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Reddi R, Chatterjee S, Matulef K, Gustafson A, Gao L, Valiyaveetil FI. A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. J Biol Chem 2024; 300:105517. [PMID: 38042487 PMCID: PMC10790091 DOI: 10.1016/j.jbc.2023.105517] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Amide-to-ester substitutions are used to study the role of the amide bonds of the protein backbone in protein structure, function, and folding. An amber suppressor tRNA/synthetase pair has been reported for incorporation of p-hydroxy-phenyl-L-lactic acid (HPLA), thereby introducing ester substitution at tyrosine residues. However, the application of this approach was limited due to the low yields of the modified proteins and the high cost of HPLA. Here we report the in vivo generation of HPLA from the significantly cheaper phenyl-L-lactic acid. We also construct an optimized plasmid with the HPLA suppressor tRNA/synthetase pair that provides higher yields of the modified proteins. The combination of the new plasmid and the in-situ generation of HPLA provides a facile and economical approach for introducing tyrosine ester substitutions. We demonstrate the utility of this approach by introducing tyrosine ester substitutions into the K+ channel KcsA and the integral membrane enzyme GlpG. We introduce the tyrosine ester in the selectivity filter of the M96V mutant of the KcsA to probe the role of the second ion binding site in the conformation of the selectivity filter and the process of inactivation. We use tyrosine ester substitutions in GlpG to perturb backbone H-bonds to investigate the contribution of these H-bonds to membrane protein stability. We anticipate that the approach developed in this study will facilitate further investigations using tyrosine ester substitutions.
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Affiliation(s)
- Ravikumar Reddi
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Satyaki Chatterjee
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Kimberly Matulef
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Andrew Gustafson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Lujia Gao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA
| | - Francis I Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Multnomah County, Portland, Oregon, USA.
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2
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Veit S, Paweletz LC, Günther Pomorski T. Determination of membrane protein orientation upon liposomal reconstitution down to the single vesicle level. Biol Chem 2023; 404:647-661. [PMID: 36857289 DOI: 10.1515/hsz-2022-0325] [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: 11/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Reconstitution of membrane proteins into liposomal membranes represents a key technique in enabling functional analysis under well-defined conditions. In this review, we provide a brief introduction to selected methods that have been developed to determine membrane protein orientation after reconstitution in liposomes, including approaches based on proteolytic digestion with proteases, site-specific labeling, fluorescence quenching and activity assays. In addition, we briefly highlight new strategies based on single vesicle analysis to address the problem of sample heterogeneity.
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Affiliation(s)
- Sarina Veit
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Laura Charlotte Paweletz
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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3
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Bakhtiari S, Manshadi MKD, Candas M, Beskok A. Changes in Electrical Capacitance of Cell Membrane Reflect Drug Partitioning-Induced Alterations in Lipid Bilayer. MICROMACHINES 2023; 14:316. [PMID: 36838014 PMCID: PMC9961635 DOI: 10.3390/mi14020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The plasma membrane is a lipid bilayer that establishes the outer boundary of a living cell. The composition of the lipid bilayer influences the membrane's biophysical properties, including fluidity, thickness, permeability, phase behavior, charge, elasticity, and formation of flat sheet or curved structures. Changes in the biophysical properties of the membrane can be occasioned when new entities, such as drug molecules, are partitioned in the bilayer. Therefore, assessing drugs for their effect on the biophysical properties of the lipid bilayer of a cell membrane is critical to understanding specific and non-specific drug action. Previously, we reported a non-invasive technique for real-time characterization of cellular dielectric properties, such as membrane capacitance and cytoplasmic conductivity. In this study, we discuss the potential application of the technique in assessing the biophysical properties of the cell membrane in response to interaction with amiodarone compared to aspirin/acetylsalicylic acid and glucose. Amiodarone is a potent drug used to treat cardiac arrhythmia, but it also exerts various non-specific effects. Compared to aspirin and glucose, we measured a rapid and higher magnitude increase in membrane capacitance on cells under amiodarone treatment. Increased membrane capacitance induced by aspirin and glucose quickly returned to baseline in 15 s, while amiodarone-induced increased capacitance sustained and decreased slowly, approaching baseline or another asymptotic limit in ~2.5 h. Because amiodarone has a strong lipid partitioning property, we reason that drug partitioning alters the lipid bilayer context and subsequently reduces bilayer thickness, leading to an increase in the electrical capacitance of the cell membrane. The presented microfluidic system promises a new approach to assess drug-membrane interactions and delineate specific and non-specific actions of the drug on cells.
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Affiliation(s)
- Shide Bakhtiari
- Mechanical Engineering Department, Southern Methodist University, Dallas, TX 75275, USA
| | | | - Mehmet Candas
- Department of Biological Sciences, University of Texas at Dallas, Dallas, TX 75080, USA
| | - Ali Beskok
- Mechanical Engineering Department, Southern Methodist University, Dallas, TX 75275, USA
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4
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Esquembre R, Renart ML, Poveda JA, Mateo CR. Silica/Proteoliposomal Nanocomposite as a Potential Platform for Ion Channel Studies. Molecules 2022; 27:molecules27196658. [PMID: 36235195 PMCID: PMC9571612 DOI: 10.3390/molecules27196658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
The nanostructuration of solid matrices with lipid nanoparticles containing membrane proteins is a promising tool for the development of high-throughput screening devices. Here, sol-gel silica-derived nanocomposites loaded with liposome-reconstituted KcsA, a prokaryotic potassium channel, have been synthesized. The conformational and functional stability of these lipid nanoparticles before and after sol-gel immobilization have been characterized by using dynamic light scattering, and steady-state and time-resolved fluorescence spectroscopy methods. The lipid-reconstituted KcsA channel entrapped in the sol-gel matrix retained the conformational and stability changes induced by the presence of blocking or permeant cations in the buffer (associated with the conformation of the selectivity filter) or by a drop in the pH (associated with the opening of the activation gate of the protein). Hence, these results indicate that this novel device has the potential to be used as a screening platform to test new modulating drugs of potassium channels.
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5
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Reddi R, Matulef K, Riederer E, Moenne-Loccoz P, Valiyaveetil FI. Structures of Gating Intermediates in a K + channel. J Mol Biol 2021; 433:167296. [PMID: 34627789 DOI: 10.1016/j.jmb.2021.167296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
Regulation of ion conduction through the pore of a K+ channel takes place through the coordinated action of the activation gate at the bundle crossing of the inner helices and the inactivation gate located at the selectivity filter. The mechanism of allosteric coupling of these gates is of key interest. Here we report new insights into this allosteric coupling mechanism from studies on a W67F mutant of the KcsA channel. W67 is in the pore helix and is highly conserved in K+ channels. The KcsA W67F channel shows severely reduced inactivation and an enhanced rate of activation. We use continuous wave EPR spectroscopy to establish that the KcsA W67F channel shows an altered pH dependence of activation. Structural studies on the W67F channel provide the structures of two intermediate states: a pre- open state and a pre-inactivated state of the KcsA channel. These structures highlight key nodes in the allosteric pathway. The structure of the KcsA W67F channel with the activation gate open shows altered ion occupancy at the second ion binding site (S2) in the selectivity filter. This finding in combination with previous studies strongly support a requirement for ion occupancy at the S2 site for the channel to inactivate.
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Affiliation(s)
- Ravikumar Reddi
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States. https://twitter.com/Ravi_K_Reddi
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Erika Riederer
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Pierre Moenne-Loccoz
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States.
