1
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Schloßhauer JL, Dondapati SK, Kubick S, Zemella A. A Cost-Effective Pichia pastoris Cell-Free System Driven by Glycolytic Intermediates Enables the Production of Complex Eukaryotic Proteins. Bioengineering (Basel) 2024; 11:92. [PMID: 38247969 PMCID: PMC10813726 DOI: 10.3390/bioengineering11010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Cell-free systems are particularly attractive for screening applications and the production of difficult-to-express proteins. However, the production of cell lysates is difficult to implement on a larger scale due to large time requirements, cultivation costs, and the supplementation of cell-free reactions with energy regeneration systems. Consequently, the methylotrophic yeast Pichia pastoris, which is widely used in recombinant protein production, was utilized in the present study to realize cell-free synthesis in a cost-effective manner. Sensitive disruption conditions were evaluated, and appropriate signal sequences for translocation into ER vesicles were identified. An alternative energy regeneration system based on fructose-1,6-bisphosphate was developed and a ~2-fold increase in protein production was observed. Using a statistical experiment design, the optimal composition of the cell-free reaction milieu was determined. Moreover, functional ion channels could be produced, and a G-protein-coupled receptor was site-specifically modified using the novel cell-free system. Finally, the established P. pastoris cell-free protein production system can economically produce complex proteins for biotechnological applications in a short time.
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Affiliation(s)
- Jeffrey L. Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Located at the Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, 14469 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
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2
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Coutinho A, Poveda JA, Renart ML. Conformational Dynamic Studies of Prokaryotic Potassium Channels Explored by Homo-FRET Methodologies. Methods Mol Biol 2024; 2796:35-72. [PMID: 38856894 DOI: 10.1007/978-1-0716-3818-7_3] [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] [Indexed: 06/11/2024]
Abstract
Fluorescence techniques have been widely used to shed light over the structure-function relationship of potassium channels for the last 40-50 years. In this chapter, we describe how a Förster resonance energy transfer between identical fluorophores (homo-FRET) approach can be applied to study the gating behavior of the prokaryotic channel KcsA. Two different gates have been described to control the K+ flux across the channel's pore, the helix-bundle crossing and the selectivity filter, located at the opposite sides of the channel transmembrane section. Both gates can be studied individually or by using a double-reporter system. Due to its homotetrameric structural arrangement, KcsA presents a high degree of symmetry that fulfills the first requisite to calculate intersubunit distances through this technique. The results obtained through this work have helped to uncover the conformational plasticity of the selectivity filter under different experimental conditions and the importance of its allosteric coupling to the opening of the activation (inner) gate. This biophysical approach usually requires low protein concentration and presents high sensitivity and reproducibility, complementing the high-resolution structural information provided by X-ray crystallography, cryo-EM, and NMR studies.
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Affiliation(s)
- Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain
| | - María Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain.
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3
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Renart ML, Giudici AM, Coll-Díez C, González-Ros JM, Poveda JA. Anionic Phospholipids Shift the Conformational Equilibrium of the Selectivity Filter in the KcsA Channel to the Conductive Conformation: Predicted Consequences on Inactivation. Biomedicines 2023; 11:biomedicines11051376. [PMID: 37239046 DOI: 10.3390/biomedicines11051376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Here, we report an allosteric effect of an anionic phospholipid on a model K+ channel, KcsA. The anionic lipid in mixed detergent-lipid micelles specifically induces a change in the conformational equilibrium of the channel selectivity filter (SF) only when the channel inner gate is in the open state. Such change consists of increasing the affinity of the channel for K+, stabilizing a conductive-like form by maintaining a high ion occupancy in the SF. The process is highly specific in several aspects: First, lipid modifies the binding of K+, but not that of Na+, which remains unperturbed, ruling out a merely electrostatic phenomenon of cation attraction. Second, no lipid effects are observed when a zwitterionic lipid, instead of an anionic one, is present in the micelles. Lastly, the effects of the anionic lipid are only observed at pH 4.0, when the inner gate of KcsA is open. Moreover, the effect of the anionic lipid on K+ binding to the open channel closely emulates the K+ binding behaviour of the non-inactivating E71A and R64A mutant proteins. This suggests that the observed increase in K+ affinity caused by the bound anionic lipid should result in protecting the channel against inactivation.
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Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Carlos Coll-Díez
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
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4
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Molecular Events behind the Selectivity and Inactivation Properties of Model NaK-Derived Ion Channels. Int J Mol Sci 2022; 23:ijms23169246. [PMID: 36012519 PMCID: PMC9409022 DOI: 10.3390/ijms23169246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
Y55W mutants of non-selective NaK and partly K+-selective NaK2K channels have been used to explore the conformational dynamics at the pore region of these channels as they interact with either Na+ or K+. A major conclusion is that these channels exhibit a remarkable pore conformational flexibility. Homo-FRET measurements reveal a large change in W55–W55 intersubunit distances, enabling the selectivity filter (SF) to admit different species, thus, favoring poor or no selectivity. Depending on the cation, these channels exhibit wide-open conformations of the SF in Na+, or tight induced-fit conformations in K+, most favored in the four binding sites containing NaK2K channels. Such conformational flexibility seems to arise from an altered pattern of restricting interactions between the SF and the protein scaffold behind it. Additionally, binding experiments provide clues to explain such poor selectivity. Compared to the K+-selective KcsA channel, these channels lack a high affinity K+ binding component and do not collapse in Na+. Thus, they cannot properly select K+ over competing cations, nor reject Na+ by collapsing, as K+-selective channels do. Finally, these channels do not show C-type inactivation, likely because their submillimolar K+ binding affinities prevent an efficient K+ loss from their SF, thus favoring permanently open channel states.
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5
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Reddi R, Matulef K, Riederer EA, Whorton MR, Valiyaveetil FI. Structural basis for C-type inactivation in a Shaker family voltage-gated K + channel. SCIENCE ADVANCES 2022; 8:eabm8804. [PMID: 35452285 PMCID: PMC9032944 DOI: 10.1126/sciadv.abm8804] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
C-type inactivation is a process by which ion flux through a voltage-gated K+ (Kv) channel is regulated at the selectivity filter. While prior studies have indicated that C-type inactivation involves structural changes at the selectivity filter, the nature of the changes has not been resolved. Here, we report the crystal structure of the Kv1.2 channel in a C-type inactivated state. The structure shows that C-type inactivation involves changes in the selectivity filter that disrupt the outer two ion binding sites in the filter. The changes at the selectivity filter propagate to the extracellular mouth and the turret regions of the channel pore. The structural changes observed are consistent with the functional hallmarks of C-type inactivation. This study highlights the intricate interplay between K+ occupancy at the ion binding sites and the interactions of the selectivity filter in determining the balance between the conductive and the inactivated conformations of the filter.
