4102447 DOI: 10.1371/journal.pcbi.1003729] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/02/2014] [Indexed: 01/04/2023] Open
Abstract
Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance. Cancers can eventually confer drug resistance to the continued medication. In most cases, mutations occurred in a drug target can attenuate the binding affinity of the drugs. Here, we studied the drug resistance mechanisms of the mutations G2032R in the ROS1 tyrosine kinase in fusion-type NSCLC. It is well known that the phosphate-binding loop (P-loop) plays a vital role in the binding of competitive inhibitors in tyrosine kinases, and numerous mutations have been found occurred around the P-loop, which may affect the binding/unbinding process of a drug. Free energy surfaces were constructed to characterize the impact of the mutation to the binding/unbinding process of a well-known NSCLC drug, crizotinib. Two advanced free energy calculation methods, namely funnel based well-tempered metadynamics and umbrella sampling based absolute binding free energy calculation achieved consistent results with the experimental data, suggesting that the rigid P-loop of the mutated target was mainly responsible for the crizotinib resistance to ROS1 tyrosine kinase.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Sheng Tian
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Junmei Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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39
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Stelzl LS, Fowler PW, Sansom MS, Beckstein O. Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol 2014; 426:735-51. [PMID: 24513108 PMCID: PMC3905165 DOI: 10.1016/j.jmb.2013.10.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 12/29/2022]
Abstract
The major facilitator superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling molecular dynamics method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free-energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepTSo, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin–spin distance measurements that have been interpreted to show occluded conformations. During the simulations, a salt bridge that has been postulated to be involved in driving the conformational transition formed. Our results argue against a simple rigid-body domain motion as implied by a strict “rocker-switch mechanism” and instead hint at an intricate coupling between two flexible gates. The transport mechanism of LacY is hypothesized to involve an intermediate “occluded” state. Such a state is observed in computer simulations of the conformational transitions. Simulation data are validated with experimental double electron–electron spin resonance measurements. The structural gating elements of LacY are identified. Occluded LacY is similar to known occluded structures of homologous proteins.
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Affiliation(s)
- Lukas S. Stelzl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philip W. Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author Department of Physics, Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287-1504, USA.
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40
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Fowler P, Abad E, Beckstein O, Sansom MSP. Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels. J Chem Theory Comput 2013; 9:5176-5189. [PMID: 24353479 PMCID: PMC3864263 DOI: 10.1021/ct4005933] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 12/18/2022]
Abstract
Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion-water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.
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Affiliation(s)
- Philip
W. Fowler
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Enrique Abad
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Oliver Beckstein
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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41
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Fowler P, Beckstein O, Abad E, Sansom MSP. Detailed Examination of a Single Conduction Event in a Potassium Channel. J Phys Chem Lett 2013; 4:3104-3109. [PMID: 24143269 PMCID: PMC3797101 DOI: 10.1021/jz4014079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/29/2013] [Indexed: 06/02/2023]
Abstract
Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using stratified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.1 paddle chimera and thereby identifies the expected stable configurations of ions and waters in the selectivity filter of the channel. We describe in detail the motions of the ions and waters during a conduction event, focusing on how waters and ions enter the filter, the rotation of water molecules inside the filter, and how potassium ions are coordinated as they move from a water to a protein environment. Finally, we analyze the small conformational changes undergone by the protein, showing that the stable configurations are most similar to the experimental crystal structure.
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Affiliation(s)
- Philip
W. Fowler
- Department of Biochemistry, University
of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | | | - Mark S. P. Sansom
- Department of Biochemistry, University
of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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