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6
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Mechanisms underlying drug-mediated regulation of membrane protein function. Proc Natl Acad Sci U S A 2021; 118:2113229118. [PMID: 34753824 DOI: 10.1073/pnas.2113229118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
The hydrophobic coupling between membrane proteins and their host lipid bilayer provides a mechanism by which bilayer-modifying drugs may alter protein function. Drug regulation of membrane protein function thus may be mediated by both direct interactions with the protein and drug-induced alterations of bilayer properties, in which the latter will alter the energetics of protein conformational changes. To tease apart these mechanisms, we examine how the prototypical, proton-gated bacterial potassium channel KcsA is regulated by bilayer-modifying drugs using a fluorescence-based approach to quantify changes in both KcsA function and lipid bilayer properties (using gramicidin channels as probes). All tested drugs inhibited KcsA activity, and the changes in the different gating steps varied with bilayer thickness, suggesting a coupling to the bilayer. Examining the correlations between changes in KcsA gating steps and bilayer properties reveals that drug-induced regulation of membrane protein function indeed involves bilayer-mediated mechanisms. Both direct, either specific or nonspecific, binding and bilayer-mediated mechanisms therefore are likely to be important whenever there is overlap between the concentration ranges at which a drug alters membrane protein function and bilayer properties. Because changes in bilayer properties will impact many diverse membrane proteins, they may cause indiscriminate changes in protein function.
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7
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Ueki M, Iwamoto M. Fluorescent labeling in size-controlled liposomes reveals membrane curvature-induced structural changes in the KcsA potassium channel. FEBS Lett 2021; 595:1914-1919. [PMID: 34080704 DOI: 10.1002/1873-3468.14141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 11/06/2022]
Abstract
Biological structures with highly curved membranes, such as caveolae and transport vesicles, are essential for signal transduction and membrane trafficking. Although membrane proteins in these structures are subjected to physical stress due to the curvature of the lipid bilayers, the effect of this membrane curvature on protein structure and function remains unclear. In this study, we established an experimental procedure to evaluate membrane curvature-induced structural changes in the prototypical potassium channel KcsA. The effect of a large membrane curvature was estimated using fluorescently labeled KcsA by incorporating it into liposomes with a small diameter (< 30 nm). We found that a large membrane curvature significantly affects the activation gate conformation of the KcsA channel.
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Affiliation(s)
- Misuzu Ueki
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Japan
| | - Masayuki Iwamoto
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Japan
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8
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Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
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9
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Laucirica G, Toum Terrones Y, Cayón VM, Cortez ML, Toimil-Molares ME, Trautmann C, Marmisollé WA, Azzaroni O. High-sensitivity detection of dopamine by biomimetic nanofluidic diodes derivatized with poly(3-aminobenzylamine). NANOSCALE 2020; 12:18390-18399. [PMID: 32941586 DOI: 10.1039/d0nr03634j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During the last few years, much scientific effort has been devoted to the control of ionic transport properties of solid state nanochannels and the rational integration of chemical systems to induce changes in the ionic transport by interaction with selected target molecules for (bio)sensing purposes. In this work, we present the construction and functional evaluation of a highly sensitive dopamine-responsive iontronic device by functionalization of bullet-shaped track-etched single nanochannels in PET membranes with poly(3-aminobenzylamine) (PABA). The variety of basic groups in this amino-appended polyaniline derivative allows programming of the ion selectivity of the channel by setting the pH conditions. On the other hand, the amino-pendant groups of PABA become suitable binding sites for the selective chemical reaction with dopamine, leading to a change in the nanochannel surface charge. Thus, the exposure of the PABA-modified nanochannel to dopamine solutions selectively produces changes in the iontronic response. By rationally selecting the conditions for both the dopamine binding step and the iontronic reading, we obtained a correlation between the rectification efficiency and dopamine concentration down to the nanomolar range, which was also successfully interpreted in terms of a simple binding model.
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Affiliation(s)
- Gregorio Laucirica
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - Yamili Toum Terrones
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - Vanina M Cayón
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - M Lorena Cortez
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
| | | | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany and Technische Universität Darmstadt, Materialwissenschaft, 64287 Darmstadt, Germany
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, 1900 La Plata, Argentina.
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10
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Callahan KM, Mondou B, Sasseville L, Schwartz JL, D'Avanzo N. The influence of membrane bilayer thickness on KcsA channel activity. Channels (Austin) 2020; 13:424-439. [PMID: 31608774 PMCID: PMC6802934 DOI: 10.1080/19336950.2019.1676367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Atomic resolution structures have provided significant insight into the gating and permeation mechanisms of various ion channels, including potassium channels. However, ion channels may also be regulated by numerous factors, including the physiochemical properties of the membrane in which they are embedded. For example, the matching of the bilayer's hydrophobic region to the hydrophobic external surface of the ion channel is thought to minimize the energetic penalty needed to solvate hydrophobic residues or exposed lipid tails. To understand the molecular basis of such regulation by hydrophobic matching requires examining channels in the presence of the lipid membrane. Here we examine the role of hydrophobic matching in regulating the activity of the model potassium channel, KcsA. 86Rb+ influx assays and single-channel recordings indicate that the non-inactivating E71A KcsA channel is most active in thin bilayers (<diC18:1PC). Bilayer thickness affects the open probability of KcsA and not its unitary conductance. Molecular dynamics simulations indicate that the bilayer can sufficiently modify its dimensions to accommodate KcsA channels without major perturbations in the protein helical packing within the nanosecond timescale. Based on experimental results and MD simulations, we present a model in which bilayer thickness influences the stability of the open and closed conformations of the intracellular gate of KcsA, with minimal impact on the stability of the selectivity filter of the non-inactivating mutant, E71A.
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Affiliation(s)
- Karen M Callahan
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Benoit Mondou
- Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
| | - Louis Sasseville
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Jean-Louis Schwartz
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada.,Centre SÈVE, Université de Sherbrooke , Sherbrooke , Canada
| | - Nazzareno D'Avanzo
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
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11
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Peng P, Wang Q, Du Y, Wang H, Shi L, Li T. Extracellular Ion-Responsive Logic Sensors Utilizing DNA Dimeric Nanoassemblies on Cell Surface and Application to Boosting AS1411 Internalization. Anal Chem 2020; 92:9273-9280. [PMID: 32521996 DOI: 10.1021/acs.analchem.0c01612] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High levels of extracellular H+ and K+ are unique features of the tumor microenvironment and have shown great promise for use in cancer-targeted drug delivery. Here, we design H+- and/or K+-responsive logic sensors utilizing in situ dimeric framework nucleic acid (FNA) assembly on the cell surface and for the first time apply the logic sensors to boosting cellular internalization of molecular payloads in tumor-mimicking extracellular environments. An anticancer aptamer AS1411 is blocked on branched FNA vertexes where a bimolecular i-motif is tethered as the controlling unit to enable a dimeric DNA nanoassembly in response to extracellular pH change. K+ promotes AS1411 to fold into a G-quadruplex and thereby release from dimeric FNA in which a proximity DNA hybridization-based FRET happens. Furthermore, such an AND-gated nanosensor functions more efficiently for AS1411 internalization than the conventional pathway. This finding shows significant implications for tumor-microenvironment-recognizing target drug delivery and precision cancer therapy.