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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, USA
| | - 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, USA
| | - Erika A. Riederer
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Matthew R. Whorton
- Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - 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, USA
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6
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A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V. Nat Commun 2022; 13:1574. [PMID: 35322021 PMCID: PMC8943062 DOI: 10.1038/s41467-022-28866-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/01/2022] [Indexed: 11/08/2022] Open
Abstract
C-type inactivation is of great physiological importance in voltage-activated K+ channels (Kv), but its structural basis remains unresolved. Knowledge about C-type inactivation has been largely deduced from the bacterial K+ channel KcsA, whose selectivity filter constricts under inactivating conditions. However, the filter is highly sensitive to its molecular environment, which is different in Kv channels than in KcsA. In particular, a glutamic acid residue at position 71 along the pore helix in KcsA is substituted by a valine conserved in most Kv channels, suggesting that this side chain is a molecular determinant of function. Here, a combination of X-ray crystallography, solid-state NMR and MD simulations of the E71V KcsA mutant is undertaken to explore inactivation in this Kv-like construct. X-ray and ssNMR data show that the filter of the Kv-like mutant does not constrict under inactivating conditions. Rather, the filter adopts a conformation that is slightly narrowed and rigidified. On the other hand, MD simulations indicate that the constricted conformation can nonetheless be stably established in the mutant channel. Together, these findings suggest that the Kv-like KcsA mutant may be associated with different modes of C-type inactivation, showing that distinct filter environments entail distinct C-type inactivation mechanisms.
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7
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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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8
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Puiggalí-Jou A, Molina BG, Lopes-Rodrigues M, Michaux C, Perpète EA, Zanuy D, Alemán C. Self-standing, conducting and capacitive biomimetic hybrid nanomembranes for selective molecular ion separation. Phys Chem Chem Phys 2021; 23:16157-16164. [PMID: 34297025 DOI: 10.1039/d1cp01840j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hybrid free-standing biomimetic materials are developed by integrating the VDAC36 β-barrel protein into robust and flexible three-layered polymer nanomembranes. The first and third layers are prepared by spin-coating a mixture of poly(lactic acid) (PLA) and poly(vinyl alcohol) (PVA). PVA nanofeatures are transformed into controlled nanoperforations by solvent-etching. The two nanoperforated PLA layers are separated by an electroactive layer, which is successfully electropolymerized by introducing a conducting sacrificial substrate under the first PLA nanosheet. Finally, the nanomaterial is consolidated by immobilizing the VDAC36 protein, active as an ion channel, into the nanoperforations of the upper layer. The integration of the protein causes a significant reduction of the material resistance, which decreases from 21.9 to 3.9 kΩ cm2. Electrochemical impedance spectroscopy studies using inorganic ions and molecular metabolites (i.e.l-lysine and ATP) not only reveal that the hybrid films behave as electrochemical supercapacitors but also indicate the most appropriate conditions to obtain selective responses against molecular ions as a function of their charge. The combination of polymers and proteins is promising for the development of new devices for engineering, biotechnological and biomedical applications.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Edif. I2, 08019, Barcelona, Spain.
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9
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Giudici AM, Díaz-García C, Renart ML, Coutinho A, Prieto M, González-Ros JM, Poveda JA. Tetraoctylammonium, a Long Chain Quaternary Ammonium Blocker, Promotes a Noncollapsed, Resting-Like Inactivated State in KcsA. Int J Mol Sci 2021; 22:ijms22020490. [PMID: 33419017 PMCID: PMC7825302 DOI: 10.3390/ijms22020490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023] Open
Abstract
Alkylammonium salts have been used extensively to study the structure and function of potassium channels. Here, we use the hydrophobic tetraoctylammonium (TOA+) to shed light on the structure of the inactivated state of KcsA, a tetrameric prokaryotic potassium channel that serves as a model to its homologous eukaryotic counterparts. By the combined use of a thermal denaturation assay and the analysis of homo-Förster resonance energy transfer in a mutant channel containing a single tryptophan (W67) per subunit, we found that TOA+ binds the channel cavity with high affinity, either with the inner gate open or closed. Moreover, TOA+ bound at the cavity allosterically shifts the equilibrium of the channel's selectivity filter conformation from conductive to an inactivated-like form. The inactivated TOA+-KcsA complex exhibits a loss in the affinity towards permeant K+ at pH 7.0, when the channel is in its closed state, but maintains the two sets of K+ binding sites and the W67-W67 intersubunit distances characteristic of the selectivity filter in the channel resting state. Thus, the TOA+-bound state differs clearly from the collapsed channel state described by X-ray crystallography and claimed to represent the inactivated form of KcsA.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Clara Díaz-García
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Ana Coutinho
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
- Departamento de Química e Bioquímica, Faculty of Sciences, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
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10
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Cosseddu SM, Choe EJ, Khovanov IA. Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel. ENTROPY (BASEL, SWITZERLAND) 2021; 23:E72. [PMID: 33418985 PMCID: PMC7825352 DOI: 10.3390/e23010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/02/2021] [Indexed: 12/26/2022]
Abstract
The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network's residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.
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Affiliation(s)
| | | | - Igor A. Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (S.M.C.); (E.J.C.)
