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Treptow W, Liu Y, Bassetto CAZ, Pinto BI, Alves Nunes JA, Uriarte RM, Chipot CJ, Bezanilla F, Roux B. Isoleucine gate blocks K + conduction in C-type inactivation. eLife 2024; 13:e97696. [PMID: 39530849 DOI: 10.7554/elife.97696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024] Open
Abstract
Many voltage-gated potassium (Kv) channels display a time-dependent phenomenon called C-type inactivation, whereby prolonged activation by voltage leads to the inhibition of ionic conduction, a process that involves a conformational change at the selectivity filter toward a non-conductive state. Recently, a high-resolution structure of a strongly inactivated triple-mutant channel kv1.2-kv2.1-3m revealed a novel conformation of the selectivity filter that is dilated at its outer end, distinct from the well-characterized conductive state. While the experimental structure was interpreted as the elusive non-conductive state, our molecular dynamics simulations and electrophysiological measurements show that the dilated filter of kv1.2-kv2.1-3m is conductive and, as such, cannot completely account for the inactivation of the channel observed in the structural experiments. The simulation shows that an additional conformational change, implicating isoleucine residues at position 398 along the pore lining segment S6, is required to effectively block ion conduction. The I398 residues from the four subunits act as a state-dependent hydrophobic gate located immediately beneath the selectivity filter. These observations are corroborated by electrophysiological experiments showing that ion permeation can be resumed in the kv1.2-kv2.1-3m channel when I398 is mutated to an asparagine-a mutation that does not abolish C-type inactivation since digitoxin (AgTxII) fails to block the ionic permeation of kv1.2-kv2.1-3m_I398N. As a critical piece of the C-type inactivation machinery, this structural feature is the potential target of a broad class of quaternary ammonium (QA) blockers and negatively charged activators thus opening new research directions toward the development of drugs that specifically modulate gating states of Kv channels.
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Affiliation(s)
- Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília, Brasilia, Brazil
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Yichen Liu
- Department of Neurobiology, The University of Chicago, Chicago, United States
| | - Carlos A Z Bassetto
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Bernardo I Pinto
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Joao Antonio Alves Nunes
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília, Brasilia, Brazil
| | - Ramon Mendoza Uriarte
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Christophe J Chipot
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019, Université de Lorraine, Université de Lorraine, Vandœuvre-lès-Nancy, France
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
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Kacher J, Sokolova OS, Tarek M. A Deep Learning Approach to Uncover Voltage-Gated Ion Channels' Intermediate States. J Phys Chem B 2024; 128:8724-8736. [PMID: 39213618 DOI: 10.1021/acs.jpcb.4c03182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Owing to recent advancements in cryo-electron microscopy, voltage-gated ion channels have gained a greater comprehension of their structural characteristics. However, a significant enigma remains unsolved for a large majority of these channels: their gating mechanism. This mechanism, which encompasses the conformational changes between open and closed states, is pivotal to their proper functioning. Beyond the binary states of open and closed, an ensemble of intermediate states defines the transition path in-between. Due to the lack of experimental data, one might resort to molecular dynamics simulations as an alternative to decipher these states and the transitions between them. However, the high-energy barriers and the colossal time scales involved hinder access to the latter. We present here an application of deep learning as a reliable pipeline for a comprehensive exploration of voltage-gated ion channel conformational rearrangements during gating. We showcase the pipeline performance specifically on the Kv1.2 voltage sensor domain and confront the results with existing data. We demonstrate how our physics-based deep learning approach contributes to the theoretical understanding of these channels and how it might provide further insights into the exploration of channelopathies.
