1
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Costa ISD, Junot T, Silva FL, Felix W, Cardozo Fh JL, Pereira de Araujo AF, Pais do Amaral C, Gonçalves S, Santos NC, Leite JRSA, Bloch C, Brand GD. Occurrence and evolutionary conservation analysis of α-helical cationic amphiphilic segments in the human proteome. FEBS J 2024; 291:547-565. [PMID: 37945538 DOI: 10.1111/febs.16997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/14/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023]
Abstract
The existence of encrypted fragments with antimicrobial activity in human proteins has been thoroughly demonstrated in the literature. Recently, algorithms for the large-scale identification of these segments in whole proteomes were developed, and the pervasiveness of this phenomenon was stated. These algorithms typically mine encrypted cationic and amphiphilic segments of proteins, which, when synthesized as individual polypeptide sequences, exert antimicrobial activity by membrane disruption. In the present report, the human reference proteome was submitted to the software kamal for the uncovering of protein segments that correspond to putative intragenic antimicrobial peptides (IAPs). The assessment of the identity of these segments, frequency, functional classes of parent proteins, structural relevance, and evolutionary conservation of amino acid residues within their corresponding proteins was conducted in silico. Additionally, the antimicrobial and anticancer activity of six selected synthetic peptides was evaluated. Our results indicate that cationic and amphiphilic segments can be found in 2% of all human proteins, but are more common in transmembrane and peripheral membrane proteins. These segments are surface-exposed basic patches whose amino acid residues present similar conservation scores to other residues with similar solvent accessibility. Moreover, the antimicrobial and anticancer activity of the synthetic putative IAP sequences was irrespective to whether these are associated to membranes in the cellular setting. Our study discusses these findings in light of the current understanding of encrypted peptide sequences, offering some insights into the relevance of these segments to the organism in the context of their harboring proteins or as separate polypeptide sequences.
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Affiliation(s)
- Igor S D Costa
- Laboratório de Síntese e Análise de Biomoléculas - LSAB, Instituto de Química, Universidade de Brasília, Brazil
| | - Tiago Junot
- Laboratório de Síntese e Análise de Biomoléculas - LSAB, Instituto de Química, Universidade de Brasília, Brazil
| | - Fernanda L Silva
- Laboratório de Síntese e Análise de Biomoléculas - LSAB, Instituto de Química, Universidade de Brasília, Brazil
| | - Wanessa Felix
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada - NuPMIA, Faculdade de Medicina, Universidade de Brasília, Brazil
| | - José L Cardozo Fh
- Laboratório de Espectrometria de Massa - LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Antonio F Pereira de Araujo
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brazil
| | | | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - José R S A Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada - NuPMIA, Faculdade de Medicina, Universidade de Brasília, Brazil
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa - LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Guilherme D Brand
- Laboratório de Síntese e Análise de Biomoléculas - LSAB, Instituto de Química, Universidade de Brasília, Brazil
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2
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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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3
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Structural analysis of the S4-S5 linker of the human KCNQ1 potassium channel. Biochem Biophys Res Commun 2015; 456:410-4. [PMID: 25475720 DOI: 10.1016/j.bbrc.2014.11.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/24/2014] [Indexed: 11/23/2022]
Abstract
KCNQ1 plays important roles in the cardiac action potential and consists of an N-terminal domain, a voltage-sensor domain, a pore domain and a C-terminal domain. KCNQ1 is a voltage-gated potassium channel and its channel activity is regulated by membrane potentials. The linker between transmembrane helices 4 and 5 (S4-S5 linker) is important for transferring the conformational changes from the voltage-sensor domain to the pore domain. In this study, the structure of the S4-S5 linker of KCNQ1 was investigated by solution NMR, circular dichroism and fluorescence spectroscopic studies. The S4-S5 linker adopted a helical structure in detergent micelles. The W248 may interact with the cell membrane.