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11
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Abstract
Potassium channels are present in every living cell and essential to setting up a stable, non-zero transmembrane electrostatic potential which manifests the off-equilibrium livelihood of the cell. They are involved in other cellular activities and regulation, such as the controlled release of hormones, the activation of T-cells for immune response, the firing of action potential in muscle cells and neurons, etc. Pharmacological reagents targeting potassium channels are important for treating various human diseases linked to dysfunction of the channels. High-resolution structures of these channels are very useful tools for delineating the detailed chemical basis underlying channel functions and for structure-based design and optimization of their pharmacological and pharmaceutical agents. Structural studies of potassium channels have revolutionized biophysical understandings of key concepts in the field - ion selectivity, conduction, channel gating, and modulation, making them multi-modality targets of pharmacological regulation. In this chapter, I will select a few high-resolution structures to illustrate key structural insights, proposed allostery behind channel functions, disagreements still open to debate, and channel-lipid interactions and co-evolution. The known structural consensus allows the inference of conserved molecular mechanisms shared among subfamilies of K+ channels and makes it possible to develop channel-specific pharmaceutical agents.
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Affiliation(s)
- Qiu-Xing Jiang
- Laboratory of Molecular Physiology and Biophysics and the Cryo-EM Center, Hauptmann-Woodward Medical Research Institute, Buffalo, NY, USA.
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA.
- Departments of Materials Design and Invention and Physiology and Biophysics, University of Buffalo (SUNY), Buffalo, NY, USA.
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12
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Lipinsky M, Tobelaim WS, Peretz A, Simhaev L, Yeheskel A, Yakubovich D, Lebel G, Paas Y, Hirsch JA, Attali B. A unique mechanism of inactivation gating of the Kv channel family member Kv7.1 and its modulation by PIP2 and calmodulin. SCIENCE ADVANCES 2020; 6:eabd6922. [PMID: 33355140 PMCID: PMC11206195 DOI: 10.1126/sciadv.abd6922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Inactivation of voltage-gated K+ (Kv) channels mostly occurs by fast N-type or/and slow C-type mechanisms. Here, we characterized a unique mechanism of inactivation gating comprising two inactivation states in a member of the Kv channel superfamily, Kv7.1. Removal of external Ca2+ in wild-type Kv7.1 channels produced a large, voltage-dependent inactivation, which differed from N- or C-type mechanisms. Glu295 and Asp317 located, respectively, in the turret and pore entrance are involved in Ca2+ coordination, allowing Asp317 to form H-bonding with the pore helix Trp304, which stabilizes the selectivity filter and prevents inactivation. Phosphatidylinositol 4,5-bisphosphate (PIP2) and Ca2+-calmodulin prevented Kv7.1 inactivation triggered by Ca2+-free external solutions, where Ser182 at the S2-S3 linker relays the calmodulin signal from its inner boundary to the external pore to allow proper channel conduction. Thus, we revealed a unique mechanism of inactivation gating in Kv7.1, exquisitely controlled by external Ca2+ and allosterically coupled by internal PIP2 and Ca2+-calmodulin.
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Affiliation(s)
- Maya Lipinsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - William Sam Tobelaim
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Asher Peretz
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luba Simhaev
- The Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adva Yeheskel
- The Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel
| | - Daniel Yakubovich
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Lebel
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoav Paas
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Joel A Hirsch
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Bernard Attali
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel.
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13
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Selectivity filter ion binding affinity determines inactivation in a potassium channel. Proc Natl Acad Sci U S A 2020; 117:29968-29978. [PMID: 33154158 DOI: 10.1073/pnas.2009624117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Potassium channels can become nonconducting via inactivation at a gate inside the highly conserved selectivity filter (SF) region near the extracellular side of the membrane. In certain ligand-gated channels, such as BK channels and MthK, a Ca2+-activated K+ channel from Methanobacterium thermoautotrophicum, the SF has been proposed to play a role in opening and closing rather than inactivation, although the underlying conformational changes are unknown. Using X-ray crystallography, identical conductive MthK structures were obtained in wide-ranging K+ concentrations (6 to 150 mM), unlike KcsA, whose SF collapses at low permeant ion concentrations. Surprisingly, three of the SF's four binding sites remained almost fully occupied throughout this range, indicating high affinities (likely submillimolar), while only the central S2 site titrated, losing its ion at 6 mM, indicating low K+ affinity (∼50 mM). Molecular simulations showed that the MthK SF can also collapse in the absence of K+, similar to KcsA, but that even a single K+ binding at any of the SF sites, except S4, can rescue the conductive state. The uneven titration across binding sites differs from KcsA, where SF sites display a uniform decrease in occupancy with K+ concentration, in the low millimolar range, leading to SF collapse. We found that ions were disfavored in MthK's S2 site due to weaker coordination by carbonyl groups, arising from different interactions with the pore helix and water behind the SF. We conclude that these differences in interactions endow the seemingly identical SFs of KcsA and MthK with strikingly different inactivating phenotypes.
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14
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Lolicato M, Natale AM, Abderemane-Ali F, Crottès D, Capponi S, Duman R, Wagner A, Rosenberg JM, Grabe M, Minor DL. K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. SCIENCE ADVANCES 2020; 6:6/44/eabc9174. [PMID: 33127683 PMCID: PMC7608817 DOI: 10.1126/sciadv.abc9174] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/10/2020] [Indexed: 05/05/2023]
Abstract
K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.
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Affiliation(s)
- Marco Lolicato
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - David Crottès
- Department of Physiology, University of California, San Francisco, CA 93858-2330, USA
| | - Sara Capponi
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Ramona Duman
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 93858-2330, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 93858-2330, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, 93858-2330, USA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
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15
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Braun N, Sheikh ZP, Pless SA. The current chemical biology tool box for studying ion channels. J Physiol 2020; 598:4455-4471. [DOI: 10.1113/jp276695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- N. Braun
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - Z. P. Sheikh
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - S. A. Pless
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
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16
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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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17
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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18
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Oakes V, Furini S, Domene C. Insights into the Mechanisms of K + Permeation in K + Channels from Computer Simulations. J Chem Theory Comput 2020; 16:794-799. [PMID: 31809048 DOI: 10.1021/acs.jctc.9b00971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion permeation, selectivity, and the behavior of the K+ channel selectivity filter have been studied intensively in the previous two decades. The agreement among multiple approaches used to study ion flux in K+ channels suggests a consensus mechanism of ion permeation across the selectivity that has been put to the test in recent years with the proposal of an alternative way by which ions can cross the selectivity filter of K+ channels via direct Coulomb repulsion between contacting cations. Past experimental work by Zhou and MacKinnon (J. Mol. Biol. 2004, 338, 839) showed that mutation of the site S4 reduces the total occupancy of the selectivity filter to less than two ions on average by lowering the occupancy of the S2-S4 configuration without changing the S1-S3 configuration much, and this reduction of occupancy means that ion configurations different from the ones involved in the canonical mechanism are likely to be involved. At that time, calculations using complicated kinetic networks to relate occupancy to conduction did not provide deeper insight into the conduction mechanism. Here, to help solve this enigma, umbrella sampling simulations have been performed to evaluate the potential of mean force of two KcsA mutant channels where the S4 site is substituted. Our new results provide insights into the significance of threonine in this position, revealing the effect of substitution on the alternate mechanisms of conduction proposed, involving either water or vacant sites.