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Affiliation(s)
- Julia Kacher
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia
- Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
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Tibery DV, Nunes JAA, da Mata DO, Menezes LFS, de Souza ACB, Fernandes-Pedrosa MDF, Treptow W, Schwartz EF. Unveiling Tst3, a Multi-Target Gating Modifier Scorpion α Toxin from Tityus stigmurus Venom of Northeast Brazil: Evaluation and Comparison with Well-Studied Ts3 Toxin of Tityus serrulatus. Toxins (Basel) 2024; 16:257. [PMID: 38922152 PMCID: PMC11209618 DOI: 10.3390/toxins16060257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Studies on the interaction sites of peptide toxins and ion channels typically involve site-directed mutations in toxins. However, natural mutant toxins exist among them, offering insights into how the evolutionary process has conserved crucial sequences for activities and molecular target selection. In this study, we present a comparative investigation using electrophysiological approaches and computational analysis between two alpha toxins from evolutionarily close scorpion species of the genus Tityus, namely, Tst3 and Ts3 from T. stigmurus and T. serrulatus, respectively. These toxins exhibit three natural substitutions near the C-terminal region, which is directly involved in the interaction between alpha toxins and Nav channels. Additionally, we characterized the activity of the Tst3 toxin on Nav1.1-Nav1.7 channels. The three natural changes between the toxins did not alter sensitivity to Nav1.4, maintaining similar intensities regarding their ability to alter opening probabilities, delay fast inactivation, and induce persistent currents. Computational analysis demonstrated a preference for the down conformation of VSD4 and a shift in the conformational equilibrium towards this state. This illustrates that the sequence of these toxins retained the necessary information, even with alterations in the interaction site region. Through electrophysiological and computational analyses, screening of the Tst3 toxin on sodium isoform revealed its classification as a classic α-NaTx with a broad spectrum of activity. It effectively delays fast inactivation across all tested isoforms. Structural analysis of molecular energetics at the interface of the VSD4-Tst3 complex further confirmed this effect.
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Affiliation(s)
- Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (D.V.T.); (D.O.d.M.); (L.F.S.M.); (A.C.B.d.S.)
| | - João Antonio Alves Nunes
- Laboratório de Biologia Teórica e Computacional (LBTC), Departamento de Biologia Celular, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (J.A.A.N.); (W.T.)
| | - Daniel Oliveira da Mata
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (D.V.T.); (D.O.d.M.); (L.F.S.M.); (A.C.B.d.S.)
| | - Luis Felipe Santos Menezes
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (D.V.T.); (D.O.d.M.); (L.F.S.M.); (A.C.B.d.S.)
| | - Adolfo Carlos Barros de Souza
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (D.V.T.); (D.O.d.M.); (L.F.S.M.); (A.C.B.d.S.)
| | - Matheus de Freitas Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte (UFRN), Natal 59012-570, Rio Grande do Norte, Brazil;
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Departamento de Biologia Celular, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (J.A.A.N.); (W.T.)
| | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília (UnB), Brasília 70910-900, Distrito Federal, Brazil; (D.V.T.); (D.O.d.M.); (L.F.S.M.); (A.C.B.d.S.)
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4
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Arcos-Hernández C, Nishigaki T. Ion currents through the voltage sensor domain of distinct families of proteins. J Biol Phys 2023; 49:393-413. [PMID: 37851173 PMCID: PMC10651576 DOI: 10.1007/s10867-023-09645-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
The membrane potential of a cell (Vm) regulates several physiological processes. The voltage sensor domain (VSD) is a region that confers voltage sensitivity to different types of transmembrane proteins such as the following: voltage-gated ion channels, the voltage-sensing phosphatase (Ci-VSP), and the sperm-specific Na+/H+ exchanger (sNHE). VSDs contain four transmembrane segments (S1-S4) and several positively charged amino acids in S4, which are essential for the voltage sensitivity of the protein. Generally, in response to changes of the Vm, the positive residues of S4 displace along the plasma membrane without generating ionic currents through this domain. However, some native (e.g., Hv1 channel) and mutants of VSDs produce ionic currents. These gating pore currents are usually observed in VSDs that lack one or more of the conserved positively charged amino acids in S4. The gating pore currents can also be induced by the isolation of a VSD from the rest of the protein domains. In this review, we summarize gating pore currents from all families of proteins with VSDs with classification into three cases: (1) pathological, (2) physiological, and (3) artificial currents. We reinforce the model in which the position of S4 that lacks the positively charged amino acid determines the voltage dependency of the gating pore current of all VSDs independent of protein families.