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4
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Conservation analysis of residues in the S4-S5 linker and the terminal part of the S5-P-S6 pore modulus in Kv and HCN channels: flexible determinants for the electromechanical coupling. Pflugers Arch 2014; 467:2069-79. [PMID: 25398373 DOI: 10.1007/s00424-014-1647-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 11/03/2014] [Indexed: 12/22/2022]
Abstract
Protein mobility is important to achieve protein function. Intrinsic flexibility associated with motion underlies this important issue and the analysis of side chain flexibility gives insights to understand it. In this work, the S5-P-S6 pore modulus (PM) of members of Kv and HCN channels was examined by a combination of sequence alignment, residue composition analysis, and intrinsic side chain flexibility. The PM sequences were organized as a database that was used to reveal and correlate the functional diversity of each analyzed family. Specifically, we focused our attention on the crucial role of the S4-S5 linker and its well-described interaction with the S6 T during the electromechanical coupling. Our analysis suggests the presence of a Gly-hinge in the middle of the S4-S5 linkers. This apparent Gly-hinge links a flexible N-terminal segment with a rigid C-terminal one, although in Kv7 channels, the latter segment is even more flexible. Instead, HCN channels exhibit a putative Thr-hinge and is rich in aromatic residues, in consequence, their linker is more rigid. Concerning S6, we confirm the presence of the two flexible kinks previously described and we provide the complete segmental flexibility profiles for the different families. Our results are discussed in terms of the relation between residue composition, conservation, and local conformational flexibility. This provides important insights to understand and differentiate the characteristic gating properties of these channels as well as their implications in cell physiology.
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5
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Zhang J, Qu X, Covarrubias M, Germann MW. Insight into the modulation of Shaw2 Kv channels by general anesthetics: structural and functional studies of S4-S5 linker and S6 C-terminal peptides in micelles by NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:595-601. [PMID: 23031574 DOI: 10.1016/j.bbamem.2012.09.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 12/20/2022]
Abstract
The modulation of the Drosophila Shaw2 Kv channel by 1-alkanols and inhaled anesthetics is correlated with the involvement of the S4-S5 linker and C-terminus of S6, and consistent with stabilization of the channel's closed state. Structural analysis of peptides from S4-S5 (L45) and S6 (S6c), by nuclear magnetic resonance and circular dichroism spectroscopy supports that an α-helical conformation was adopted by L45, while S6c was only in an unstable/dynamic partially folded α-helix in dodecylphosphocholine micelles. Solvent accessibility and paramagnetic probing of L45 revealed that L45 lies parallel to the surface of micelles with charged and polar residues pointing towards the solution while hydrophobic residues are buried inside the micelles. Chemical shift perturbation introduced by 1-butanol on residues Gln320, Thr321, Phe322 and Arg323 of L45, as well as Thr423 and Gln424 of S6c indicates possible anesthetic binding sites on these two important components in the channel activation apparatus. Diffusion measurements confirmed the association of L45, S6c and 1-butanol with micelles which suggests the capability of 1-butanol to influence a possible interaction of L45 and S6c in the micelle environment.
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Affiliation(s)
- Jin Zhang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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6
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Vardanyan V, Pongs O. Coupling of voltage-sensors to the channel pore: a comparative view. Front Pharmacol 2012; 3:145. [PMID: 22866036 PMCID: PMC3406610 DOI: 10.3389/fphar.2012.00145] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 07/07/2012] [Indexed: 12/11/2022] Open
Abstract
The activation of voltage-dependent ion channels is initiated by potential-induced conformational rearrangements in the voltage-sensor domains that propagates to the pore domain (PD) and finally opens the ion conduction pathway. In potassium channels voltage-sensors are covalently linked to the pore via S4-S5 linkers at the cytoplasmic site of the PD. Transformation of membrane electric energy into the mechanical work required for the opening or closing of the channel pore is achieved through an electromechanical coupling mechanism, which involves local interaction between residues in S4-S5 linker and pore-forming alpha helices. In this review we discuss present knowledge and open questions related to the electromechanical coupling mechanism in most intensively studied voltage-gated Shaker potassium channel and compare structure-functional aspects of coupling with those observed in distantly related ion channels. We focus particularly on the role of electromechanical coupling in modulation of the constitutive conductance of ion channels.