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Affiliation(s)
- Victoria Oakes
- Department of Chemistry , University of Bath , Claverton Down, Bath BA2 7AY , U.K
| | - Simone Furini
- Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Carmen Domene
- Department of Chemistry , University of Bath , Claverton Down, Bath BA2 7AY , U.K.,Department of Chemistry , University of Oxford , Oxford OX1 3TA , U.K
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19
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Meisel E, Tobelaim W, Dvir M, Haitin Y, Peretz A, Attali B. Inactivation gating of Kv7.1 channels does not involve concerted cooperative subunit interactions. Channels (Austin) 2019; 12:89-99. [PMID: 29451064 PMCID: PMC5972808 DOI: 10.1080/19336950.2018.1441649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Inactivation is an intrinsic property of numerous voltage-gated K+ (Kv) channels and can occur by N-type or/and C-type mechanisms. N-type inactivation is a fast, voltage independent process, coupled to activation, with each inactivation particle of a tetrameric channel acting independently. In N-type inactivation, a single inactivation particle is necessary and sufficient to occlude the pore. C-type inactivation is a slower process, involving the outermost region of the pore and is mediated by a concerted, highly cooperative interaction between all four subunits. Inactivation of Kv7.1 channels does not exhibit the hallmarks of N- and C-type inactivation. Inactivation of WT Kv7.1 channels can be revealed by hooked tail currents that reflects the recovery from a fast and voltage-independent inactivation process. However, several Kv7.1 mutants such as the pore mutant L273F generate an additional voltage-dependent slow inactivation. The subunit interactions during this slow inactivation gating remain unexplored. The goal of the present study was to study the nature of subunit interactions along Kv7.1 inactivation gating, using concatenated tetrameric Kv7.1 channel and introducing sequentially into each of the four subunits the slow inactivating pore mutation L273F. Incorporating an incremental number of inactivating mutant subunits did not affect the inactivation kinetics but slowed down the recovery kinetics from inactivation. Results indicate that Kv7.1 inactivation gating is not compatible with a concerted cooperative process. Instead, adding an inactivating subunit L273F into the Kv7.1 tetramer incrementally stabilizes the inactivated state, which suggests that like for activation gating, Kv7.1 slow inactivation gating is not a concerted process.
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Affiliation(s)
- Eshcar Meisel
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
| | - William Tobelaim
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
| | - Meidan Dvir
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
| | - Yoni Haitin
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
| | - Asher Peretz
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
| | - Bernard Attali
- a Department of Physiology & Pharmacology , the Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University , Tel Aviv , Israel
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20
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Gating modules of the AMPA receptor pore domain revealed by unnatural amino acid mutagenesis. Proc Natl Acad Sci U S A 2019; 116:13358-13367. [PMID: 31213549 DOI: 10.1073/pnas.1818845116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are responsible for fast synaptic transmission throughout the vertebrate nervous system. Conformational changes of the transmembrane domain (TMD) underlying ion channel activation and desensitization remain poorly understood. Here, we explored the dynamics of the TMD of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type iGluRs using genetically encoded unnatural amino acid (UAA) photocross-linkers, p-benzoyl-l-phenylalanine (BzF) and p-azido-l-phenylalanine (AzF). We introduced these UAAs at sites throughout the TMD of the GluA2 receptor and characterized the mutants in patch-clamp recordings, exposing them to glutamate and ultraviolet (UV) light. This approach revealed a range of optical effects on the activity of mutant receptors. We found evidence for an interaction between the Pre-M1 and the M4 TMD helix during desensitization. Photoactivation at F579AzF, a residue behind the selectivity filter in the M2 segment, had extraordinarily broad effects on gating and desensitization. This observation suggests coupling to other parts of the receptor and like in other tetrameric ion channels, selectivity filter gating.
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21
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Xu Y, McDermott AE. Inactivation in the potassium channel KcsA. JOURNAL OF STRUCTURAL BIOLOGY-X 2019; 3:100009. [PMID: 32647814 PMCID: PMC7337057 DOI: 10.1016/j.yjsbx.2019.100009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 05/17/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022]
Abstract
C-type inactivation in potassium channels is a nearly universal regulatory mechanism. A major hypothesis states that C-type inactivation involves ion loss at the selectivity filter as an allosteric response to activation. NMR is used to probe protein conformational changes in response to pH and [K+], demonstrating that H+ and K+ binding are allosterically coupled in KcsA. The lipids are integrated parts of potassium channels in terms of structure, energetics and function.
Inactivation, the slow cessation of transmission after activation, is a general feature of potassium channels. It is essential for their function, and malfunctions in inactivation leads to numerous pathologies. The detailed mechanism for the C-type inactivation, distinct from the N-type inactivation, remains an active area of investigation. Crystallography, computational simulations, and NMR have greatly enriched our understanding of the process. Here we review the major hypotheses regarding C-type inactivation, particularly focusing on the key role played by NMR studies of the prokaryotic potassium channel KcsA, which serves as a good model for voltage gated mammalian channels.
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Affiliation(s)
- Yunyao Xu
- Department of Chemistry, Columbia University, New York, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, United States
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22
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Conformational plasticity in the KcsA potassium channel pore helix revealed by homo-FRET studies. Sci Rep 2019; 9:6215. [PMID: 30996281 PMCID: PMC6470172 DOI: 10.1038/s41598-019-42405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
Potassium channels selectivity filter (SF) conformation is modulated by several factors, including ion-protein and protein-protein interactions. Here, we investigate the SF dynamics of a single Trp mutant of the potassium channel KcsA (W67) using polarized time-resolved fluorescence measurements. For the first time, an analytical framework is reported to analyze the homo-Förster resonance energy transfer (homo-FRET) within a symmetric tetrameric protein with a square geometry. We found that in the closed state (pH 7), the W67-W67 intersubunit distances become shorter as the average ion occupancy of the SF increases according to cation type and concentration. The hypothesis that the inactivated SF at pH 4 is structurally similar to its collapsed state, detected at low K+, pH 7, was ruled out, emphasizing the critical role played by the S2 binding site in the inactivation process of KcsA. This homo-FRET approach provides complementary information to X-ray crystallography in which the protein conformational dynamics is usually compromised.