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Affiliation(s)
- César Arcos-Hernández
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
| | - Takuya Nishigaki
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
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5
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Kostritskii AY, Machtens JP. Domain- and state-specific shape of the electric field tunes voltage sensing in voltage-gated sodium channels. Biophys J 2023; 122:1807-1821. [PMID: 37077046 PMCID: PMC10209041 DOI: 10.1016/j.bpj.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023] Open
Abstract
The ability to sense transmembrane voltage underlies most physiological roles of voltage-gated sodium (Nav) channels. Whereas the key role of their voltage-sensing domains (VSDs) in channel activation is well established, the molecular underpinnings of voltage coupling remain incompletely understood. Voltage-dependent energetics of the activation process can be described in terms of the gating charge that is defined by coupling of charged residues to the external electric field. The shape of the electric field within VSDs is therefore crucial for the activation of voltage-gated ion channels. Here, we employed molecular dynamics simulations of cardiac Nav1.5 and bacterial NavAb, together with our recently developed tool g_elpot, to gain insights into the voltage-sensing mechanisms of Nav channels via high-resolution quantification of VSD electrostatics. In contrast to earlier low-resolution studies, we found that the electric field within VSDs of Nav channels has a complex isoform- and domain-specific shape, which prominently depends on the activation state of a VSD. Different VSDs vary not only in the length of the region where the electric field is focused but also differ in their overall electrostatics, with possible implications in the diverse ion selectivity of their gating pores. Due to state-dependent field reshaping, not only translocated basic but also relatively immobile acidic residues contribute significantly to the gating charge. In the case of NavAb, we found that the transition between structurally resolved activated and resting states results in a gating charge of 8e, which is noticeably lower than experimental estimates. Based on the analysis of VSD electrostatics in the two activation states, we propose that the VSD likely adopts a deeper resting state upon hyperpolarization. In conclusion, our results provide an atomic-level description of the gating charge, demonstrate diversity in VSD electrostatics, and reveal the importance of electric-field reshaping for voltage sensing in Nav channels.
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Affiliation(s)
- Andrei Y Kostritskii
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany; Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany.
| | - Jan-Philipp Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany; Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany.
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6
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Pantazis A, Kaneko M, Angelini M, Steccanella F, Westerlund AM, Lindström SH, Nilsson M, Delemotte L, Saitta SC, Olcese R. Tracking the motion of the K V1.2 voltage sensor reveals the molecular perturbations caused by a de novo mutation in a case of epilepsy. J Physiol 2020; 598:5245-5269. [PMID: 32833227 PMCID: PMC8923147 DOI: 10.1113/jp280438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
KEY POINTS KV1.2 channels, encoded by the KCNA2 gene, regulate neuronal excitability by conducting K+ upon depolarization. A new KCNA2 missense variant was discovered in a patient with epilepsy, causing amino acid substitution F302L at helix S4, in the KV1.2 voltage-sensing domain. Immunocytochemistry and flow cytometry showed that F302L does not impair KCNA2 subunit surface trafficking. Molecular dynamics simulations indicated that F302L alters the exposure of S4 residues to membrane lipids. Voltage clamp fluorometry revealed that the voltage-sensing domain of KV1.2-F302L channels is more sensitive to depolarization. Accordingly, KV1.2-F302L channels opened faster and at more negative potentials; however, they also exhibited enhanced inactivation: that is, F302L causes both gain- and loss-of-function effects. Coexpression of KCNA2-WT and -F302L did not fully rescue these effects. The proband's symptoms are more characteristic of patients with loss of KCNA2 function. Enhanced KV1.2 inactivation could lead to increased synaptic release in excitatory neurons, steering neuronal circuits towards epilepsy. ABSTRACT An exome-based diagnostic panel in an infant with epilepsy revealed a previously unreported de novo missense variant in KCNA2, which encodes voltage-gated K+ channel KV1.2. This variant causes substitution F302L, in helix S4 of the KV1.2 voltage-sensing domain (VSD). F302L does not affect KCNA2 subunit membrane trafficking. However, it does alter channel functional properties, accelerating channel opening at more hyperpolarized membrane potentials, indicating gain of function. F302L also caused loss of KV1.2 function via accelerated inactivation onset, decelerated recovery and shifted inactivation voltage dependence to more negative potentials. These effects, which are not fully rescued by coexpression of wild-type and mutant KCNA2 subunits, probably result from the enhancement of VSD function, as demonstrated by optically tracking VSD depolarization-evoked conformational rearrangements. In turn, molecular dynamics simulations suggest altered VSD exposure to membrane lipids. Compared to other encephalopathy patients with KCNA2 mutations, the proband exhibits mild neurological impairment, more characteristic of patients with KCNA2 loss of function. Based on this information, we propose a mechanism of epileptogenesis based on enhanced KV1.2 inactivation leading to increased synaptic release preferentially in excitatory neurons, and hence the perturbation of the excitatory/inhibitory balance of neuronal circuits.
