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Brahma R, Raghuraman H. Characterization of a novel MgtE homolog and its structural dynamics in membrane mimetics. Biophys J 2024; 123:1968-1983. [PMID: 38042987 PMCID: PMC11309985 DOI: 10.1016/j.bpj.2023.11.3402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 12/04/2023] Open
Abstract
Magnesium (Mg2+) is the most abundant divalent cation in the cell and is critical for numerous cellular processes. Despite its importance, the mechanisms of intracellular Mg2+ transport and its regulation are poorly understood. MgtE is the main Mg2+ transport system in almost half of bacterial species and is an ortholog of mammalian SLC41A1 transporters, which are implicated in neurodegenerative diseases and cancer. To date, only MgtE from Thermus thermophilus (MgtETT) has been extensively characterized, mostly in detergent micelles, and gating-related structural dynamics in biologically relevant membranes are scarce. The MgtE homolog from Bacillus firmus (MgtEBF) is unique since it lacks the entire Mg2+-sensing N-domain but has conserved structural motifs in the TM-domain for Mg2+ transport. In this work, we have successfully purified this novel homolog in a stable and functional form, and ColabFold structure prediction analysis suggests a homodimer. Further, microscale thermophoresis experiments show that MgtEBF binds Mg2+ and ATP, similar to MgtETT. Importantly, we show that, despite lacking the N-domain, MgtEBF mediates Mg2+ transport function in the presence of an inwardly directed Mg2+ gradient in reconstituted proteoliposomes. Furthermore, comparison of the organization and dynamics of Trp residues in the TM-domain of MgtEBF in membrane mimetics, in apo- and Mg2+-bound forms, suggests that the cytoplasmic binding of Mg2+ might involve modest gating-related conformational changes at the TM-domain. Overall, our results show that the gating-related structural dynamics (hydration dynamics, conformational heterogeneity) of the full-length MgtEBF is significantly changed in functionally pertinent membrane environment, emphasizing the importance of lipid-protein interactions in MgtE gating mechanisms.
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Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Training School Complex, Mumbai, India.
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2
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Pahlavan B, Buitrago N, Santamaria F. Macromolecular rate theory explains the temperature dependence of membrane conductance kinetics. Biophys J 2023; 122:522-532. [PMID: 36567527 PMCID: PMC9941726 DOI: 10.1016/j.bpj.2022.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/19/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
The factor Q10 is used in neuroscience to adjust reaction rates of voltage-activated membrane conductances to different temperatures and is widely assumed to be constant. By performing an analysis of published data of the reaction rates of sodium, potassium, and calcium membrane conductances, we demonstrate that 1) Q10 is temperature dependent, 2) this relationship is similar across conductances, and 3) there is a strong effect at low temperatures (<15°C). We show that macromolecular rate theory (MMRT) explains this temperature dependency. MMRT predicts the existence of optimal temperatures at which reaction rates decrease as temperature increases, a phenomenon that we also found in the published data sets. We tested the consequences of using MMRT-adjusted reaction rates in the Hodgkin-Huxley model of the squid's giant axon. The MMRT-adjusted model reproduces the temperature dependence of the rising and falling times of the action potential. Furthermore, the model also reproduces these properties for different squid species that live in different climates. In a second example, we compare spiking patterns of biophysical models based on human pyramidal neurons from the Allen Cell Types database at room and physiological temperatures. The original models, calibrated at 34°C, failed to generate realistic spikes at room temperature in more than half of the tested models, while the MMRT produces realistic spiking in all conditions. In another example, we show that using the MMRT correction in hippocampal pyramidal cell models results in 100% differences in voltage responses. Finally, we show that the shape of the Q10 function results in systematic errors in predicting reaction rates. We propose that the optimal temperature could be a thermodynamical barrier to avoid over excitation in neurons. While this study is centered on membrane conductances, our results have important consequences for all biochemical reactions involved in cell signaling.
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Affiliation(s)
- Bahram Pahlavan
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, Texas
| | - Nicolas Buitrago
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, Texas
| | - Fidel Santamaria
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, Texas.