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Affiliation(s)
- Vitya Vardanyan
- Ion Channel Research Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia Yerevan, Armenia
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Cheng YM, Claydon TW. Voltage-dependent gating of HERG potassium channels. Front Pharmacol 2012; 3:83. [PMID: 22586397 PMCID: PMC3347040 DOI: 10.3389/fphar.2012.00083] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 04/16/2012] [Indexed: 12/20/2022] Open
Abstract
The mechanisms by which voltage-gated channels sense changes in membrane voltage and energetically couple this with opening of the ion conducting pore has been the source of significant interest. In voltage-gated potassium (Kv) channels, much of our knowledge in this area comes from Shaker-type channels, for which voltage-dependent gating is quite rapid. In these channels, activation and deactivation are associated with rapid reconfiguration of the voltage-sensing domain unit that is electromechanically coupled, via the S4-S5 linker helix, to the rate-limiting opening of an intracellular pore gate. However, fast voltage-dependent gating kinetics are not typical of all Kv channels, such as Kv11.1 (human ether-à-go-go related gene, hERG), which activates and deactivates very slowly. Compared to Shaker channels, our understanding of the mechanisms underlying slow hERG gating is much poorer. Here, we present a comparative review of the structure-function relationships underlying activation and deactivation gating in Shaker and hERG channels, with a focus on the roles of the voltage-sensing domain and the S4-S5 linker that couples voltage sensor movements to the pore. Measurements of gating current kinetics and fluorimetric analysis of voltage sensor movement are consistent with models suggesting that the hERG activation pathway contains a voltage independent step, which limits voltage sensor transitions. Constraints upon hERG voltage sensor movement may result from loose packing of the S4 helices and additional intra-voltage sensor counter-charge interactions. More recent data suggest that key amino acid differences in the hERG voltage-sensing unit and S4-S5 linker, relative to fast activating Shaker-type Kv channels, may also contribute to the increased stability of the resting state of the voltage sensor.
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Affiliation(s)
- Yen May Cheng
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University Burnaby, BC, Canada
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8
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Gayen S, Li Q, Kang C. The solution structure of the S4-S5 linker of the hERG potassium channel. J Pept Sci 2011; 18:140-5. [DOI: 10.1002/psc.1427] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/15/2011] [Accepted: 09/22/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Shovanlal Gayen
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore 138669 Singapore
| | - Qingxin Li
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore 138669 Singapore
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9
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Kusch J, Zimmer T, Holschuh J, Biskup C, Schulz E, Nache V, Benndorf K. Role of the S4-S5 linker in CNG channel activation. Biophys J 2011; 99:2488-96. [PMID: 20959089 DOI: 10.1016/j.bpj.2010.07.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 06/22/2010] [Accepted: 07/19/2010] [Indexed: 10/18/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) channels mediate sensory signal transduction in retinal and olfactory cells. The channels are activated by the binding of cyclic nucleotides to a cyclic nucleotide-binding domain (CNBD) in the C-terminus that is located at the intracellular side. The molecular events translating the ligand binding to the pore opening are still unknown. We investigated the role of the S4-S5 linker in the activation process by quantifying its interaction with other intracellular regions. To this end, we constructed chimeric channels in which the N-terminus, the S4-S5 linker, the C-linker, and the CNBD of the retinal CNGA1 subunit were systematically replaced by the respective regions of the olfactory CNGA2 subunit. Macroscopic concentration-response relations were analyzed, yielding the apparent affinity to cGMP and the Hill coefficient. The degree of functional coupling of intracellular regions in the activation gating was determined by thermodynamic double-mutant cycle analysis. We observed that all four intracellular regions, including the relatively short S4-S5 linker, are involved in controlling the apparent affinity of the channel to cGMP and, moreover, in determining the degree of cooperativity between the subunits, as derived from the Hill coefficient. The interaction energies reveal an interaction of the S4-S5 linker with both the N-terminus and the C-linker, but no interaction with the CNBD.