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Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
- Wallenberg Center for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Maki Kaneko
- Center for Personalized Medicine, Children's Hospital, Los Angeles, Los Angeles, CA, USA
- Division of Genomic Medicine, Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Marina Angelini
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Federica Steccanella
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah H Lindström
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Michelle Nilsson
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sulagna C Saitta
- Department of Obstetrics and Gynecology and Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Brain Research Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
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7
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Silva MA, Kiametis AS, Treptow W. Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature. J Chem Inf Model 2020; 60:3463-3471. [PMID: 32096991 DOI: 10.1021/acs.jcim.9b01073] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Donepezil is a second generation acetylcholinesterase (AChE) inhibitor for treatment of Alzheimer's disease (AD). AChE is important for neurotransmission at neuromuscular junctions and cholinergic brain synapses by hydrolyzing acetylcholine into acetate and choline. In vitro data support that donepezil is a reversible, mixed competitive and noncompetitive inhibitor of AChE. The experimental fact then suggests a more complex binding mechanism beyond the molecular view in X-ray models resolved at cryogenic temperatures that show a unique binding mode of donepezil in the active site of the enzyme. Aiming at clarifying the mechanism behind that mixed competitive and noncompetitive nature of the inhibitor, we have applied molecular dynamics (MD) simulations and docking and free-energy calculations to investigate microscopic details and energetics of donepezil association for conditions of substrate-free and -bound states of the enzyme. Liquid-phase MD simulation at room temperature shows AChE transits between "open" and "closed" conformations to control accessibility to the active site and ligand binding. As shown by docking and free-energy calculations, association of donepezil involves its reversible axial displacement and reorientation in the active site of the enzyme, assisted by water molecules. Donepezil binds equally well the main-door anionic binding site PAS, the acyl pocket, and the catalytic site CAS by respectively adopting outward-inward-inward orientations regardless of substrate occupancy-the overall stability of that reaction process depends however on co-occupancy of the enzyme being preferential for its substrate-free state. All together, our findings support a physiologically relevant mechanism of AChE inhibition by donepezil involving multistable interactions modes at the molecular origin of the inhibitor's activity.
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Affiliation(s)
- Monica A Silva
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
| | - Alessandra S Kiametis
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
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8
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Kasimova MA, Tewari D, Cowgill JB, Ursuleaz WC, Lin JL, Delemotte L, Chanda B. Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating. eLife 2019; 8:e53400. [PMID: 31774399 PMCID: PMC6904216 DOI: 10.7554/elife.53400] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/19/2022] Open
Abstract
In contrast to most voltage-gated ion channels, hyperpolarization- and cAMP gated (HCN) ion channels open on hyperpolarization. Structure-function studies show that the voltage-sensor of HCN channels are unique but the mechanisms that determine gating polarity remain poorly understood. All-atom molecular dynamics simulations (~20 μs) of HCN1 channel under hyperpolarization reveals an initial downward movement of the S4 voltage-sensor but following the transfer of last gating charge, the S4 breaks into two sub-helices with the lower sub-helix becoming parallel to the membrane. Functional studies on bipolar channels show that the gating polarity strongly correlates with helical turn propensity of the substituents at the breakpoint. Remarkably, in a proto-HCN background, the replacement of breakpoint serine with a bulky hydrophobic amino acid is sufficient to completely flip the gating polarity from inward to outward-rectifying. Our studies reveal an unexpected mechanism of inward rectification involving a linker sub-helix emerging from HCN S4 during hyperpolarization.