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Affiliation(s)
- Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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12
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Modulation of Function, Structure and Clustering of K + Channels by Lipids: Lessons Learnt from KcsA. Int J Mol Sci 2020; 21:ijms21072554. [PMID: 32272616 PMCID: PMC7177331 DOI: 10.3390/ijms21072554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
KcsA, a prokaryote tetrameric potassium channel, was the first ion channel ever to be structurally solved at high resolution. This, along with the ease of its expression and purification, made KcsA an experimental system of choice to study structure–function relationships in ion channels. In fact, much of our current understanding on how the different channel families operate arises from earlier KcsA information. Being an integral membrane protein, KcsA is also an excellent model to study how lipid–protein and protein–protein interactions within membranes, modulate its activity and structure. In regard to the later, a variety of equilibrium and non-equilibrium methods have been used in a truly multidisciplinary effort to study the effects of lipids on the KcsA channel. Remarkably, both experimental and “in silico” data point to the relevance of specific lipid binding to two key arginine residues. These residues are at non-annular lipid binding sites on the protein and act as a common element to trigger many of the lipid effects on this channel. Thus, processes as different as the inactivation of channel currents or the assembly of clusters from individual KcsA channels, depend upon such lipid binding.
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13
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Otsuka R, Hirata K, Sasaki Y, Lisy JM, Ishiuchi S, Fujii M. Alkali and Alkaline Earth Metal Ions Complexes with a Partial Peptide of the Selectivity Filter in K
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Channels Studied by a Cold Ion Trap Infrared Spectroscopy. Chemphyschem 2020; 21:712-724. [DOI: 10.1002/cphc.202000033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/12/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Remina Otsuka
- Laboratory for Chemistry and Life ScienceInstitute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and TechnologyTokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8503 Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life ScienceInstitute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and TechnologyTokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8503 Japan
| | - Yuta Sasaki
- Laboratory for Chemistry and Life ScienceInstitute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and TechnologyTokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8503 Japan
| | - James M. Lisy
- Tokyo Tech World Research Hub Initiative (WRHI)Institute of Innovation Research, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- Department of ChemistryUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Shun‐ichi Ishiuchi
- Laboratory for Chemistry and Life ScienceInstitute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and TechnologyTokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8503 Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life ScienceInstitute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
- School of Life Science and TechnologyTokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8503 Japan
- Tokyo Tech World Research Hub Initiative (WRHI)Institute of Innovation Research, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokohama 226-8503 Japan
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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15
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Chill JH, Qasim A, Sher I, Gross R. NMR Perspectives of the KcsA Potassium Channel in the Membrane Environment. Isr J Chem 2019. [DOI: 10.1002/ijch.201900107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordan H. Chill
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Arwa Qasim
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Inbal Sher
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Renana Gross
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
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16
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Qasim A, Sher I, Hirschhorn O, Shaked H, Qasem Z, Ruthstein S, Chill JH. Investigation of a KcsA Cytoplasmic pH Gate in Lipoprotein Nanodiscs. Chembiochem 2019; 20:813-821. [PMID: 30565824 DOI: 10.1002/cbic.201800627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 12/14/2022]
Abstract
The bacterial potassium channel KcsA is gated by pH, opening for conduction under acidic conditions. Molecular determinants responsible for this effect have been identified at the extracellular selectivity filter, at the membrane-cytoplasm interface (TM2 gate), and in the cytoplasmic C-terminal domain (CTD), an amphiphilic four-helix bundle mediated by hydrophobic and electrostatic interactions. Here we have employed NMR and EPR to provide a structural view of the pH-induced open-to-closed CTD transition. KcsA was embedded in lipoprotein nanodiscs (LPNs), selectively methyl-protonated at Leu/Val residues to allow observation of both states by NMR, and spin-labeled for the purposes of EPR studies. We observed a pHinduced structural change between an associated structured CTD at neutral pH and a dissociated flexible CTD at acidic pH, with a transition in the 5.0-5.5 range, consistent with a stabilization of the CTD by channel architecture. A double mutant constitutively open at the TM2 gate exhibited reduced stability of associated CTD, as indicated by weaker spin-spin interactions, a shift to higher transition pH values, and a tenfold reduction in the population of the associated "closed" channels. We extended these findings for isolated CTD-derived peptides to full-length KcsA and have established a contribution of the CTD to KcsA pH-controlled gating, which exhibits a strong correlation with the state of the proximal TM2 gate.
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Affiliation(s)
- Arwa Qasim
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Inbal Sher
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Orel Hirschhorn
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Zena Qasem
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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17
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Zhang X, Han X, Qian S, Yang Y, Hu N. Tuning Ion Transport through a Nanopore by Self-Oscillating Chemical Reactions. Anal Chem 2019; 91:4600-4607. [DOI: 10.1021/acs.analchem.8b05823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoling Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
| | - Xianwei Han
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Yuanjian Yang
- School of Safety Engineering, Chongqing University of Science and Technology, Chongqing 401331, PR China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
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18
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Gamal El-Din TM, Lenaeus MJ, Ramanadane K, Zheng N, Catterall WA. Molecular dissection of multiphase inactivation of the bacterial sodium channel Na VAb. J Gen Physiol 2018; 151:174-185. [PMID: 30510035 PMCID: PMC6363407 DOI: 10.1085/jgp.201711884] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/22/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Voltage-gated sodium channels have a conserved multiphase slow-inactivation process. Gamal El-Din et al. show that the early phase involves conformational changes at a critical threonine in the S6 segment, which are followed by a late phase mediated by the intracellular C-terminal domain. Homotetrameric bacterial voltage-gated sodium channels share major biophysical features with their more complex eukaryotic counterparts, including a slow-inactivation mechanism that reduces ion-conductance activity during prolonged depolarization through conformational changes in the pore. The bacterial sodium channel NaVAb activates at very negative membrane potentials and inactivates through a multiphase slow-inactivation mechanism. Early voltage-dependent inactivation during one depolarization is followed by late use-dependent inactivation during repetitive depolarization. Mutations that change the molecular volume of Thr206 in the pore-lining S6 segment can enhance or strongly block early voltage-dependent inactivation, suggesting that this residue serves as a molecular hub controlling the coupling of activation to inactivation. In contrast, truncation of the C-terminal tail enhances the early phase of inactivation yet completely blocks late use-dependent inactivation. Determination of the structure of a C-terminal tail truncation mutant and molecular modeling of conformational changes at Thr206 and the S6 activation gate led to a two-step model of these gating processes. First, bending of the S6 segment, local protein interactions dependent on the size of Thr206, and exchange of hydrogen-bonding partners at the level of Thr206 trigger pore opening followed by the early phase of voltage-dependent inactivation. Thereafter, conformational changes in the C-terminal tail lead to late use-dependent inactivation. These results have important implications for the sequence of conformational changes that lead to multiphase inactivation of NaVAb and other sodium channels.
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Affiliation(s)
| | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA.,Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, WA
| | - Karthik Ramanadane
- Department of Pharmacology, University of Washington, Seattle, WA.,École Normal Supérieure, Cachan, France
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
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19
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Gamal El-Din TM, Lenaeus MJ, Catterall WA. Structural and Functional Analysis of Sodium Channels Viewed from an Evolutionary Perspective. Handb Exp Pharmacol 2018; 246:53-72. [PMID: 29043505 DOI: 10.1007/164_2017_61] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels initiate and propagate action potentials in excitable cells. They respond to membrane depolarization through opening, followed by fast inactivation that terminates the sodium current. This ON-OFF behavior of voltage-gated sodium channels underlays the coding of information and its transmission from one location in the nervous system to another. In this review, we explore and compare structural and functional data from prokaryotic and eukaryotic channels to infer the effects of evolution on sodium channel structure and function.