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Affiliation(s)
- Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Germany
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10
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Labro AJ, Boulet IR, Choveau FS, Mayeur E, Bruyns T, Loussouarn G, Raes AL, Snyders DJ. The S4-S5 linker of KCNQ1 channels forms a structural scaffold with the S6 segment controlling gate closure. J Biol Chem 2010; 286:717-25. [PMID: 21059661 DOI: 10.1074/jbc.m110.146977] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In vivo, KCNQ1 α-subunits associate with the β-subunit KCNE1 to generate the slowly activating cardiac potassium current (I(Ks)). Structurally, they share their topology with other Kv channels and consist out of six transmembrane helices (S1-S6) with the S1-S4 segments forming the voltage-sensing domain (VSD). The opening or closure of the intracellular channel gate, which localizes at the bottom of the S6 segment, is directly controlled by the movement of the VSD via an electromechanical coupling. In other Kv channels, this electromechanical coupling is realized by an interaction between the S4-S5 linker (S4S5(L)) and the C-terminal end of S6 (S6(T)). Previously we reported that substitutions for Leu(353) in S6(T) resulted in channels that failed to close completely. Closure could be incomplete because Leu(353) itself is the pore-occluding residue of the channel gate or because of a distorted electromechanical coupling. To resolve this and to address the role of S4S5(L) in KCNQ1 channel gating, we performed an alanine/tryptophan substitution scan of S4S5(L). The residues with a "high impact" on channel gating (when mutated) clustered on one side of the S4S5(L) α-helix. Hence, this side of S4S5(L) most likely contributes to the electromechanical coupling and finds its residue counterparts in S6(T). Accordingly, substitutions for Val(254) resulted in channels that were partially constitutively open and the ability to close completely was rescued by combination with substitutions for Leu(353) in S6(T). Double mutant cycle analysis supported this cross-talk indicating that both residues come in close contact and stabilize the closed state of the channel.
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Affiliation(s)
- Alain J Labro
- Laboratory for Molecular Biophysics, Physiology and Pharmacology, Department of Biomedical Sciences, University of Antwerp, CDE, Universiteitsplein 1, 2610 Antwerp, Belgium
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11
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Labro AJ, Raes AL, Grottesi A, Van Hoorick D, Sansom MSP, Snyders DJ. Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues. ACTA ACUST UNITED AC 2009; 132:667-80. [PMID: 19029374 PMCID: PMC2585865 DOI: 10.1085/jgp.200810048] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Voltage-dependent K+ channels transfer the voltage sensor movement into gate opening or closure through an electromechanical coupling. To test functionally whether an interaction between the S4-S5 linker (L45) and the cytoplasmic end of S6 (S6T) constitutes this coupling, the L45 in hKv1.5 was replaced by corresponding hKv2.1 sequence. This exchange was not tolerated but could be rescued by also swapping S6T. Exchanging both L45 and S6T transferred hKv2.1 kinetics to an hKv1.5 background while preserving the voltage dependence. A one-by-one residue substitution scan of L45 and S6T in hKv1.5 further shows that S6T needs to be α-helical and forms a “crevice” in which residues I422 and T426 of L45 reside. These residues transfer the mechanical energy onto the S6T crevice, whereas other residues in S6T and L45 that are not involved in the interaction maintain the correct structure of the coupling.
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Affiliation(s)
- Alain J Labro
- Laboratory for Molecular Biophysics, Physiology, and Pharmacology, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
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12
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Varga K, Tian L, McDermott AE. Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1604-13. [PMID: 17974509 DOI: 10.1016/j.bbapap.2007.08.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 08/15/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly (13)C, (15)N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.