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Affiliation(s)
- Marina A Kasimova
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Debanjan Tewari
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
| | - John B Cowgill
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | | | - Jenna L Lin
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Baron Chanda
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Department of Biomolecular ChemistryUniversity of Wisconsin-MadisonMadisonUnited States
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9
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Catacuzzeno L, Franciolini F. Simulation of Gating Currents of the Shaker K Channel Using a Brownian Model of the Voltage Sensor. Biophys J 2019; 117:2005-2019. [PMID: 31653450 DOI: 10.1016/j.bpj.2019.09.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/07/2019] [Accepted: 09/27/2019] [Indexed: 01/18/2023] Open
Abstract
The physical mechanism underlying the voltage-dependent gating of K channels is usually addressed theoretically using molecular dynamics simulations. However, besides being computationally very expensive, this approach is presently unable to fully predict the behavior of fundamental variables of channel gating such as the macroscopic gating current, and hence, it is presently unable to validate the model. To fill this gap, here we propose a voltage-gating model that treats the S4 segment as a Brownian particle moving through a gating channel pore and adjacent internal and external vestibules. In our model, charges on the S4 segment are screened by charged residues localized on neighboring segments of the channel protein and by ions present in the vestibules, whose dynamics are assessed using a flux conservation equation. The electrostatic voltage spatial profile is consistently assessed by applying the Poisson equation to all the charges present in the system. The treatment of the S4 segment as a Brownian particle allows description of the dynamics of a single S4 segment using the Langevin stochastic differential equation or the behavior of a population of S4 segments-useful for assessing the macroscopic gating current-using the Fokker-Planck equation. The proposed model confirms the gating charge transfer hypothesis with the movement of the S4 segment among five different stable positions where the gating charges interact in succession with the negatively charged residues on the channel protein. This behavior produces macroscopic gating currents quite similar to those experimentally found.
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Affiliation(s)
- Luigi Catacuzzeno
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy.
| | - Fabio Franciolini
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
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10
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Romero F, Nishigaki T. Comparative genomic analysis suggests that the sperm-specific sodium/proton exchanger and soluble adenylyl cyclase are key regulators of CatSper among the Metazoa. ZOOLOGICAL LETTERS 2019; 5:25. [PMID: 31372239 PMCID: PMC6660944 DOI: 10.1186/s40851-019-0141-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND CatSper is a sperm-specific calcium ion (Ca2+) channel, which regulates sperm flagellar beating by tuning cytoplasmic Ca2+ concentrations. Although this Ca2+ channel is essential for mammalian fertilization, recent bioinformatics analyses have revealed that genes encoding CatSper are heterogeneously distributed throughout the eukaryotes, including vertebrates. As this channel is activated by cytoplasmic alkalization in mammals and sea urchins, it has been proposed that the sperm-specific Na+/H+ exchanger (sNHE, a product of the SLC9C gene family) positively regulates its activity. In mouse, sNHE is functionally coupled to soluble adenylyl cyclase (sAC). CatSper, sNHE, and sAC have thus been considered functionally interconnected in the control of sperm motility, at least in mouse and sea urchin. RESULTS We carried out a comparative genomic analysis to explore phylogenetic relationships among CatSper, sNHE and sAC in eukaryotes. We found that sNHE occurs only in Metazoa, although sAC occurs widely across eukaryotes. In animals, we found correlated and restricted distribution patterns of the three proteins, suggesting coevolution among them in the Metazoa. Namely, nearly all species in which CatSper is conserved also preserve sNHE and sAC. In contrast, in species without sAC, neither CatSper nor sNHE is conserved. On the other hand, the distribution of another testis-specific NHE (NHA, a product of the SLC9B gene family) does not show any apparent association with that of CatSper. CONCLUSIONS Our results suggest that CatSper, sNHE and sAC form prototypical machinery that functions in regulating sperm flagellar beating in Metazoa. In non-metazoan species, CatSper may be regulated by other H+ transporters, or its activity might be independent of cytoplasmic pH.
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Affiliation(s)
- Francisco Romero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México (IBT-UNAM). Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos Mexico
| | - Takuya Nishigaki
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México (IBT-UNAM). Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos Mexico
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11
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Fernandes JRC, Bleicher L, Beirão PSL. Closed- and open-state models of human skeletal muscle sodium channel. Biochem Biophys Res Commun 2018; 506:826-832. [PMID: 30389137 DOI: 10.1016/j.bbrc.2018.10.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
Abstract
Voltage-gated sodium channels play important roles in human physiology. However, their complexity hinders the understanding of their physiology and pathology at atomic level. We took advantage of the structural reports of similar channels obtained by cryo-EM (EeNav1.4, and NavPaS), and constructed models of human Nav1.4 channels at closed and open states. The open-state model is very similar to the recently published cryo-EM structure of hNav1.4. The comparison of both models shows shifts of the voltage sensors (VS) of DIII and DIV. The activated position of VS-DII in the closed model was demonstrated by Ts1 docking, thereby confirming the requirement that VS-DI, VS-DII and VS-DIII must be activated for the channel to open. The interactions observed with VS-DIII suggest a stepwise, yet fast, transition from resting to activated state. These models provide structural insights on the closed-open transition of the channel.