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Affiliation(s)
- Tamer M Gamal El-Din
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA.
| | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
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20
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Rondelli V, Del Favero E, Brocca P, Fragneto G, Trapp M, Mauri L, Ciampa M, Romani G, Braun C, Winterstein L, Schroeder I, Thiel G, Moroni A, Cantu' L. Directional K+ channel insertion in a single phospholipid bilayer: Neutron reflectometry and electrophysiology in the joint exploration of a model membrane functional platform. Biochim Biophys Acta Gen Subj 2018; 1862:1742-1750. [DOI: 10.1016/j.bbagen.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/27/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
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21
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Hirano M, Ide T. Electrostatic state of the cytoplasmic domain influences inactivation at the selectivity filter of the KcsA potassium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:220-227. [PMID: 30053405 DOI: 10.1016/j.bbamem.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022]
Abstract
KcsA is a proton-activated K+ channel that is regulated at two gates: an activation gate located in the inner entrance of the pore and an inactivation gate at the selectivity filter. Previously, we revealed that the cytoplasmic domain (CPD) of KcsA senses proton and that electrostatic changes of the CPD influences the opening and closing of the activation gate. However, our previous studies did not reveal the effect of CPD on the inactivation gate because we used a non-inactivating mutant (E71A). In the present study, we used mutants that did not harbor the E71A mutation, and showed that the electrostatic state of the CPD influences the inactivation gate. Three novel CPD mutants were generated in which some negatively charged amino acids were replaced with neutral amino acids. These CPD mutants conducted K+, but showed various inactivation properties. Mutants carrying the D149N mutation showed high open probability and slow inactivation, whereas those without the D149N mutation showed low open probability and fast inactivation, similar to wild-type KcsA. In addition, mutants with D149N showed poor K+ selectivity, and permitted Na+ to flow. These results indicated that electrostatic changes in the CPD by D149N mutation triggered the loss of fast inactivation and changes in the conformation of selectivity filter. Additionally, the loss of fast inactivation induced by D149N was reversed by R153A mutation, suggesting that not only the electrostatic state of D149, but also that of R153 affects inactivation.
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Affiliation(s)
- Minako Hirano
- Bio Photonics Laboratory, The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
| | - Toru Ide
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka Kita-ku, Okayama-shi, Okayama 700-8530, Japan
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22
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CW-EPR Spectroscopy and Site-Directed Spin Labeling to Study the Structural Dynamics of Ion Channels. Methods Mol Biol 2018; 1684:279-288. [PMID: 29058199 DOI: 10.1007/978-1-4939-7362-0_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Continuous-wave electron paramagnetic resonance spectroscopy (CW-EPR) and site-directed spin labeling (SDSL) are proven experimental approaches to assess the structural dynamics of proteins in general (Hubbell et al., Curr Opin Struct Biol 8(5):649-656, 1998; Kazmier et al., Curr Opin Struct Biol 45:100-108, 2016; Perozo et al., Science 285(5424):73-78, 1999). These techniques have been particularly effective assessing the structure of integral membrane proteins embedded in a lipid bilayer (Cortes et al., J Gen Physiol 117(2):165-180, 2001; Cuello et al., Science 306(5695):491-495, 2004; Dalmas et al., Structure 18(7):868-878, 2010; Li et al., Proc Natl Acad Sci U S A 112(44):E5926-5935, 2015; Perozo et al., J Gen Physiol 118(2):193-206, 2001), as well as determining the conformational changes associated with their biological function (Kazmier et al., Curr Opin Struct Biol 45:100-108, 2016; Perozo et al., Science 285(5424):73-78, 1999; Arrigoni et al., Cell 164(5):922-936, 2016; Dalmas et al., Nat Commun 5:3590, 2014; Dong et al., Science 308(5724):1023-1028, 2005; Farrens et al., Science 274(5288):768-770, 1996; Perozo et al., Nat Struct Biol 5(6):459-469, 1998; Perozo et al., Nature 418(6901):942-948, 2002). In this chapter, we described a practical guide for the spin-labeling, liposome reconstitution, and CW-EPR measurements of the prototypical bacterial K+ channel, KcsA.
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23
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Mitchell MR, Leibler S. Elastic strain and twist analysis of protein structural data and allostery of the transmembrane channel KcsA. Phys Biol 2018; 15:036004. [PMID: 29116053 DOI: 10.1088/1478-3975/aa9906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The abundance of available static protein structural data makes the more effective analysis and interpretation of this data a valuable tool to supplement the experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins. Here, we demonstrate that other transformations of displacements yield additional insights. We calculate the divergence and curl of deformations of the transmembrane channel KcsA. Additionally, we introduce quantities analogous to bend, splay, and twist deformation energies of nematic liquid crystals. These transformations enable the decomposition of displacements into different modes of deformation, helping to characterize the type of deformation a protein undergoes. We apply these calculations to study the filter and gating regions of KcsA. We observe a continuous path of rotational deformations physically coupling these two regions, and, we propose, underlying the allosteric interaction between these regions. Bend, splay, and twist distinguish KcsA gate opening, filter opening, and filter-gate coupling, respectively. In general, physically meaningful representations of deformations (like strain, curl, bend, splay, and twist) can make testable predictions and yield insights into protein mechanics, augmenting experimental methods and more fully exploiting available structural data.
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Affiliation(s)
- Michael R Mitchell
- Laboratory of Living Matter and the Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, United States of America
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24
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Visscher KM, Medeiros-Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolekulare Organisation und funktionale Auswirkungen von Ballungen von K +
-Kanälen in Membranen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
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25
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Visscher KM, Medeiros‐Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolecular Organization and Functional Implications of K + Channel Clusters in Membranes. Angew Chem Int Ed Engl 2017; 56:13222-13227. [PMID: 28685953 PMCID: PMC5655921 DOI: 10.1002/anie.201705723] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/29/2017] [Indexed: 11/19/2022]
Abstract
The segregation of cellular surfaces in heterogeneous patches is considered to be a common motif in bacteria and eukaryotes that is underpinned by the observation of clustering and cooperative gating of signaling membrane proteins such as receptors or channels. Such processes could represent an important cellular strategy to shape signaling activity. Hence, structural knowledge of the arrangement of channels or receptors in supramolecular assemblies represents a crucial step towards a better understanding of signaling across membranes. We herein report on the supramolecular organization of clusters of the K+ channel KcsA in bacterial membranes, which was analyzed by a combination of DNP-enhanced solid-state NMR experiments and MD simulations. We used solid-state NMR spectroscopy to determine the channel-channel interface and to demonstrate the strong correlation between channel function and clustering, which suggests a yet unknown mechanism of communication between K+ channels.
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Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João Medeiros‐Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
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26
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van der Cruijsen EAW, Prokofyev AV, Pongs O, Baldus M. Probing Conformational Changes during the Gating Cycle of a Potassium Channel in Lipid Bilayers. Biophys J 2017; 112:99-108. [PMID: 28076820 DOI: 10.1016/j.bpj.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/08/2016] [Accepted: 12/01/2016] [Indexed: 01/10/2023] Open
Abstract
Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K+ channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K+ gating. Yet, the direct observation of the full gating cycle of KcsA has remained structurally elusive, and crystal structures mimicking these gating events require mutations in or stabilization of functionally relevant channel segments. Here, we found that changes in lipid composition strongly increased the KcsA open probability. This enabled us to probe all four major gating states in native-like membranes by combining electrophysiological and solid-state NMR experiments. In contrast to previous crystallographic views, we found that the selectivity filter and turret region, coupled to the surrounding bilayer, were actively involved in channel gating. The increase in overall steady-state open probability was accompanied by a reduction in activation-gate opening, underscoring the important role of the surrounding lipid bilayer in the delicate conformational coupling of the inactivation and activation gates.