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3
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Esquembre R, Renart ML, Poveda JA, Mateo CR. Silica/Proteoliposomal Nanocomposite as a Potential Platform for Ion Channel Studies. Molecules 2022; 27:molecules27196658. [PMID: 36235195 PMCID: PMC9571612 DOI: 10.3390/molecules27196658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
The nanostructuration of solid matrices with lipid nanoparticles containing membrane proteins is a promising tool for the development of high-throughput screening devices. Here, sol-gel silica-derived nanocomposites loaded with liposome-reconstituted KcsA, a prokaryotic potassium channel, have been synthesized. The conformational and functional stability of these lipid nanoparticles before and after sol-gel immobilization have been characterized by using dynamic light scattering, and steady-state and time-resolved fluorescence spectroscopy methods. The lipid-reconstituted KcsA channel entrapped in the sol-gel matrix retained the conformational and stability changes induced by the presence of blocking or permeant cations in the buffer (associated with the conformation of the selectivity filter) or by a drop in the pH (associated with the opening of the activation gate of the protein). Hence, these results indicate that this novel device has the potential to be used as a screening platform to test new modulating drugs of potassium channels.
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4
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Barrera FN. On 'Fourier transform infrared study of proteins with parallel β-chains' by Heino Susi, D. Michael Byler. Arch Biochem Biophys 2022; 726:109114. [PMID: 34973205 DOI: 10.1016/j.abb.2021.109114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022]
Abstract
In 1987, Susi & Byler published a groundbreaking paper for the determination of the secondary structure of proteins. Notably, they determined the characteristic signature of the β-strand in the infrared spectrum. As a result, Fourier-transform infrared spectroscopy became a general method to determine protein structure.
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Affiliation(s)
- Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee Knoxville, USA.
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5
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Single-molecule fluorescence vistas of how lipids regulate membrane proteins. Biochem Soc Trans 2021; 49:1685-1694. [PMID: 34346484 DOI: 10.1042/bst20201074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
The study of membrane proteins is undergoing a golden era, and we are gaining unprecedented knowledge on how this key group of proteins works. However, we still have only a basic understanding of how the chemical composition and the physical properties of lipid bilayers control the activity of membrane proteins. Single-molecule (SM) fluorescence methods can resolve sample heterogeneity, allowing to discriminate between the different molecular populations that biological systems often adopt. This short review highlights relevant examples of how SM fluorescence methodologies can illuminate the different ways in which lipids regulate the activity of membrane proteins. These studies are not limited to lipid molecules acting as ligands, but also consider how the physical properties of the bilayer can be determining factors on how membrane proteins function.
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6
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Chatterjee S, Brahma R, Raghuraman H. Gating-related Structural Dynamics of the MgtE Magnesium Channel in Membrane-Mimetics Utilizing Site-Directed Tryptophan Fluorescence. J Mol Biol 2020; 433:166691. [PMID: 33203509 DOI: 10.1016/j.jmb.2020.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022]
Abstract
Magnesium is the most abundant divalent cation present in the cell, and an abnormal Mg2+ homeostasis is associated with several diseases in humans. However, among ion channels, the mechanisms of intracellular regulation and transport of Mg2+ are poorly understood. MgtE is a homodimeric Mg2+-selective channel and is negatively regulated by high intracellular Mg2+ concentration where the cytoplasmic domain of MgtE acts as a Mg2+ sensor. Most of the previous biophysical studies on MgtE have been carried out in detergent micelles and the information regarding gating-related structural dynamics of MgtE in physiologically-relevant membrane environment is scarce. In this work, we monitored the changes in gating-related structural dynamics, hydration dynamics and conformational heterogeneity of MgtE in micelles and membranes using the intrinsic site-directed Trp fluorescence. For this purpose, we have engineered six single-Trp mutants in the functional Trp-less background of MgtE to obtain site-specific information on the gating-related structural dynamics of MgtE in membrane-mimetic systems. Our results indicate that Mg2+-induced gating might involve the possibility of a 'conformational wave' from the cytosolic N-domain to transmembrane domain of MgtE. Although MgtE is responsive to Mg2+-induced gating in both micelles and membranes, the organization and dynamics of MgtE is substantially altered in physiologically important phospholipid membranes compared to micelles. This is accompanied by significant changes in hydration dynamics and conformational heterogeneity. Overall, our results highlight the importance of lipid-protein interactions and are relevant for understanding gating mechanism of magnesium channels in general, and MgtE in particular.