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Affiliation(s)
- João R C Fernandes
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil
| | - Paulo S L Beirão
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil.
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12
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Stock L, Hosoume J, Cirqueira L, Treptow W. Binding of the general anesthetic sevoflurane to ion channels. PLoS Comput Biol 2018; 14:e1006605. [PMID: 30475796 PMCID: PMC6283617 DOI: 10.1371/journal.pcbi.1006605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/06/2018] [Accepted: 10/26/2018] [Indexed: 11/21/2022] Open
Abstract
The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia. Despite advancements in the field, a first principle all-atom demonstration of this structure-function premise is still missing. We focus on the clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds protein’s well-characterized open and closed structures in a conformation-dependent manner to shift channel equilibrium. We employ an innovative approach relying on extensive docking calculations and free-energy perturbation of all potential binding sites revealed by the latter, and find sevoflurane binds open and closed structures at multiple sites under complex saturation and concentration effects. Results point to a non-trivial interplay of site and conformation-dependent modes of action involving distinct binding sites that increase channel open-probability at diluted ligand concentrations. Given the challenge in exploring more complex processes potentially impacting channel-anesthetic interaction, the result is revealing as it demonstrates the process of multiple anesthetic binding events alone may account for open-probability shifts recorded in measurements. General anesthetics are central to modern medicine, yet their microscopic mechanism of action is still unknown. Here, we demonstrate that a clinically used anesthetic, sevoflurane, binds the mammalian voltage-gated potassium channel Kv1.2 effecting a shift in its open probability, even at low concentrations. The results, supported by recent experimental measurements, are promising as they demonstrate that the molecular process of direct binding of anesthetic to ion channels play a relevant role in anesthesia.
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Affiliation(s)
- Letícia Stock
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Juliana Hosoume
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Leonardo Cirqueira
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
- * E-mail:
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13
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Gating-induced large aqueous volumetric remodeling and aspartate tolerance in the voltage sensor domain of Shaker K + channels. Proc Natl Acad Sci U S A 2018; 115:8203-8208. [PMID: 30038023 DOI: 10.1073/pnas.1806578115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurons encode electrical signals with critically tuned voltage-gated ion channels and enzymes. Dedicated voltage sensor domains (VSDs) in these membrane proteins activate coordinately with an unresolved structural change. Such change conveys the transmembrane translocation of four positively charged arginine side chains, the voltage-sensing residues (VSRs; R1-R4). Countercharges and lipid phosphohead groups likely stabilize these VSRs within the low-dielectric core of the protein. However, the role of hydration, a sign-independent charge stabilizer, remains unclear. We replaced all VSRs and their neighboring residues with negatively charged aspartates in a voltage-gated potassium channel. The ensuing mild functional effects indicate that hydration is also important in VSR stabilization. The voltage dependency of the VSR aspartate variants approached the expected arithmetic summation of charges at VSR positions, as if negative and positive side chains faced similar pathways. In contrast, aspartates introduced between R2 and R3 did not affect voltage dependence as if the side chains moved outside the electric field or together with it, undergoing a large displacement and volumetric remodeling. Accordingly, VSR performed osmotic work at both internal and external aqueous interfaces. Individual VSR contributions to volumetric works approached arithmetical additivity but were largely dissimilar. While R1 and R4 displaced small volumes, R2 and R3 volumetric works were massive and vectorially opposed, favoring large aqueous remodeling during VSD activation. These diverse volumetric works are, at least for R2 and R3, not compatible with VSR translocation across a unique stationary charge transfer center. Instead, VSRs may follow separated pathways across a fluctuating low-dielectric septum.