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Affiliation(s)
- Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Alexander V Prokofyev
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany
| | - Olaf Pongs
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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27
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Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017; 7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA.
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- SETI Institute, 189 N Bernardo Ave #200, Mountain View, CA 94043, USA.
| | - Gareth Shannon
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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28
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Montoya E, Lourdes Renart M, Marcela Giudici A, Poveda JA, Fernández AM, Morales A, González-Ros JM. Differential binding of monovalent cations to KcsA: Deciphering the mechanisms of potassium channel selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:779-788. [PMID: 28088447 DOI: 10.1016/j.bbamem.2017.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/16/2016] [Accepted: 01/10/2017] [Indexed: 11/19/2022]
Abstract
This work explores whether the ion selectivity and permeation properties of a model potassium channel, KcsA, could be explained based on ion binding features. Non-permeant Na+ or Li+ bind with low affinity (millimolar KD's) to a single set of sites contributed by the S1 and S4 sites seen at the selectivity filter in the KcsA crystal structure. Conversely, permeant K+, Rb+, Tl+ and even Cs+ bind to two different sets of sites as their concentration increases, consistent with crystallographic evidence on the ability of permeant species to induce concentration-dependent transitions between conformational states (non-conductive and conductive) of the channel's selectivity filter. The first set of such sites, assigned also to the crystallographic S1 and S4 sites, shows similarly high affinities for all permeant species (micromolar KD's), thus, securing displacement of potentially competing non-permeant cations. The second set of sites, available only to permeant cations upon the transition to the conductive filter conformation, shows low affinity (millimolar KD's), thus, favoring cation dissociation and permeation and results from the contribution of all S1 through S4 crystallographic sites. The differences in affinities between permeant and non-permeant cations and the similarities in binding behavior within each of these two groups, correlate fully with their permeabilities relative to K+, suggesting that binding is an important determinant of the channel's ion selectivity. Conversely, the complexity observed in permeation features cannot be explained just in terms of binding and likely relates to reported differences in the occupancy of the S2 and S3 sites by the permeant cations.
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Affiliation(s)
- Estefanía Montoya
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - M Lourdes Renart
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - A Marcela Giudici
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - José A Poveda
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - Asia M Fernández
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - Andrés Morales
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - José M González-Ros
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain.
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Kim DM, Dikiy I, Upadhyay V, Posson DJ, Eliezer D, Nimigean CM. Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles. J Gen Physiol 2016; 148:119-32. [PMID: 27432996 PMCID: PMC4969796 DOI: 10.1085/jgp.201611602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 12/27/2022] Open
Abstract
The process of ion channel gating-opening and closing-involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Igor Dikiy
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
| | - Vikrant Upadhyay
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
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30
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Tilegenova C, Vemulapally S, Cortes DM, Cuello LG. An improved method for the cost-effective expression and purification of large quantities of KcsA. Protein Expr Purif 2016; 127:53-60. [PMID: 27393071 DOI: 10.1016/j.pep.2016.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/22/2016] [Accepted: 07/04/2016] [Indexed: 11/30/2022]
Abstract
KcsA, the bacterial K(+) channel from Streptomyces lividans, is the prototypical model system to study the functional and structural correlations of the pore domain of eukaryotic voltage-gated K(+) channels (Kv channels). It contains all the molecular elements responsible for ion conduction, activation, deactivation and inactivation gating [1]. KcsA's structural simplicity makes it highly amenable for structural studies. Therefore, it is methodological advantageous to produce large amounts of functional and properly folded KcsA in a cost-effective manner. In the present study, we show an optimized protocol for the over-expression and purification of large amounts of high-quality, fully functional and crystallizable KcsA using inexpensive detergents, which significantly lowered the cost of the purification process.
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Affiliation(s)
- Cholpon Tilegenova
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6551, Lubbock, TX 79430, USA
| | - Spandana Vemulapally
- Current address: Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Doris M Cortes
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6551, Lubbock, TX 79430, USA
| | - Luis G Cuello
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6551, Lubbock, TX 79430, USA.
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31
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Niemeyer MI, Cid LP, González W, Sepúlveda FV. Gating, Regulation, and Structure in K2P K+ Channels: In Varietate Concordia? Mol Pharmacol 2016; 90:309-17. [DOI: 10.1124/mol.116.103895] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/31/2016] [Indexed: 11/22/2022] Open
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Individual Ion Binding Sites in the K(+) Channel Play Distinct Roles in C-type Inactivation and in Recovery from Inactivation. Structure 2016; 24:750-761. [PMID: 27150040 DOI: 10.1016/j.str.2016.02.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/08/2016] [Accepted: 02/16/2016] [Indexed: 01/14/2023]
Abstract
The selectivity filter of K(+) channels contains four ion binding sites (S1-S4) and serves dual functions of discriminating K(+) from Na(+) and acting as a gate during C-type inactivation. C-type inactivation is modulated by ion binding to the selectivity filter sites, but the underlying mechanism is not known. Here we evaluate how the ion binding sites in the selectivity filter of the KcsA channel participate in C-type inactivation and in recovery from inactivation. We use unnatural amide-to-ester substitutions in the protein backbone to manipulate the S1-S3 sites and a side-chain substitution to perturb the S4 site. We develop an improved semisynthetic approach for generating these amide-to-ester substitutions in the selectivity filter. Our combined electrophysiological and X-ray crystallographic analysis of the selectivity filter mutants show that the ion binding sites play specific roles during inactivation and provide insights into the structural changes at the selectivity filter during C-type inactivation.
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33
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Rivera-Torres IO, Jin TB, Cadene M, Chait BT, Poget SF. Discovery and characterisation of a novel toxin from Dendroaspis angusticeps, named Tx7335, that activates the potassium channel KcsA. Sci Rep 2016; 6:23904. [PMID: 27044983 PMCID: PMC4820689 DOI: 10.1038/srep23904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/16/2016] [Indexed: 02/07/2023] Open
Abstract
Due to their central role in essential physiological processes, potassium channels are common targets for animal toxins. These toxins in turn are of great value as tools for studying channel function and as lead compounds for drug development. Here, we used a direct toxin pull-down assay with immobilised KcsA potassium channel to isolate a novel KcsA-binding toxin (called Tx7335) from eastern green mamba snake (Dendroaspis angusticeps) venom. Sequencing of the toxin by Edman degradation and mass spectrometry revealed a 63 amino acid residue peptide with 4 disulphide bonds that belongs to the three-finger toxin family, but with a unique modification of its disulphide-bridge scaffold. The toxin induces a dose-dependent increase in both open probabilities and mean open times on KcsA in artificial bilayers. Thus, it unexpectedly behaves as a channel activator rather than an inhibitor. A charybdotoxin-sensitive mutant of KcsA exhibits similar susceptibility to Tx7335 as wild-type, indicating that the binding site for Tx7335 is distinct from that of canonical pore-blocker toxins. Based on the extracellular location of the toxin binding site (far away from the intracellular pH gate), we propose that Tx7335 increases potassium flow through KcsA by allosterically reducing inactivation of the channel.