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Affiliation(s)
- Krisztina Varga
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, NY 10027, USA
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13
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Rainey JK, Fliegel L, Sykes BD. Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides. Biochem Cell Biol 2007; 84:918-29. [PMID: 17215879 DOI: 10.1139/o06-178] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely indicative of kinks in the full-length protein. This minireview focuses on methods and protocols for NMR structure calculation and analysis of peptide structures under conditions of conformational sampling. The methods outlined allow the identification and analysis of structured peptides containing break points owing to conformational sampling and the differentiation between oligomerization and ensemble-averaged observation of multiple peptide conformations.
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Affiliation(s)
- Jan K Rainey
- Protein Engineering Network of Centres of Excellence and Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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14
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Bhattacharji A, Kaplan B, Harris T, Qu X, Germann MW, Covarrubias M. The concerted contribution of the S4-S5 linker and the S6 segment to the modulation of a Kv channel by 1-alkanols. Mol Pharmacol 2006; 70:1542-54. [PMID: 16887933 DOI: 10.1124/mol.106.026187] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gating of voltage-gated K(+) channels (K(v) channels) depends on the electromechanical coupling between the voltage sensor and activation gate. The main activation gate of K(v) channels involves the COOH-terminal section of the S6 segment (S6-b) and the S4-S5 linker at the intracellular mouth of the pore. In this study, we have expanded our earlier work to probe the concerted contribution of these regions to the putative amphipathic 1-alkanol site in the Shaw2 K(+) channel. In the S4-S5 linker, we found a direct energetic correlation between alpha-helical propensity and the inhibition of the Shaw2 channel by 1-butanol. Spectroscopic structural analyses of the S4-S5 linker supported this correlation. Furthermore, the analysis of chimeric Shaw2 and K(v)3.4 channels that exchanged their corresponding S4-S5 linkers showed that the potentiation induced by 1-butanol depends on the combination of a single mutation in the S6 PVPV motif (PVAV) and the presence of the Shaw2 S4-S5 linker. Then, using tandem-heterodimer subunits, we determined that this potentiation also depends on the number of S4-S5 linkers and PVAV mutations in the K(v) channel tetramer. Consistent with the critical contribution of the Shaw2 S4-S5 linker, the equivalent PVAV mutation in certain mammalian K(v) channels with divergent S4-S5 linkers conferred weak potentiation by 1-butanol. Overall, these results suggest that 1-alkanol action in Shaw2 channels depends on interactions involving the S4-S5 linker and the S6-b segment. Therefore, we propose that amphiphilic general anesthetic agents such as 1-alkanols may modulate gating of the Shaw2 K(+) channel by an interaction with its activation gate.
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Affiliation(s)
- Aditya Bhattacharji
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College of Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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15
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Emerick MC, Stein R, Kunze R, McNulty MM, Regan MR, Hanck DA, Agnew WS. Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations. Proteins 2006; 64:320-42. [PMID: 16671074 DOI: 10.1002/prot.20877] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development.
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Affiliation(s)
- Mark C Emerick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Li F, Li H, Hu L, Kwan M, Chen G, He QY, Sun H. Structure, Assembly, and Topology of the G185R Mutant of the Fourth Transmembrane Domain of Divalent Metal Transporter. J Am Chem Soc 2005; 127:1414-23. [PMID: 15686373 DOI: 10.1021/ja047148t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mammalian iron transporter, divalent metal transporter (DMT1), is a 12-transmembrane domain integral protein, responsible for dietary iron uptake in the duodenum and iron acquisition from transferrin in peripheral tissues. Two disease-causing mutants in animals have been found and attributed to the same missense mutation (G185R), which occurs within the putative transmembrane domain 4 (TM4) of DMT1. We have characterized a synthetic 24-mer peptide, corresponding to the sequence of the TM4 of DMT1 with G185R mutation using circular dichroism (CD) and NMR spectroscopy and show that the G185R peptide assumes mainly alpha-helical conformations in various membrane-mimetic environments. Solution structures derived from NMR and molecular dynamics/simulated annealing calculations demonstrate that the peptide exhibits a highly defined alpha-helix in its middle portion, flanked by a highly flexible N-terminus and a relatively ordered C-terminus. Both the folding and location of the C-terminus in SDS micelles are regulated by pH values. Paramagnetic broadening on peptide NMR signals by spin-labeled 5- and 16-doxylstearic acids and Mn(2+) ion suggests that both the N-terminus and the helical region of the peptide are embedded in SDS micelles. Surprisingly, self-association of the peptides for both the wild type and the G185R mutant studied by CD, electrospray ionization mass spectrometry, and NMR diffusion-ordered spectroscopy demonstrated that mutation of the Gly185 to a bulky and positively charged arginine causes a different self-assembly of the peptide, e.g., from a trimer to a hexamer, which implies that the quaternary structure of integral DMT1 may be crucial for its function in vivo.