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14
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Modeling squid axon K + channel by a nucleation and growth kinetic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:505-514. [PMID: 29155211 DOI: 10.1016/j.bbamem.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/09/2017] [Accepted: 11/15/2017] [Indexed: 01/28/2023]
Abstract
A kinetic model accounting for all salient features of the K+ channel of the squid giant axon, including the rising phase of the ON gating charge and the Cole-Moore effect, is provided. Upon accounting for a significant feature distinguishing K+, Na+ and Ca2+ channels from channel-forming peptides modeled in our previous 2016 BBA paper, the nucleation-and-growth kinetic model developed therein is extended to simulate ON ionic and gating currents of the K+ channel of the squid giant axon at different depolarization potentials by the use of only two free parameters. K+ channel opening is considered to proceed by progressive aggregation of single subunits, while they are moving their gating charge outward under depolarizing conditions within their tetrameric structure; K+ channel closing proceeds in the opposite direction, by repolarization-induced disaggregation of subunits, accompanied by inward movement of their gating charge.
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15
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Concentration-Dependent Binding of Small Ligands to Multiple Saturable Sites in Membrane Proteins. Sci Rep 2017; 7:5734. [PMID: 28720769 PMCID: PMC5516019 DOI: 10.1038/s41598-017-05896-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022] Open
Abstract
Membrane proteins are primary targets for most therapeutic indications in cancer and neurological diseases, binding over 50% of all known small molecule drugs. Understanding how such ligands impact membrane proteins requires knowledge on the molecular structure of ligand binding, a reasoning that has driven relentless efforts in drug discovery and translational research. Binding of small ligands appears however highly complex involving interaction to multiple transmembrane protein sites featuring single or multiple occupancy states. Within this scenario, looking for new developments in the field, we investigate the concentration-dependent binding of ligands to multiple saturable sites in membrane proteins. The study relying on docking and free-energy perturbation provides us with an extensive description of the probability density of protein-ligand states that allows for computation of thermodynamic properties of interest. It also provides one- and three-dimensional spatial descriptions for the ligand density across the protein-membrane system which can be of interest for structural purposes. Illustration and discussion of the results are shown for binding of the general anesthetic sevoflurane against Kv1.2, a mammalian ion channel for which experimental data are available.
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16
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Sun RN, Gong H. Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field. J Phys Chem Lett 2017; 8:901-908. [PMID: 28171721 DOI: 10.1021/acs.jpclett.7b00023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Voltage-gated sodium (NaV) channels play vital roles in the signal transduction of excitable cells. Upon activation of a NaV channel, the change of transmembrane voltage triggers conformational change of the voltage sensing domain, which then elicits opening of the pore domain and thus allows an influx of Na+ ions. Description of this process with atomistic details is in urgent demand. In this work, we simulated the partial activation process of the voltage sensing domain of a prokaryotic NaV channel using a polarizable force field. We not only observed the conformational change of the voltage sensing domain from resting to preactive state, but also rigorously estimated the free energy profile along the identified reaction pathway. Comparison with the control simulation using an additive force field indicates that voltage-gating thermodynamics of NaV channels may be inaccurately described without considering the electrostatic polarization effect.
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Affiliation(s)
- Rui-Ning Sun
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
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17
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Vickery ON, Machtens JP, Tamburrino G, Seeliger D, Zachariae U. Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure 2016; 24:997-1007. [PMID: 27210286 PMCID: PMC4906246 DOI: 10.1016/j.str.2016.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
G-protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins and one-third of all drug targets in humans. A number of recent studies have reported evidence for substantial voltage regulation of GPCRs. However, the structural basis of GPCR voltage sensing has remained enigmatic. Here, we present atomistic simulations on the δ-opioid and M2 muscarinic receptors, which suggest a structural and mechanistic explanation for the observed voltage-induced functional effects. The simulations reveal that the position of an internal Na(+) ion, recently detected to bind to a highly conserved aqueous pocket in receptor crystal structures, strongly responds to voltage changes. The movements give rise to gating charges in excellent agreement with previous experimental recordings. Furthermore, free energy calculations show that these rearrangements of Na(+) can be induced by physiological membrane voltages. Due to its role in receptor function and signal bias, the repositioning of Na(+) has important general implications for signal transduction in GPCRs.