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23
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Giudici AM, Renart ML, Díaz-García C, Morales A, Poveda JA, González-Ros JM. Accessibility of Cations to the Selectivity Filter of KcsA in the Inactivated State: An Equilibrium Binding Study. Int J Mol Sci 2019; 20:ijms20030689. [PMID: 30764559 PMCID: PMC6387330 DOI: 10.3390/ijms20030689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/29/2022] Open
Abstract
Cation binding under equilibrium conditions has been used as a tool to explore the accessibility of permeant and nonpermeant cations to the selectivity filter in three different inactivated models of the potassium channel KcsA. The results show that the stack of ion binding sites (S1 to S4) in the inactivated filter models remain accessible to cations as they are in the resting channel state. The inactivated state of the selectivity filter is therefore “resting-like” under such equilibrium conditions. Nonetheless, quantitative differences in the apparent KD’s of the binding processes reveal that the affinity for the binding of permeant cations to the inactivated channel models, mainly K+, decreases considerably with respect to the resting channel. This is likely to cause a loss of K+ from the inactivated filter and consequently, to promote nonconductive conformations. The most affected site by the affinity loss seems to be S4, which is interesting because S4 is the first site to accommodate K+ coming from the channel vestibule when K+ exits the cell. Moreover, binding of the nonpermeant species, Na+, is not substantially affected by inactivation, meaning that the inactivated channels are also less selective for permeant versus nonpermeant cations under equilibrium conditions.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - Clara Díaz-García
- CQFM-IN and IBB-Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.
| | - Andrés Morales
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, E-03080 Alicante, Spain.
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - José Manuel González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
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24
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Identifying coupled clusters of allostery participants through chemical shift perturbations. Proc Natl Acad Sci U S A 2019; 116:2078-2085. [PMID: 30679272 DOI: 10.1073/pnas.1811168116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Allosteric couplings underlie many cellular signaling processes and provide an exciting avenue for development of new diagnostics and therapeutics. A general method for identifying important residues in allosteric mechanisms would be very useful, but remains elusive due to the complexity of long-range phenomena. Here, we introduce an NMR method to identify residues involved in allosteric coupling between two ligand-binding sites in a protein, which we call chemical shift detection of allostery participants (CAP). Networks of functional groups responding to each ligand are defined through correlated NMR perturbations. In this process, we also identify allostery participants, groups that respond to both binding events and likely play a role in the coupling between the binding sites. Such residues exhibit multiple functional states with distinct NMR chemical shifts, depending on binding status at both binding sites. Such a strategy was applied to the prototypical ion channel KcsA. We had previously shown that the potassium affinity at the extracellular selectivity filter is strongly dependent on proton binding at the intracellular pH sensor. Here, we analyzed proton and potassium binding networks and identified groups that depend on both proton and potassium binding (allostery participants). These groups are viewed as candidates for transmitting information between functional units. The vital role of one such identified amino acid was validated through site-specific mutagenesis, electrophysiology functional studies, and NMR-detected thermodynamic analysis of allosteric coupling. This strategy for identifying allostery participants is likely to have applications for many other systems.
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25
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DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. J Physiol 2018; 597:679-698. [PMID: 30471114 DOI: 10.1113/jp277088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all-atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage-gated channels from the KV and NaV families, which have garnered many successes and engendered several long-standing controversies regarding the nature of their structure-function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Chemistry Department, American River College, Sacramento, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
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26
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Delemotte L. Opening leads to closing: Allosteric crosstalk between the activation and inactivation gates in KcsA. J Gen Physiol 2018; 150:1356-1359. [PMID: 30143551 PMCID: PMC6168244 DOI: 10.1085/jgp.201812161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Delemotte appraises new computational work revealing that the intracellular activation gate must open for C-type inactivation to occur in K+ channels.
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Affiliation(s)
- Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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27
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Matthies D, Bae C, Toombes GE, Fox T, Bartesaghi A, Subramaniam S, Swartz KJ. Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs. eLife 2018; 7:37558. [PMID: 30109985 PMCID: PMC6093707 DOI: 10.7554/elife.37558] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/31/2018] [Indexed: 12/17/2022] Open
Abstract
Voltage-activated potassium (Kv) channels open to conduct K+ ions in response to membrane depolarization, and subsequently enter non-conducting states through distinct mechanisms of inactivation. X-ray structures of detergent-solubilized Kv channels appear to have captured an open state even though a non-conducting C-type inactivated state would predominate in membranes in the absence of a transmembrane voltage. However, structures for a voltage-activated ion channel in a lipid bilayer environment have not yet been reported. Here we report the structure of the Kv1.2-2.1 paddle chimera channel reconstituted into lipid nanodiscs using single-particle cryo-electron microscopy. At a resolution of ~3 Å for the cytosolic domain and ~4 Å for the transmembrane domain, the structure determined in nanodiscs is similar to the previously determined X-ray structure. Our findings show that large differences in structure between detergent and lipid bilayer environments are unlikely, and enable us to propose possible structural mechanisms for C-type inactivation.