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Affiliation(s)
- Fei Li
- Department of Chemistry and Open Laboratory of Chemical Biology, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
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Treptow W, Maigret B, Chipot C, Tarek M. Coupled motions between pore and voltage-sensor domains: a model for Shaker B, a voltage-gated potassium channel. Biophys J 2004; 87:2365-79. [PMID: 15454436 PMCID: PMC1304659 DOI: 10.1529/biophysj.104.039628] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Accepted: 06/23/2004] [Indexed: 11/18/2022] Open
Abstract
A high-resolution crystal structure of KvAP, an archeabacterial voltage-gated potassium (Kv) channel, complexed with a monoclonal Fab fragment has been recently determined. Based on this structure, a mechanism for the activation (opening) of Kv channels has been put forward. This mechanism has since been criticized, suggesting that the resolved structure is not representative of the family of voltage-gated potassium channels. Here, we propose a model of the transmembrane domain of Shaker B, a well-characterized Kv channel, built by homology modeling and docking calculations. In this model, the positively charged S4 helices are oriented perpendicular to the membrane and localized in the groove between segments S5 and S6 of adjacent subunits. The structure and the dynamics of the full atomistic model embedded in a hydrated lipid bilayer were investigated by means of two large-scale molecular dynamics simulations under transmembrane-voltage conditions known to induce, respectively, the resting state (closed) and the activation (opening) of voltage-gated channels. Upon activation, the model undergoes conformational changes that lead to an increase of the hydration of the charged S4 helices, correlated with an upward translation and a tilting of the latter, concurrently with movements of the S5 helices and the activation gate. Although small, these conformational changes ultimately result in an alteration of the ion-conduction pathway. Our findings support the transporter model devised by Bezanilla and collaborators, and further underline the crucial role played by internal hydration in the activation of the channel.
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Affiliation(s)
- Werner Treptow
- Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche, Centre National de la Recherche Scientifique/Université Henri Poincaré 7565, Nancy, France
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Shahidullah M, Harris T, Germann MW, Covarrubias M. Molecular features of an alcohol binding site in a neuronal potassium channel. Biochemistry 2003; 42:11243-52. [PMID: 14503874 PMCID: PMC2219921 DOI: 10.1021/bi034738f] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aliphatic alcohols (1-alkanols) selectively inhibit the neuronal Shaw2 K(+) channel at an internal binding site. This inhibition is conferred by a sequence of 13 residues that constitutes the S4-S5 loop in the pore-forming subunit. Here, we combined functional and structural approaches to gain insights into the molecular basis of this interaction. To infer the forces that are involved, we employed a fast concentration-clamp method (10-90% exchange time = 800 micros) to examine the kinetics of the interaction of three members of the homologous series of 1-alkanols (ethanol, 1-butanol, and 1-hexanol) with Shaw2 K(+) channels in Xenopus oocyte inside-out patches. As expected for a second-order mechanism involving a receptor site, only the observed association rate constants were linearly dependent on the 1-alkanol concentration. While the alkyl chain length modestly influenced the dissociation rate constants (decreasing only approximately 2-fold between ethanol and 1-hexanol), the second-order association rate constants increased e-fold per carbon atom. Thus, hydrophobic interactions govern the probability of productive collisions at the 1-alkanol binding site, and short-range polar interactions help to stabilize the complex. We also examined the relationship between the energetics of 1-alkanol binding and the structural properties of the S4-S5 loop. Circular dichroism spectroscopy applied to peptides corresponding to the S4-S5 loop of various K(+) channels revealed a correlation between the apparent binding affinity of the 1-alkanol binding site and the alpha-helical propensity of the S4-S5 loop. The data suggest that amphiphilic interactions at the Shaw2 1-alkanol binding site depend on specific structural constraints in the pore-forming subunit of the channel.