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MESH Headings
- Animals
- Crystallography, X-Ray
- Humans
- Ion Channel Gating
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Protein Structure, Secondary
- Receptor, Muscarinic M2/chemistry
- Receptor, Muscarinic M2/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Sodium/metabolism
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Affiliation(s)
- Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Jan-Philipp Machtens
- Forschungszentrum Jülich GmbH, Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Leo-Brandt-Strasse, 52428 Jülich, Germany
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Daniel Seeliger
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riss, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK.
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18
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Patel D, Mahdavi S, Kuyucak S. Computational Study of Binding of μ-Conotoxin GIIIA to Bacterial Sodium Channels NaVAb and NaVRh. Biochemistry 2016; 55:1929-38. [PMID: 26959170 DOI: 10.1021/acs.biochem.5b01324] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Structures of several voltage-gated sodium (NaV) channels from bacteria have been determined recently, but the same feat might not be achieved for the mammalian counterparts in the near future. Thus, at present, computational studies of the mammalian NaV channels have to be performed using homology models based on the bacterial crystal structures. A successful homology model for the mammalian NaV1.4 channel was recently constructed using the extensive mutation data for binding of μ-conotoxin GIIIA to NaV1.4, which was further validated through studies of binding of other μ-conotoxins and ion permeation. Understanding the similarities and differences between the bacterial and mammalian NaV channels is an important issue, and the NaV1.4-GIIIA system provides a good opportunity for such a comparison. To this end, we study the binding of GIIIA to the bacterial channels NaVAb and NaVRh. The complex structures are obtained using docking and molecular dynamics simulations, and the dissociation of GIIIA is studied through umbrella sampling simulations. The results are compared to those obtained from the NaV1.4-GIIIA system, and the differences in the binding modes arising from the changes in the selectivity filters are highlighted.
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Affiliation(s)
- Dharmeshkumar Patel
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Somayeh Mahdavi
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Serdar Kuyucak
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
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19
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Abstract
Voltage-gated potassium channels or Kv's are membrane proteins with fundamental physiological roles. They are composed of 2 main functional protein domains, the pore domain, which regulates ion permeation, and the voltage-sensing domain, which is in charge of sensing voltage and undergoing a conformational change that is later transduced into pore opening. The voltage-sensing domain or VSD is a highly conserved structural motif found in all voltage-gated ion channels and can also exist as an independent feature, giving rise to voltage sensitive enzymes and also sustaining proton fluxes in proton-permeable channels. In spite of the structural conservation of VSDs in potassium channels, there are several differences in the details of VSD function found across variants of Kvs. These differences are mainly reflected in variations in the electrostatic energy needed to open different potassium channels. In turn, the differences in detailed VSD functioning among voltage-gated potassium channels might have physiological consequences that have not been explored and which might reflect evolutionary adaptations to the different roles played by Kv channels in cell physiology.
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Affiliation(s)
- León D Islas
- a Departamento de Fisiología, Facultad de Medicina ; National Autonomous University of Mexico (UNAM), Ciudad Universitaria , México City , México
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20
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Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions. J Membr Biol 2015; 248:419-30. [PMID: 25972106 DOI: 10.1007/s00232-015-9805-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/24/2015] [Indexed: 01/06/2023]
Abstract
Voltage-sensing domains (VSDs) are integral membrane protein units that sense changes in membrane electric potential, and through the resulting conformational changes, regulate a specific function. VSDs confer voltage-sensitivity to a large superfamily of membrane proteins that includes voltage-gated Na[Formula: see text], K[Formula: see text], Ca[Formula: see text] ,and H[Formula: see text] selective channels, hyperpolarization-activated cyclic nucleotide-gated channels, and voltage-sensing phosphatases. VSDs consist of four transmembrane segments (termed S1 through S4). Their most salient structural feature is the highly conserved positions for charged residues in their sequences. S4 exhibits at least three conserved triplet repeats composed of one basic residue (mostly arginine) followed by two hydrophobic residues. These S4 basic side chains participate in a state-dependent internal salt-bridge network with at least four acidic residues in S1-S3. The signature of voltage-dependent activation in electrophysiology experiments is a transient current (termed gating or sensing current) upon a change in applied membrane potential as the basic side chains in S4 move across the membrane electric field. Thus, the unique structural features of the VSD architecture allow for competing requirements: maintaining a series of stable transmembrane conformations, while allowing charge motion, as briefly reviewed here.
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