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Affiliation(s)
- Doreen Matthies
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Chanhyung Bae
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Kenton Jon Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
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28
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Li J, Ostmeyer J, Cuello LG, Perozo E, Roux B. Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel. J Gen Physiol 2018; 150:1408-1420. [PMID: 30072373 PMCID: PMC6168234 DOI: 10.1085/jgp.201812082] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022] Open
Abstract
C-type inactivation in K+ channels is thought to be a result of constriction of the selectivity filter. By using MD simulations, Li et al. show that rapid constriction occurs within 1–2 s when the intracellular activation gate is fully open, but not when the gate is closed or partially open. C-type inactivation is a time-dependent process observed in many K+ channels whereby prolonged activation by an external stimulus leads to a reduction in ionic conduction. While C-type inactivation is thought to be a result of a constriction of the selectivity filter, the local dynamics of the process remain elusive. Here, we use molecular dynamics (MD) simulations of the KcsA channel to elucidate the nature of kinetically delayed activation/inactivation gating coupling. Microsecond-scale MD simulations based on the truncated form of the KcsA channel (C-terminal domain deleted) provide a first glimpse of the onset of C-type inactivation. We observe over multiple trajectories that the selectivity filter consistently undergoes a spontaneous and rapid (within 1–2 µs) transition to a constricted conformation when the intracellular activation gate is fully open, but remains in the conductive conformation when the activation gate is closed or partially open. Multidimensional umbrella sampling potential of mean force calculations and nonequilibrium voltage-driven simulations further confirm these observations. Electrophysiological measurements show that the truncated form of the KcsA channel inactivates faster and greater than full-length KcsA, which is consistent with truncated KcsA opening to a greater degree because of the absence of the C-terminal domain restraint. Together, these results imply that the observed kinetics underlying activation/inactivation gating reflect a rapid conductive-to-constricted transition of the selectivity filter that is allosterically controlled by the slow opening of the intracellular gate.
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Affiliation(s)
- Jing Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Luis G Cuello
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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Time-Resolved Neutron Interferometry and the Mechanism of Electromechanical Coupling in Voltage-Gated Ion Channels. Methods Enzymol 2018. [PMID: 29673535 DOI: 10.1016/bs.mie.2018.01.019] [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
The mechanism of electromechanical coupling for voltage-gated ion channels (VGICs) involved in neurological signal transmission, primarily Nav- and Kv-channels, remains unresolved. Anesthetics have been shown to directly impact this mechanism, at least for Kv-channels. Molecular dynamics computer simulations can now predict the structures of VGICs embedded within a hydrated phospholipid bilayer membrane as a function of the applied transmembrane voltage, but significant assumptions are still necessary. Nevertheless, these simulations are providing new insights into the mechanism of electromechanical coupling at the atomic level in 3-D. We show that time-resolved neutron interferometry can be used to investigate directly the profile structure of a VGIC, vectorially oriented within a single hydrated phospholipid bilayer membrane at the solid-liquid interface, as a function of the applied transmembrane voltage in the absence of any assumptions or potentially perturbing modifications of the VGIC protein and/or the host membrane. The profile structure is a projection of the membrane's 3-D structure onto the membrane normal and, in the absence of site-directed deuterium labeling, is provided at substantially lower spatial resolution than the atomic level. Nevertheless, this novel approach can be used to directly test the validity of the predictions from molecular dynamics simulations. We describe the key elements of our novel experimental approach, including why each is necessary and important to providing the essential information required for this critical comparison of "simulation" vs "experiment." In principle, the approach could be extended to higher spatial resolution and to include the effects of anesthetics on the electromechanical coupling mechanism in VGICs.
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30
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Cuello LG, Cortes DM, Perozo E. The gating cycle of a K + channel at atomic resolution. eLife 2017; 6:28032. [PMID: 29165243 PMCID: PMC5711375 DOI: 10.7554/elife.28032] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 11/21/2017] [Indexed: 11/13/2022] Open
Abstract
C-type inactivation in potassium channels helps fine-tune long-term channel activity through conformational changes at the selectivity filter. Here, through the use of cross-linked constitutively open constructs, we determined the structures of KcsA’s mutants that stabilize the selectivity filter in its conductive (E71A, at 2.25 Å) and deep C-type inactivated (Y82A at 2.4 Å) conformations. These structural snapshots represent KcsA’s transient open-conductive (O/O) and the stable open deep C-type inactivated states (O/I), respectively. The present structures provide an unprecedented view of the selectivity filter backbone in its collapsed deep C-type inactivated conformation, highlighting the close interactions with structural waters and the local allosteric interactions that couple activation and inactivation gating. Together with the structures associated with the closed-inactivated state (C/I) and in the well-known closed conductive state (C/O), this work recapitulates, at atomic resolution, the key conformational changes of a potassium channel pore domain as it progresses along its gating cycle.
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Affiliation(s)
- Luis G Cuello
- Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States
| | - D Marien Cortes
- Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
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31
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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:909-926. [PMID: 29113819 DOI: 10.1016/j.bbamem.2017.10.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 11/22/2022]
Abstract
The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.
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32
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Wu D. Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel. PLoS One 2017; 12:e0186789. [PMID: 29049423 PMCID: PMC5648213 DOI: 10.1371/journal.pone.0186789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/08/2017] [Indexed: 11/17/2022] Open
Abstract
The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation.
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Affiliation(s)
- Di Wu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
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33
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Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. Proc Natl Acad Sci U S A 2017; 114:11145-11150. [PMID: 28973956 DOI: 10.1073/pnas.1706983114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In many K+ channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a "constricted" conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these structure-conserving modifications are not believed to prevent the selectivity filter from adopting the constricted conformation. However, several untested assumptions about the structural and functional impact of these chemical modifications underlie these arguments. To make progress, molecular dynamics simulations based on atomic models of the KcsA channel were performed. The computational results support the notion that the constricted conformation of the selectivity filter corresponds to the functional C-type inactivated state of the KcsA. Importantly, MD simulations reveal that the semisynthetic KcsAD-ala77 channel can adopt an asymmetrical constricted-like nonconductive conformation and that the amide-to-ester backbone substitutions at Gly77 and Tyr78 perturb the hydrogen bonding involving the buried water molecules stabilizing the constricted conformation.
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34
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Transmembrane allosteric energetics characterization for strong coupling between proton and potassium ion binding in the KcsA channel. Proc Natl Acad Sci U S A 2017; 114:8788-8793. [PMID: 28768808 DOI: 10.1073/pnas.1701330114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The slow spontaneous inactivation of potassium channels exhibits classic signatures of transmembrane allostery. A variety of data support a model in which the loss of K+ ions from the selectivity filter is a major factor in promoting inactivation, which defeats transmission, and is allosterically coupled to protonation of key channel activation residues, more than 30 Å from the K+ ion binding site. We show that proton binding at the intracellular pH sensor perturbs the potassium affinity at the extracellular selectivity filter by more than three orders of magnitude for the full-length wild-type KcsA, a pH-gated bacterial channel, in membrane bilayers. Studies of F103 in the hinge of the inner helix suggest an important role for its bulky sidechain in the allosteric mechanism; we show that the energetic strength of coupling of the gates is strongly altered when this residue is mutated to alanine. These results provide quantitative site-specific measurements of allostery in a bilayer environment, and highlight the power of describing ion channel gating through the lens of allosteric coupling.