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Affiliation(s)
- Iván O. Rivera-Torres
- LaGuardia Community College, City University of New York, Long Island City, NY 11101, USA
| | - Tony B. Jin
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | | | | | - Sébastien F. Poget
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
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34
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Zhang H, Tian Y, Hou J, Hou X, Hou G, Ou R, Wang H, Jiang L. Bioinspired Smart Gate-Location-Controllable Single Nanochannels: Experiment and Theoretical Simulation. ACS NANO 2015; 9:12264-73. [PMID: 26474219 DOI: 10.1021/acsnano.5b05542] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
pH-activated gates intelligently govern the ion transport behaviors of a wide range of bioinspired ion channels, but the mechanisms between the gate locations and the functionalities of the ion channels remain poorly understood. Here, we construct an artificial gate-location-tunable single-nanochannel system to systematically investigate the impact of the gate location on the ion transport property of the biomimetic ion channel. The gate-location-controllable single nanochannels are prepared by asymmetrically grafting pH-responsive polymer gates on one side of single nanochannels with gradual shape transformation. Experimental ion current measurements show that the gating abilities and rectification effects of the pH-gated nanochannels can be gradually altered by precisely locating the artificial pH gates on the different sites of the channels. The experimental gate-location-dependent gating and rectification of ion current in the bioinspired ion channel system is further well confirmed by theoretical simulation. This work, as an example, provides a new avenue to optimize the smart ion transport features of diverse artificial nanogate devices via precisely locating the gates on the appropriate sites of the artificial nanochannels.
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Affiliation(s)
- Huacheng Zhang
- Laboratory of Bio-Inspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
| | - Ye Tian
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Jue Hou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Xu Hou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Guanglei Hou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Ranwen Ou
- Department of Chemical Engineering, Monash University , Clayton, Victoria 3800, Australia
| | - Huanting Wang
- Department of Chemical Engineering, Monash University , Clayton, Victoria 3800, Australia
| | - Lei Jiang
- Laboratory of Bio-Inspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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35
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Ion-binding properties of a K+ channel selectivity filter in different conformations. Proc Natl Acad Sci U S A 2015; 112:15096-100. [PMID: 26598654 DOI: 10.1073/pnas.1510526112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
K(+) channels are membrane proteins that selectively conduct K(+) ions across lipid bilayers. Many voltage-gated K(+) (KV) channels contain two gates, one at the bundle crossing on the intracellular side of the membrane and another in the selectivity filter. The gate at the bundle crossing is responsible for channel opening in response to a voltage stimulus, whereas the gate at the selectivity filter is responsible for C-type inactivation. Together, these regions determine when the channel conducts ions. The K(+) channel from Streptomyces lividians (KcsA) undergoes an inactivation process that is functionally similar to KV channels, which has led to its use as a practical system to study inactivation. Crystal structures of KcsA channels with an open intracellular gate revealed a selectivity filter in a constricted conformation similar to the structure observed in closed KcsA containing only Na(+) or low [K(+)]. However, recent work using a semisynthetic channel that is unable to adopt a constricted filter but inactivates like WT channels challenges this idea. In this study, we measured the equilibrium ion-binding properties of channels with conductive, inactivated, and constricted filters using isothermal titration calorimetry (ITC). EPR spectroscopy was used to determine the state of the intracellular gate of the channel, which we found can depend on the presence or absence of a lipid bilayer. Overall, we discovered that K(+) ion binding to channels with an inactivated or conductive selectivity filter is different from K(+) ion binding to channels with a constricted filter, suggesting that the structures of these channels are different.
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36
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Spin Labeling of Potassium Channels. Methods Enzymol 2015. [PMID: 26477258 DOI: 10.1016/bs.mie.2015.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Potassium channels are the ion channels most extensively studied by structural techniques. Whereas high-resolution crystal structures have provided key insights into the molecular architecture of these channels, spin labeling studies have helped to unveil the dynamic structural aspects underlying their function. From a practical standpoint, the popularity of spin labeling studies of potassium channels lies in their small size and relative ease of overexpression. The inherent fourfold symmetry of most potassium channels has also greatly facilitated spin labeling studies. This chapter focuses on the overexpression, purification, spin labeling, and subsequent reconstitution of modified potassium channels. It will discuss the general methods used to produce a suitable spin-labeled potassium channel sample and highlight some of the common pitfalls that can occur along the way. At the end of the chapter, we provide detailed methods to produce spin-labeled samples of KcsA and KvAP, the two most commonly studied potassium channels.
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37
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Blasic JR, Worcester DL, Gawrisch K, Gurnev P, Mihailescu M. Pore hydration states of KcsA potassium channels in membranes. J Biol Chem 2015; 290:26765-75. [PMID: 26370089 DOI: 10.1074/jbc.m115.661819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/30/2022] Open
Abstract
Water-filled hydrophobic cavities in channel proteins serve as gateways for transfer of ions across membranes, but their properties are largely unknown. We determined water distributions along the conduction pores in two tetrameric channels embedded in lipid bilayers using neutron diffraction: potassium channel KcsA and the transmembrane domain of M2 protein of influenza A virus. For the KcsA channel in the closed state, the distribution of water is peaked in the middle of the membrane, showing water in the central cavity adjacent to the selectivity filter. This water is displaced by the channel blocker tetrabutyl-ammonium. The amount of water associated with the channel was quantified, using neutron diffraction and solid state NMR. In contrast, the M2 proton channel shows a V-shaped water profile across the membrane, with a narrow constriction at the center, like the hourglass shape of its internal surface. These two types of water distribution are therefore very different in their connectivity to the bulk water. The water and protein profiles determined here provide important evidence concerning conformation and hydration of channels in membranes and the potential role of pore hydration in channel gating.
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Affiliation(s)
- Joseph R Blasic
- From the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - David L Worcester
- the Department of Physiology and Biophysics, University of California, Irvine, California 92697, the National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899
| | - Klaus Gawrisch
- the Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892
| | - Philip Gurnev
- the Physics Department, University of Massachusetts, Amherst, Massachusetts 01003, and From the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Mihaela Mihailescu
- From the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850,
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38
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Expression of the Genes Encoding the Trk and Kdp Potassium Transport Systems of Mycobacterium tuberculosis during Growth In Vitro. BIOMED RESEARCH INTERNATIONAL 2015; 2015:608682. [PMID: 26351637 PMCID: PMC4553272 DOI: 10.1155/2015/608682] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/30/2015] [Accepted: 08/02/2015] [Indexed: 11/18/2022]
Abstract
Two potassium (K(+))-uptake systems, Trk and Kdp, are operative in Mycobacterium tuberculosis (Mtb), but the environmental factors triggering their expression have not been determined. The current study has evaluated the expression of these genes in the Mtb wild-type and a trk-gene knockout strain at various stages of logarithmic growth in relation to extracellular K(+) concentrations and pH. In both strains, mRNA levels of the K(+)-uptake encoding genes were relatively low compared to those of the housekeeping gene, sigA, at the early- and mid-log phases, increasing during late-log. Increased gene expression coincided with decreased K(+) uptake in the context of a drop in extracellular pH and sustained high extracellular K(+) concentrations. In an additional series of experiments, the pH of the growth medium was manipulated by the addition of 1N HCl/NaOH. Decreasing the pH resulted in reductions in both membrane potential and K(+) uptake in the setting of significant induction of genes encoding both K(+) transporters. These observations are consistent with induction of the genes encoding the active K(+) transporters of Mtb as a strategy to compensate for loss of membrane potential-driven uptake of K(+) at low extracellular pH. Induction of these genes may promote survival in the acidic environments of the intracellular vacuole and granuloma.