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Affiliation(s)
- Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
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7
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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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8
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Das A, Chatterjee S, Raghuraman H. Structural Dynamics of the Paddle Motif Loop in the Activated Conformation of KvAP Voltage Sensor. Biophys J 2019; 118:873-884. [PMID: 31547975 DOI: 10.1016/j.bpj.2019.08.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Voltage-dependent potassium (Kv) channels play a fundamental role in neuronal and cardiac excitability and are potential therapeutic targets. They assemble as tetramers with a centrally located pore domain surrounded by a voltage-sensing domain (VSD), which is critical for sensing transmembrane potential and subsequent gating. Although the sensor is supposed to be in "Up" conformation in both n-octylglucoside (OG) micelles and phospholipid membranes in the absence of membrane potential, toxins that bind VSD and modulate the gating behavior of Kv channels exhibit dramatic affinity differences in these membrane-mimetic systems. In this study, we have monitored the structural dynamics of the S3b-S4 loop of the paddle motif in activated conformation of KvAP-VSD by site-directed fluorescence approaches, using the environment-sensitive fluorescent probe 7-nitrobenz-2-oxa-1,3-diazol-4-yl-ethylenediamine (NBD). Emission maximum of NBD-labeled loop region of KvAP-VSD (residues 110-117) suggests a significant change in the polarity of local environment in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) membranes compared to OG micelles. This indicates that S3b-S4 loop residues might be partitioning to membrane interface, which is supported by an overall increased mean fluorescence lifetimes and significantly reduced water accessibility in membranes. Further, the magnitude of red edge excitation shift (REES) supports the presence of restricted/bound water molecules in the loop region of the VSD in micelles and membranes. Quantitative analysis of REES data using Gaussian probability distribution function clearly indicates that the sensor loop has fewer discrete equilibrium conformational states when reconstituted in membranes. Interestingly, this reduced molecular heterogeneity is consistent with the site-specific NBD polarization results, which suggest that the membrane environment offers a relaxed/dynamic organization for most of the S3b-S4 loop residues of the sensor. Overall, our results are relevant for understanding toxin-VSD interaction and gating mechanisms of Kv channels in membranes.
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Affiliation(s)
- Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
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9
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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10
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Miller DM, Findlay HE, Ces O, Templer RH, Booth PJ. Light-activated control of protein channel assembly mediated by membrane mechanics. NANOTECHNOLOGY 2016; 27:494004. [PMID: 27831930 DOI: 10.1088/0957-4484/27/49/494004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, The University of Melbourne, 3052, Australia
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11
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Yamakata A, Shimizu H, Oiki S. Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field. Phys Chem Chem Phys 2015; 17:21104-11. [DOI: 10.1039/c5cp02681d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Surface-enhanced IR absorption spectroscopy coupled with an electrochemical system enables the potassium-induced specific structural change of the potassium channel.