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35
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Li JB, Tang S, Zheng JS, Tian CL, Liu L. Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins. Acc Chem Res 2017; 50:1143-1153. [PMID: 28374993 DOI: 10.1021/acs.accounts.7b00001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA. The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64-179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.
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Affiliation(s)
- Jia-Bin Li
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Ji-Shen Zheng
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Chang-Lin Tian
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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36
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Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Probing the Effects of Gating on the Ion Occupancy of the K + Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy. J Am Chem Soc 2017; 139:8837-8845. [PMID: 28472884 DOI: 10.1021/jacs.7b01594] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interplay between the intracellular gate and the selectivity filter underlies the structural basis for gating in potassium ion channels. Using a combination of protein semisynthesis, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics (MD) simulations, we probe the ion occupancy at the S1 binding site in the constricted state of the selectivity filter of the KcsA channel when the intracellular gate is open and closed. The 2D IR spectra resolve two features, whose relative intensities depend on the state of the intracellular gate. By matching the experiment to calculated 2D IR spectra of structures predicted by MD simulations, we identify the two features as corresponding to states with S1 occupied or unoccupied by K+. We learn that S1 is >70% occupied when the intracellular gate is closed and <15% occupied when the gate is open. Comparison of MD trajectories show that opening of the intracellular gate causes a structural change in the selectivity filter, which leads to a change in the ion occupancy. This work reveals the complexity of the conformational landscape of the K+ channel selectivity filter and its dependence on the state of the intracellular gate.
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Affiliation(s)
- Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Alvin W Annen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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37
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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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38
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Lueck JD, Mackey AL, Infield DT, Galpin JD, Li J, Roux B, Ahern CA. Atomic mutagenesis in ion channels with engineered stoichiometry. eLife 2016; 5. [PMID: 27710770 PMCID: PMC5092047 DOI: 10.7554/elife.18976] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022] Open
Abstract
C-type inactivation of potassium channels fine-tunes the electrical signaling in excitable cells through an internal timing mechanism that is mediated by a hydrogen bond network in the channels' selectively filter. Previously, we used nonsense suppression to highlight the role of the conserved Trp434-Asp447 indole hydrogen bond in Shaker potassium channels with a non-hydrogen bonding homologue of tryptophan, Ind (Pless et al., 2013). Here, molecular dynamics simulations indicate that the Trp434Ind hydrogen bonding partner, Asp447, unexpectedly 'flips out' towards the extracellular environment, allowing water to penetrate the space behind the selectivity filter while simultaneously reducing the local negative electrostatic charge. Additionally, a protein engineering approach is presented whereby split intein sequences are flanked by endoplasmic reticulum retention/retrieval motifs (ERret) are incorporated into the N- or C- termini of Shaker monomers or within sodium channels two-domain fragments. This system enabled stoichiometric control of Shaker monomers and the encoding of multiple amino acids within a channel tetramer. DOI:http://dx.doi.org/10.7554/eLife.18976.001
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Affiliation(s)
- John D Lueck
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, United States
| | - Adam L Mackey
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, United States
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, United States
| | - Jing Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, United States
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Kim DM, Nimigean CM. Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating. Cold Spring Harb Perspect Biol 2016; 8:a029231. [PMID: 27141052 PMCID: PMC4852806 DOI: 10.1101/cshperspect.a029231] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K(+) channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K(+) channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York 10065
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40
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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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41
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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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42
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Zhang TO, Grechko M, Moran SD, Zanni MT. Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies. Methods Mol Biol 2016; 1345:21-41. [PMID: 26453203 DOI: 10.1007/978-1-4939-2978-8_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This chapter provides protocols for isotope-labeling the human islet amyloid polypeptide (hIAPP or amylin) involved in type II diabetes and γD-crystallin involved in cataract formation. Because isotope labeling improves the structural resolution, these protocols are useful for experiments using Fourier transform infrared (FTIR), two-dimensional infrared (2D IR), and NMR spectroscopies. Our research group specializes in using 2D IR spectroscopy and isotope labeling. 2D IR spectroscopy provides structural information by measuring solvation from 2D diagonal lineshapes and vibrational couplings from cross peaks. Infrared spectroscopy can be used to study kinetics, membrane proteins, and aggregated proteins. Isotope labeling provides greater certainty in the spectral assignment, which enables new structural insights that are difficult to obtain with other methods. For amylin, we provide a protocol for (13)C/(18)O labeling backbone carbonyls at one or more desired amino acids in order to obtain residue-specific structural resolution. We also provide a protocol for expressing and purifying amylin from E. coli, which enables uniform (13)C or (13)C/(15)N labeling. Uniform labeling is useful for measuring the monomer infrared spectrum in an amyloid oligomer or fiber as well as amyloid protein bound to another polypeptide or protein, such as a chaperone or an inhibitor. In addition, our expression protocol results in 2-2.5 mg of amylin peptide per 1 L cell culture, which is a high enough yield to straightforwardly obtain the 2-10 mg needed for high resolution and solid-state NMR experiments. Finally, we provide a protocol to isotope-label either of the two domains of γD-crystallin using expressed protein ligation. Domain labeling makes it possible to resolve the structures of the two halves of the protein in FTIR and 2D IR spectra. With modifications, these strategies and protocols for isotope labeling can be applied to other amyloid polypeptides and proteins.
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Affiliation(s)
- Tianqi O Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Maksim Grechko
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sean D Moran
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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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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Semisynthetic protein nanoreactor for single-molecule chemistry. Proc Natl Acad Sci U S A 2015; 112:13768-73. [PMID: 26504203 DOI: 10.1073/pnas.1510565112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach.