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39
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Dörr JM, Koorengevel MC, Schäfer M, Prokofyev AV, Scheidelaar S, van der Cruijsen EAW, Dafforn TR, Baldus M, Killian JA. Detergent-free isolation, characterization, and functional reconstitution of a tetrameric K+ channel: the power of native nanodiscs. Proc Natl Acad Sci U S A 2014; 111:18607-12. [PMID: 25512535 PMCID: PMC4284610 DOI: 10.1073/pnas.1416205112] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A major obstacle in the study of membrane proteins is their solubilization in a stable and active conformation when using detergents. Here, we explored a detergent-free approach to isolating the tetrameric potassium channel KcsA directly from the membrane of Escherichia coli, using a styrene-maleic acid copolymer. This polymer self-inserts into membranes and is capable of extracting membrane patches in the form of nanosize discoidal proteolipid particles or "native nanodiscs." Using circular dichroism and tryptophan fluorescence spectroscopy, we show that the conformation of KcsA in native nanodiscs is very similar to that in detergent micelles, but that the thermal stability of the protein is higher in the nanodiscs. Furthermore, as a promising new application, we show that quantitative analysis of the co-isolated lipids in purified KcsA-containing nanodiscs allows determination of preferential lipid-protein interactions. Thin-layer chromatography experiments revealed an enrichment of the anionic lipids cardiolipin and phosphatidylglycerol, indicating their close proximity to the channel in biological membranes and supporting their functional relevance. Finally, we demonstrate that KcsA can be reconstituted into planar lipid bilayers directly from native nanodiscs, which enables functional characterization of the channel by electrophysiology without first depriving the protein of its native environment. Together, these findings highlight the potential of the use of native nanodiscs as a tool in the study of ion channels, and of membrane proteins in general.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexander V Prokofyev
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Timothy R Dafforn
- School of Bio Sciences, University of Birmingham, Edgbaston Birmingham B15 2TT, United Kingdom
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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40
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Rusinova R, Kim DM, Nimigean CM, Andersen OS. Regulation of ion channel function by the host lipid bilayer examined by a stopped-flow spectrofluorometric assay. Biophys J 2014; 106:1070-8. [PMID: 24606931 DOI: 10.1016/j.bpj.2014.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
To examine the function of ligand-gated ion channels in a defined membrane environment, we developed a robust sequential-mixing fluorescence-based stopped-flow assay. Channel activity is determined using a channel-permeable quencher (e.g., thallium, Tl(+)) of a water-soluble fluorophore (8-aminonaphthalene-1,3,6-trisulfonic acid) encapsulated in large unilamellar vesicles in which the channel of interest has been reconstituted, which allows for rapid solution changes. To validate the method, we explored the activation of wild-type KcsA channel, as well as it's noninactivating (E71A) KcsA mutant, by extravesicular protons (H(+)). For both channel types, the day-to-day variability in the reconstitution yield (as judged from the time course of fluorescence quenching) is <10%. The activation curve for E71A KcsA is similar to that obtained previously using single-channel electrophysiology, and the activation curves for wild-type and E71A KcsA are indistinguishable, indicating that channel activation and inactivation are separate processes. We then investigated the regulation of KcsA activation by changes in lipid bilayer composition. Increasing the acyl chain length (from C18:1 to C22:1 in diacylphosphatidylcholine), but not the mole fraction of POPG (>0.25) in the bilayer-forming phospholipid mixture, alters KcsA H(+) gating. The bilayer-thickness-dependent shift in the activation curve is suggestive of a decrease in an apparent H(+) affinity and cooperativity. The control over bilayer environment and time resolution makes this method a powerful assay for exploring ligand activation and inactivation of ion channels, and how channel gating varies with changes in the channels' lipid bilayer environment or other regulatory processes.
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Affiliation(s)
- Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York.
| | - Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Crina M Nimigean
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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41
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Kamnesky G, Hirschhorn O, Shaked H, Chen J, Yao L, Chill JH. Molecular determinants of tetramerization in the KcsA cytoplasmic domain. Protein Sci 2014; 23:1403-16. [PMID: 25042120 DOI: 10.1002/pro.2525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/11/2022]
Abstract
The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels.
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Affiliation(s)
- Guy Kamnesky
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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42
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General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels. Nat Commun 2014; 5:4641. [PMID: 25105557 PMCID: PMC4133698 DOI: 10.1038/ncomms5641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/09/2014] [Indexed: 12/20/2022] Open
Abstract
The pore-lining helix (PLH) bundles are central to the function of all ion channels,
as their conformational rearrangements dictate channel gating. Here we explore all
plausible oligomeric arrangements of the PLH bundles within homomeric ion channels
by building models using generic restraints. In particular, the distance between two
neighbouring PLHs was bounded both below and above in order to avoid steric clash
and allow proper packing. The resulting models provide a theoretical representation
of the accessible space for oligomeric arrangements. While the represented space is
confined, it encompasses nearly all the ion channel PLH bundles for which the
structures are currently known. For a multitude of channels, gating models suggested
by paths within the confined accessible space are in qualitative agreement with
those established in previous structural and computational studies. Rearrangements of the pore-lining helix (PLH) bundles of ion channels
are central to their gating mechanisms. Here, Dai et al. use a modelling approach
to define the general rules that govern the arrangements and gating motions of the PLHs
in homomeric ion channels.
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43
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Hirano M, Okuno D, Onishi Y, Ide T. A single amino acid gates the KcsA channel. Biochem Biophys Res Commun 2014; 450:1537-40. [PMID: 25019991 DOI: 10.1016/j.bbrc.2014.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 12/19/2022]
Abstract
The KcsA channel is a proton-activated potassium channel. We have previously shown that the cytoplasmic domain (CPD) acts as a pH-sensor, and the charged states of certain negatively charged amino acids in the CPD play an important role in regulating the pH-dependent gating. Here, we demonstrate the KcsA channel is constitutively open independent of pH upon mutating E146 to a neutrally charged amino acid. In addition, we found that rearrangement of the CPD following this mutation was not large. Our results indicate that minimal rearrangement of the CPD, particularly around E146, is sufficient for opening of the KcsA channel.
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Affiliation(s)
- Minako Hirano
- Bio Photonics Laboratory, The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu Nishi-ku Hamamatsu, Shizuoka 431-1202, Japan; Laboratory for Cell Dynamics Observation, Quantitative Biology Center, RIKEN, 6-2-3 Furue-dai Suita, Osaka 565-0874, Japan.
| | - Daichi Okuno
- Laboratory for Cell Dynamics Observation, Quantitative Biology Center, RIKEN, 6-2-3 Furue-dai Suita, Osaka 565-0874, Japan.
| | - Yukiko Onishi
- Laboratory for Cell Dynamics Observation, Quantitative Biology Center, RIKEN, 6-2-3 Furue-dai Suita, Osaka 565-0874, Japan.
| | - Toru Ide
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka Kita-ku Okayama-shi, Okayama 700-8530, Japan.