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Affiliation(s)
- Akira Yamakata
- Graduate School of Engineering
- Toyota Technological Institute
- Tempaku
- Japan
| | - Hirofumi Shimizu
- Department of Molecular Physiology and Biophysics
- Faculty of Medical Sciences
- University of Fukui
- Fukui 910-1193
- Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics
- Faculty of Medical Sciences
- University of Fukui
- Fukui 910-1193
- Japan
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12
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Poveda J, Giudici A, Renart M, Molina M, Montoya E, Fernández-Carvajal A, Fernández-Ballester G, Encinar J, González-Ros J. Lipid modulation of ion channels through specific binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1560-7. [DOI: 10.1016/j.bbamem.2013.10.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 01/08/2023]
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13
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Structural changes of the KcsA potassium channel upon application of the electrode potential studied by surface-enhanced IR absorption spectroscopy. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Vernier G, Wang J, Jennings LD, Sun J, Fischer A, Song L, Collier RJ. Solubilization and characterization of the anthrax toxin pore in detergent micelles. Protein Sci 2009; 18:1882-95. [PMID: 19609933 DOI: 10.1002/pro.199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteolytically activated Protective Antigen (PA) moiety of anthrax toxin self-associates to form a heptameric ring-shaped oligomer (the prepore). Acidic pH within the endosome converts the prepore to a pore that serves as a passageway for the toxin's enzymatic moieties to cross the endosomal membrane. Prepore is stable in solution under mildly basic conditions, and lowering the pH promotes a conformational transition to an insoluble pore-like state. N-tetradecylphosphocholine (FOS14) was the only detergent among 110 tested that prevented aggregation without dissociating the multimer into its constituent subunits. FOS14 maintained the heptamers as monodisperse, insertion-competent 440-kDa particles, which formed channels in planar phospholipid bilayers with the same unitary conductance and ability to translocate a model substrate protein as channels formed in the absence of detergent. Electron paramagnetic resonance analysis detected pore-like conformational changes within PA on solubilization with FOS14, and electron micrograph images of FOS14-solubilized pore showed an extended, mushroom-shaped structure. Circular dichroïsm measurements revealed an increase in alpha helix and a decrease in beta structure in pore formation. Spectral changes caused by a deletion mutation support the hypothesis that the 2beta2-2beta3 loop transforms into the transmembrane segment of the beta-barrel stem of the pore. Changes caused by selected point mutations indicate that the transition to alpha structure is dependent on residues of the luminal 2beta11-2beta12 loop that are known to affect pore formation. Stabilizing the PA pore in solution with FOS14 may facilitate further structural analysis and a more detailed understanding of the folding pathway by which the pore is formed.
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Affiliation(s)
- Gregory Vernier
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Boston, Massachusetts 02115, USA
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15
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Miller D, Charalambous K, Rotem D, Schuldiner S, Curnow P, Booth PJ. In vitro Unfolding and Refolding of the Small Multidrug Transporter EmrE. J Mol Biol 2009; 393:815-32. [DOI: 10.1016/j.jmb.2009.08.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 11/28/2022]
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16
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Pozo-Dengra J, Martínez-Rodríguez S, Contreras LM, Prieto J, Andújar-Sánchez M, Clemente-Jiménez JM, Las Heras-Vázquez FJ, Rodríguez-Vico F, Neira JL. Structure and conformational stability of a tetrameric thermostableN-succinylamino acid racemase. Biopolymers 2009; 91:757-72. [DOI: 10.1002/bip.21226] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Molina ML, Barrera FN, Encinar JA, Renart ML, Fernández AM, Poveda JA, Santoro J, Bruix M, Gavilanes F, Fernández-Ballester G, Neira JL, González-Ros JM. N-type inactivation of the potassium channel KcsA by the Shaker B "ball" peptide: mapping the inactivating peptide-binding epitope. J Biol Chem 2008; 283:18076-85. [PMID: 18430729 DOI: 10.1074/jbc.m710132200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effects of the inactivating peptide from the eukaryotic Shaker BK(+) channel (the ShB peptide) on the prokaryotic KcsA channel have been studied using patch clamp methods. The data show that the peptide induces rapid, N-type inactivation in KcsA through a process that includes functional uncoupling of channel gating. We have also employed saturation transfer difference (STD) NMR methods to map the molecular interactions between the inactivating peptide and its channel target. The results indicate that binding of the ShB peptide to KcsA involves the ortho and meta protons of Tyr(8), which exhibit the strongest STD effects; the C4H in the imidazole ring of His(16); the methyl protons of Val(4), Leu(7), and Leu(10) and the side chain amine protons of one, if not both, the Lys(18) and Lys(19) residues. When a noninactivating ShB-L7E mutant is used in the studies, binding to KcsA is still observed but involves different amino acids. Thus, the strongest STD effects are now seen on the methyl protons of Val(4) and Leu(10), whereas His(16) seems similarly affected as before. Conversely, STD effects on Tyr(8) are strongly diminished, and those on Lys(18) and/or Lys(19) are abolished. Additionally, Fourier transform infrared spectroscopy of KcsA in presence of (13)C-labeled peptide derivatives suggests that the ShB peptide, but not the ShB-L7E mutant, adopts a beta-hairpin structure when bound to the KcsA channel. Indeed, docking such a beta-hairpin structure into an open pore model for K(+) channels to simulate the inactivating peptide/channel complex predicts interactions well in agreement with the experimental observations.