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45
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Kwon B, Tietze D, White PB, Liao SY, Hong M. Chemical ligation of the influenza M2 protein for solid-state NMR characterization of the cytoplasmic domain. Protein Sci 2015; 24:1087-99. [PMID: 25966817 PMCID: PMC4500309 DOI: 10.1002/pro.2690] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022]
Abstract
Solid-state NMR-based structure determination of membrane proteins and large protein complexes faces the challenge of limited spectral resolution when the proteins are uniformly (13)C-labeled. A strategy to meet this challenge is chemical ligation combined with site-specific or segmental labeling. While chemical ligation has been adopted in NMR studies of water-soluble proteins, it has not been demonstrated for membrane proteins. Here we show chemical ligation of the influenza M2 protein, which contains a transmembrane (TM) domain and two extra-membrane domains. The cytoplasmic domain, which contains an amphipathic helix (AH) and a cytoplasmic tail, is important for regulating virus assembly, virus budding, and the proton channel activity. A recent study of uniformly (13)C-labeled full-length M2 by spectral simulation suggested that the cytoplasmic tail is unstructured. To further test this hypothesis, we conducted native chemical ligation of the TM segment and part of the cytoplasmic domain. Solid-phase peptide synthesis of the two segments allowed several residues to be labeled in each segment. The post-AH cytoplasmic residues exhibit random-coil chemical shifts, low bond order parameters, and a surface-bound location, thus indicating that this domain is a dynamic random coil on the membrane surface. Interestingly, the protein spectra are similar between a model membrane and a virus-mimetic membrane, indicating that the structure and dynamics of the post-AH segment is insensitive to the lipid composition. This chemical ligation approach is generally applicable to medium-sized membrane proteins to provide site-specific structural constraints, which complement the information obtained from uniformly (13)C, (15)N-labeled proteins.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Daniel Tietze
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Paul B White
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Shu Y Liao
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
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Pless SA, Kim RY, Ahern CA, Kurata HT. Atom-by-atom engineering of voltage-gated ion channels: magnified insights into function and pharmacology. J Physiol 2015; 593:2627-34. [PMID: 25640301 DOI: 10.1113/jphysiol.2014.287714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
Unnatural amino acid incorporation into ion channels has proven to be a valuable approach to interrogate detailed hypotheses arising from atomic resolution structures. In this short review, we provide a brief overview of some of the basic principles and methods for incorporation of unnatural amino acids into proteins. We also review insights into the function and pharmacology of voltage-gated ion channels that have emerged from unnatural amino acid mutagenesis approaches.
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Affiliation(s)
- Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Robin Y Kim
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | | | - Harley T Kurata
- Department of Anesthesiology, Pharmacology, and Therapeutics, University of British Columbia, Vancouver, BC, Canada
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Ariyaratne A, Zocchi G. Artificial phosphorylation sites modulate the activity of a voltage-gated potassium channel. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032701. [PMID: 25871138 DOI: 10.1103/physreve.91.032701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Indexed: 06/04/2023]
Abstract
The KvAP potassium channel is representative of a family of voltage-gated ion channels where the membrane potential is sensed by a transmembrane helix containing several positively charged arginines. Previous work by Wang and Zocchi [A. Wang and G. Zocchi, PLoS ONE 6, e18598 (2011)] showed how a negatively charged polyelectrolyte attached in proximity to the voltage sensing element can bias the opening probability of the channel. Here we introduce three phosphorylation sites at the same location and show that the response curve of the channel shifts by about 20 mV upon phosphorylation, while other characteristics such as the single-channel conductance are unaffected. In summary, we construct an artificial phosphorylation site which confers allosteric regulation to the channel.
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Affiliation(s)
- Amila Ariyaratne
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095-1547, USA
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095-1547, USA
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48
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Marchesi A, Arcangeletti M, Mazzolini M, Torre V. Proton transfer unlocks inactivation in cyclic nucleotide-gated A1 channels. J Physiol 2015; 593:857-70. [PMID: 25480799 DOI: 10.1113/jphysiol.2014.284216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/28/2014] [Indexed: 01/12/2023] Open
Abstract
KEY POINTS Desensitization and inactivation provide a form of short-term memory controlling the firing patterns of excitable cells and adaptation in sensory systems. Unlike many of their cousin K(+) channels, cyclic nucleotide-gated (CNG) channels are thought not to desensitize or inactivate. Here we report that CNG channels do inactivate and that inactivation is controlled by extracellular protons. Titration of a glutamate residue within the selectivity filter destabilizes the pore architecture, which collapses towards a non-conductive, inactivated state in a process reminiscent of the usual C-type inactivation observed in many K(+) channels. These results indicate that inactivation in CNG channels represents a regulatory mechanism that has been neglected thus far, with possible implications in several physiological processes ranging from signal transduction to growth cone navigation. ABSTRACT Ion channels control ionic fluxes across biological membranes by residing in any of three functionally distinct states: deactivated (closed), activated (open) or inactivated (closed). Unlike many of their cousin K(+) channels, cyclic nucleotide-gated (CNG) channels do not desensitize or inactivate. Using patch recording techniques, we show that when extracellular pH (pHo ) is decreased from 7.4 to 6 or lower, wild-type CNGA1 channels inactivate in a voltage-dependent manner. pHo titration experiments show that at pHo < 7 the I-V relationships are outwardly rectifying and that inactivation is coupled to current rectification. Single-channel recordings indicate that a fast mechanism of proton blockage underlines current rectification while inactivation arises from conformational changes downstream from protonation. Furthermore, mutagenesis and ionic substitution experiments highlight the role of the selectivity filter in current decline, suggesting analogies with the C-type inactivation observed in K(+) channels. Analysis with Markovian models indicates that the non-independent binding of two protons within the transmembrane electrical field explains both the voltage-dependent blockage and the inactivation. Low pH, by inhibiting the CNGA1 channels in a state-dependent manner, may represent an unrecognized endogenous signal regulating CNG physiological functions in diverse tissues.
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Affiliation(s)
- Arin Marchesi
- Neurobiology Sector, International School for Advanced Studies (SISSA), Trieste, Italy
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Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
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50
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Zuo C, Tang S, Zheng JS. Chemical synthesis and biophysical applications of membrane proteins. J Pept Sci 2014; 21:540-9. [DOI: 10.1002/psc.2721] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Chao Zuo
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Tang
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei 230031 China
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