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Lee J, Miller BT, Damjanović A, Brooks BR. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. J Chem Theory Comput 2014; 10:2738-2750. [PMID: 25061443 PMCID: PMC4095908 DOI: 10.1021/ct500175m] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/21/2022]
Abstract
We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Benjamin T Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ana Damjanović
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States ; Department of Biophysics, Johns Hopkins University , Baltimore, Maryland, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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45
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Yao Z, Olvera de la Cruz M. Ruled surface underlying KcsA potassium channels. SOFT MATTER 2014; 10:540-543. [PMID: 24652100 DOI: 10.1039/c3sm52612g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent experiments have revealed that the opening and closing of the channel is controlled by concertedly rotating and tilting the ends of the alpha-helices in the KcsA ion channels. We recognize these transmembrane alpha-helices as the generating lines of the ruled surface: the hyperboloid of one sheet. The twist-to-shrink feature of the hyperboloid is adopted by KcsA channels in gating the pore as observed in experiments. Our model may shed light on understanding nature's design principles of ion channels. And the conclusions drawn from this study have implications for the design of artificial channels.
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Affiliation(s)
- Zhenwei Yao
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208-3108, USA.
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46
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Posson DJ, Thompson AN, McCoy JG, Nimigean CM. Molecular interactions involved in proton-dependent gating in KcsA potassium channels. ACTA ACUST UNITED AC 2013; 142:613-24. [PMID: 24218397 PMCID: PMC3840921 DOI: 10.1085/jgp.201311057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The bacterial potassium channel KcsA is gated open by the binding of protons to amino acids on the intracellular side of the channel. We have identified, via channel mutagenesis and x-ray crystallography, two pH-sensing amino acids and a set of nearby residues involved in molecular interactions that influence gating. We found that the minimal mutation of one histidine (H25) and one glutamate (E118) near the cytoplasmic gate completely abolished pH-dependent gating. Mutation of nearby residues either alone or in pairs altered the channel's response to pH. In addition, mutations of certain pairs of residues dramatically increased the energy barriers between the closed and open states. We proposed a Monod-Wyman-Changeux model for proton binding and pH-dependent gating in KcsA, where H25 is a "strong" sensor displaying a large shift in pKa between closed and open states, and E118 is a "weak" pH sensor. Modifying model parameters that are involved in either the intrinsic gating equilibrium or the pKa values of the pH-sensing residues was sufficient to capture the effects of all mutations.
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Affiliation(s)
- David J Posson
- Department of Anesthesiology, 2 Department of Physiology and Biophysics, and 3 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
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47
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Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels. Proc Natl Acad Sci U S A 2013; 110:17886-91. [PMID: 24128761 DOI: 10.1073/pnas.1314356110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
K(+) channels distinguish K(+) from Na(+) in the selectivity filter, which consists of four ion-binding sites (S1-S4, extracellular to intracellular) that are built mainly using the carbonyl oxygens from the protein backbone. In addition to ionic discrimination, the selectivity filter regulates the flow of ions across the membrane in a gating process referred to as C-type inactivation. A characteristic of C-type inactivation is a dependence on the permeant ion, but the mechanism by which permeant ions modulate C-type inactivation is not known. To investigate, we used amide-to-ester substitutions in the protein backbone of the selectivity filter to alter ion binding at specific sites and determined the effects on inactivation. The amide-to-ester substitutions in the protein backbone were introduced using protein semisynthesis or in vivo nonsense suppression approaches. We show that an ester substitution at the S1 site in the KcsA channel does not affect inactivation whereas ester substitutions at the S2 and S3 sites dramatically reduce inactivation. We determined the structure of the KcsA S2 ester mutant and found that the ester substitution eliminates K(+) binding at the S2 site. We also show that an ester substitution at the S2 site in the KvAP channel has a similar effect of slowing inactivation. Our results link C-type inactivation to ion occupancy at the S2 site. Furthermore, they suggest that the differences in inactivation of K(+) channels in K(+) compared with Rb(+) are due to different ion occupancies at the S2 site.
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48
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Tunuguntla R, Bangar M, Kim K, Stroeve P, Ajo-Franklin C, Noy A. Lipid bilayer composition can influence the orientation of proteorhodopsin in artificial membranes. Biophys J 2013; 105:1388-96. [PMID: 24047990 PMCID: PMC3785883 DOI: 10.1016/j.bpj.2013.07.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/26/2022] Open
Abstract
Artificial membrane systems allow researchers to study the structure and function of membrane proteins in a matrix that approximates their natural environment and to integrate these proteins in ex vivo devices such as electronic biosensors, thin-film protein arrays, or biofuel cells. Given that most membrane proteins have vectorial functions, both functional studies and applications require effective control over protein orientation within a lipid bilayer. In this work, we explored the role of the bilayer surface charge in determining transmembrane protein orientation and functionality during formation of proteoliposomes. We reconstituted a model vectorial ion pump, proteorhodopsin, in liposomes of opposite charges and varying charge densities and determined the resultant protein orientation. Antibody-binding assay and proteolysis of proteoliposomes showed physical evidence of preferential orientation, and functional assays verified the vectorial nature of ion transport in this system. Our results indicate that the manipulation of lipid composition can indeed control orientation of an asymmetrically charged membrane protein, proteorhodopsin, in liposomes.
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Affiliation(s)
- Ramya Tunuguntla
- Department of Chemical Engineering and Materials Science, University of California, Davis, Davis, California
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Mangesh Bangar
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kyunghoon Kim
- Mechanical Engineering Department, University of California, Berkeley, Berkeley, California
| | - Pieter Stroeve
- Department of Chemical Engineering and Materials Science, University of California, Davis, Davis, California
| | - Caroline M. Ajo-Franklin
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Aleksandr Noy
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
- School of Natural Sciences, University of California, Merced, Merced, California
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
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49
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Semisynthetic K+ channels show that the constricted conformation of the selectivity filter is not the C-type inactivated state. Proc Natl Acad Sci U S A 2013; 110:15698-703. [PMID: 24019483 DOI: 10.1073/pnas.1308699110] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
C-type inactivation of K(+) channels plays a key role in modulating cellular excitability. During C-type inactivation, the selectivity filter of a K(+) channel changes conformation from a conductive to a nonconductive state. Crystal structures of the KcsA channel determined at low K(+) or in the open state revealed a constricted conformation of the selectivity filter, which was proposed to represent the C-type inactivated state. However, structural studies on other K(+) channels do not support the constricted conformation as the C-type inactivated state. In this study, we address whether the constricted conformation of the selectivity filter is in fact the C-type inactivated state. The constricted conformation can be blocked by substituting the first conserved glycine in the selectivity filter with the unnatural amino acid d-Alanine. Protein semisynthesis was used to introduce d-Alanine into the selectivity filters of the KcsA channel and the voltage-gated K(+) channel KvAP. For semisynthesis of the KvAP channel, we developed a modular approach in which chemical synthesis is limited to the selectivity filter whereas the rest of the protein is obtained by recombinant means. Using the semisynthetic KcsA and KvAP channels, we show that blocking the constricted conformation of the selectivity filter does not prevent inactivation, which suggests that the constricted conformation is not the C-type inactivated state.
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50
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Giudici AM, Molina ML, Ayala JL, Montoya E, Renart ML, Fernández AM, Encinar JA, Ferrer-Montiel AV, Poveda JA, González-Ros JM. Detergent-labile, supramolecular assemblies of KcsA: Relative abundance and interactions involved. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:193-200. [DOI: 10.1016/j.bbamem.2012.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 08/22/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022]
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