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Qiao P, Odenkirk MT, Zheng W, Wang Y, Chen J, Xu W, Baker ES. Elucidating the role of lipid interactions in stabilizing the membrane protein KcsA. Biophys J 2024:S0006-3495(24)00478-8. [PMID: 39030907 DOI: 10.1016/j.bpj.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024] Open
Abstract
The significant effects of lipid binding on the functionality of potassium channel KcsA have been validated by brilliant studies. However, the specific interactions between lipids and KcsA, such as binding parameters for each binding event, have not been fully elucidated. In this study, we employed native mass spectrometry to investigate the binding of lipids to KcsA and their effects on the channel. The tetrameric structure of KcsA remains intact even in the absence of lipid binding. However, the subunit architecture of the E71A mutant, which is constantly open at low pH, relies on tightly associated copurified lipids. Furthermore, we observed that lipids exhibit weak binding to KcsA at high pH when the channel is at a closed/inactivation state in the absence of permeant cation K+. This feeble interaction potentially facilitates the association of K+ ions, leading to the transition of the channel to a resting closed/open state. Interestingly, both anionic and zwitterionic lipids strongly bind to KcsA at low pH when the channel is in an open/inactivation state. We also investigated the binding patterns of KcsA with natural lipids derived from E. coli and Streptomyces lividans. Interestingly, lipids from E. coli exhibited much stronger binding affinity compared to the lipids from S. lividans. Among the natural lipids from S. lividans, free fatty acids and triacylglycerols demonstrated the tightest binding to KcsA, whereas no detectable binding events were observed with natural phosphatidic acid lipids. These findings suggest that the lipid association pattern in S. lividans, the natural host for KcsA, warrants further investigation. In conclusion, our study sheds light on the role of lipids in stabilizing KcsA and highlights the importance of specific lipid-protein interactions in modulating its conformational states.
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Affiliation(s)
- Pei Qiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Weiyi Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuchen Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jinhui Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wenhao Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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2
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High-Resolution Magic Angle Spinning NMR of KcsA in Liposomes: The Highly Mobile C-Terminus. Biomolecules 2022; 12:biom12081122. [PMID: 36009016 PMCID: PMC9405666 DOI: 10.3390/biom12081122] [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: 06/27/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
The structure of the transmembrane domain of the pH-activated bacterial potassium channel KcsA has been extensively characterized, yet little information is available on the structure of its cytosolic, functionally critical N- and C-termini. This study presents high-resolution magic angle spinning (HR-MAS) and fractional deuteration as tools to study these poorly resolved regions for proteoliposome-embedded KcsA. Using 1H-detected HR-MAS NMR, we show that the C-terminus transitions from a rigid structure to a more dynamic structure as the solution is rendered acidic. We make previously unreported assignments of residues in the C-terminus of lipid-embedded channels. These data agree with functional models of the C-terminus-stabilizing KcsA tetramers at a neutral pH with decreased stabilization effects at acidic pH. We present evidence that a C-terminal truncation mutation has a destabilizing effect on the KcsA selectivity filter. Finally, we show evidence of hydrolysis of lipids in proteoliposome samples during typical experimental timeframes.
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Kiya T, Takeshita K, Kawanabe A, Fujiwara Y. Intermolecular functional coupling between phosphoinositides and the potassium channel KcsA. J Biol Chem 2022; 298:102257. [PMID: 35839854 PMCID: PMC9396063 DOI: 10.1016/j.jbc.2022.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
Biological membranes are composed of a wide variety of lipids. Phosphoinositides (PIPns) in the membrane inner leaflet only account for a small percentage of the total membrane lipids but modulate the functions of various membrane proteins, including ion channels, which play important roles in cell signaling. KcsA, a prototypical K+ channel that is small, simple, and easy to handle, has been broadly examined regarding its crystallography, in silico molecular analysis, and electrophysiology. It has been reported that KcsA activity is regulated by membrane phospholipids, such as phosphatidylglycerol. However, there has been no quantitative analysis of the correlation between direct lipid binding and the functional modification of KcsA, and it is unknown whether PIPns modulate KcsA function. Here, using contact bubble bilayer recording, we observed that the open probability of KcsA increased significantly (from about 10% to 90%) when the membrane inner leaflet contained only a small percentage of PIPns. In addition, we found an increase in the electrophysiological activity of KcsA correlated with a larger number of negative charges on PIPns. We further analyzed the affinity of the direct interaction between PIPns and KcsA using microscale thermophoresis and observed a strong correlation between direct lipid binding and the functional modification of KcsA. In conclusion, our approach was able to reconstruct the direct modification of KcsA by PIPns, and we propose that it can also be applied to elucidate the mechanism of modification of other ion channels by PIPns.