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Affiliation(s)
- Mohammad Shahidullah
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College of Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
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Vais H, Atkinson S, Pluteanu F, Goodson SJ, Devonshire AL, Williamson MS, Usherwood PNR. Mutations of the para Sodium Channel of Drosophila melanogaster Identify Putative Binding Sites for Pyrethroids. Mol Pharmacol 2003; 64:914-22. [PMID: 14500748 DOI: 10.1124/mol.64.4.914] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The effects of two pyrethroids on recombinant wild-type and mutant (pyrethroid-resistant) Na+ channels of Drosophila melanogaster have been studied. Three mutations that confer resistance (kdr/superkdr) to pyrethroids were inserted, either individually or in combination, into the para Na+ channel of D. melanogaster: L1014F in domain IIS6, M918T in the IIS4-S5 linker, and T929I in domain IIS5. Channels were expressed in Xenopus laevis oocytes and the effects of the pyrethroids permethrin (type I) and deltamethrin (type II) on Na+ currents were investigated using voltage clamp. The Na+ channels deactivated slowly after deltamethrin treatment, the resultant "tail" currents being used to quantify the effects of this pyrethroid. The Hill slope of 2 for deltamethrin action on the wild-type channel and the mutant L1014F channel is indicative of cooperative binding at two or more sites on these channels. In contrast, binding to the mutants M918T and T929I is noncooperative. Tail currents for the wild-type channel and L1014F channel decayed biphasically, whereas those for M918T and T929I mutants decayed monophasically. The L1014F mutant was approximately 20-fold less sensitive than the wild-type to deltamethrin. Surprisingly, the sensitivity of the double mutant M918T+L1014F to deltamethrin was similar to that of M918T alone, whereas the sensitivity of T929I+L1014F was >30,000-fold lower than that of T929I. Permethrin was less potent than deltamethrin, and its binding to all channel types was noncooperative. The decays of permethrin-induced tail currents were exclusively monophasic. These findings are discussed in terms of the properties and possible locations of pyrethroid binding sites on the D. melanogaster Na+ channel.
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Affiliation(s)
- H Vais
- Division of Molecular Toxicology, School of Life and Environmental Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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Abstract
The cytoplasmic ends of the four S6 transmembrane segments of voltage-gated potassium channels converge in a bundle crossing that acts as the activation gate that opens in response to a depolarization. To explore whether the cytoplasmic extension of the S6 segment (the S6 tail) plays a role in coupling voltage sensor and activation gate movements, we examined the effect of cysteine substitution from residues N482 to T489 on the kinetics and voltage-dependence of S4 charge movement and on the kinetics of deactivation of ionic current. Among these mutants, F484C has the steepest voltage-dependent charge movement, the largest Q-V shift, and the fastest OFF gating currents. Further study of the residue at position 484, using mutagenesis and modification of F484C by cysteine reagents, suggests that aromaticity at this position is essential to maintain normal coupling. We used periodicity analysis to appraise the possibility that the S6 tail has an alpha-helical structure. Although we obtained an alpha-periodicity index of 2.41 for gating current parameters, a new randomization test produced an indecisive conclusion about the secondary structure of this region. Taken together, our results suggest that the tail end of S6 plays an important role in coupling between activation gating and charge movement.
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Affiliation(s)
- Shinghua Ding
- Department of Physiology, Institute of Hyperexcitability, Jefferson Medical College, Philadelphia, Pennsylvania 19107, USA
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