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Affiliation(s)
- Takunari Kiya
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan
| | - Kohei Takeshita
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Hyogo 679-5148, Japan
| | - Akira Kawanabe
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan.
| | - Yuichiro Fujiwara
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kagawa 761-0793, Japan.
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Pipatpolkai T, Quetschlich D, Stansfeld PJ. From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels. J Mol Biol 2021; 433:167105. [PMID: 34139216 PMCID: PMC8361781 DOI: 10.1016/j.jmb.2021.167105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022]
Abstract
Potassium (K+) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K+ conductance, returning a cell to its resting potential. K+ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K+ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K+ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K+ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Physiology Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, UK
| | - Daniel Quetschlich
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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5
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Solid state NMR of membrane proteins: methods and applications. Biochem Soc Trans 2021; 49:1505-1513. [PMID: 34397082 DOI: 10.1042/bst20200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.
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Pérez-Conesa S, Keeler EG, Zhang D, Delemotte L, McDermott AE. Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel. J Chem Phys 2021; 154:165102. [PMID: 33940802 PMCID: PMC9250420 DOI: 10.1063/5.0040649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, complexation with antibodies, and substitution of detergents in place of lipids, examining the channel under more native conditions is desirable. Solid-state nuclear magnetic resonance (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the activated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible x-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs fully open ensembles from MD simulations. The simulated NMR chemical shifts for those specific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discriminate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change.
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Affiliation(s)
- Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Eric G Keeler
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Dongyu Zhang
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Warschawski DE, Lakshmi KV, Marcotte I. Foreword to: Biophysical studies of membrane systems and interactions - Commemorative issue in honour of Professor Michèle Auger. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183609. [PMID: 33794169 DOI: 10.1016/j.bbamem.2021.183609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Dror E Warschawski
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005 Paris, France
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, H3C 3P8 Montreal, Canada.
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Fortea E, Accardi A. A quantitative flux assay for the study of reconstituted Cl - channels and transporters. Methods Enzymol 2021; 652:243-272. [PMID: 34059284 DOI: 10.1016/bs.mie.2021.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The recent deluge of high-resolution structural information on membrane proteins has not been accompanied by a comparable increase in our ability to functionally interrogate these proteins. Current functional assays often are not quantitative or are performed in conditions that significantly differ from those used in structural experiments, thus limiting the mechanistic correspondence between structural and functional experiments. A flux assay to determine quantitatively the functional properties of purified and reconstituted Cl- channels and transporters in membranes of defined lipid compositions is described. An ion-sensitive electrode is used to measure the rate of Cl- efflux from proteoliposomes reconstituted with the desired protein and the fraction of vesicles containing at least one active protein. These measurements enable the quantitative determination of key molecular parameters such as the unitary transport rate, the fraction of proteins that are active, and the molecular mass of the transport protein complex. The approach is illustrated using CLC-ec1, a CLC-type H+/Cl- exchanger as an example. The assay enables the quantitative study of a wide range of Cl- transporting molecules and proteins whose activity is modulated by ligands, voltage, and membrane composition as well as the investigation of the effects of compounds that directly inhibit or activate the reconstituted transport systems. The present assay is readily adapted to the study of transport systems with diverse substrate specificities and molecular characteristics, and the necessary modifications needed are discussed.
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Affiliation(s)
- Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States; Department of Anesthesiology, Weill Cornell Medical College, New York, NY, United States; Department of Biochemistry, Weill Cornell Medical College, New York, NY, United States.
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