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Affiliation(s)
- M Luisa Molina
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
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18
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Barrera FN, Renart ML, Poveda JA, de Kruijff B, Killian JA, González-Ros JM. Protein Self-Assembly and Lipid Binding in the Folding of the Potassium Channel KcsA. Biochemistry 2008; 47:2123-33. [DOI: 10.1021/bi700778c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco N. Barrera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - M. Lourdes Renart
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - José A. Poveda
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ben de Kruijff
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J. Antoinette Killian
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - José M. González-Ros
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain, and Biochemistry of Membranes, Bijvoetcenter, and Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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19
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Phosphatidic acid plays a special role in stabilizing and folding of the tetrameric potassium channel KcsA. FEBS Lett 2007; 581:5715-22. [DOI: 10.1016/j.febslet.2007.11.039] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Revised: 11/09/2007] [Accepted: 11/13/2007] [Indexed: 11/22/2022]
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Vásquez V, Cortes DM, Furukawa H, Perozo E. An Optimized Purification and Reconstitution Method for the MscS Channel: Strategies for Spectroscopical Analysis†. Biochemistry 2007; 46:6766-73. [PMID: 17500538 DOI: 10.1021/bi700322k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanosensitive channel of small conductance (MscS) plays a critical role in the osmoregulation of prokaryotic cells. The crystal structure of MscS revealed a homoheptamer with three transmembrane segments and a large cytoplasmic domain. It has been suggested that the crystal structure depicts an open state, but its actual functional conformation remains controversial. In the pursuit of spectroscopical approaches to MscS gating, we determined that standard purification methods yield two forms of MscS, with a considerable amount of unfolded channel. Here, we present an improved high-yield purification method based on Escherichia coli expression and a biochemical characterization of the reconstituted channel, optimized to yield approximately 4 mg of a single monodisperse product. Upon reconstitution into lipid vesicles, MscS is unusually prone to lateral aggregation depending on the lipid composition, particularly after sample freezing. Strategies for minimizing MscS aggregation in two dimensions for spectroscopic analyses of gating have been developed.
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Affiliation(s)
- Valeria Vásquez
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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21
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Boiteux C, Kraszewski S, Ramseyer C, Girardet C. Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. J Mol Model 2007; 13:699-713. [PMID: 17415597 DOI: 10.1007/s00894-007-0202-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 03/08/2007] [Accepted: 03/19/2007] [Indexed: 12/29/2022]
Abstract
KcsA potassium channel belongs to a wide family of allosteric proteins that switch between closed and open states conformations in response to a stimulus, and act as a regulator of cation activity in living cells. The gating mechanism and cation selectivity of such channels have been extensively studied in the literature, with a revival emphasis these latter years, due to the publication of the crystallized structure of KcsA. Despite the increasing number of research and review papers on these topics, quantitative interpretation of these processes at the atomic scale is far from achieved. On the basis of available experimental and theoretical data, and by including our recent results, we review the progresses in this field of activity and discuss the weaknesses that should be corrected. In this spirit, we partition the channel into the filter, cavity, extra and intracellular media, in order to analyze separately the specificity of each region. Special emphasis is brought to the study of an open state for the channel and to the different properties generated by the opening. The influence of water as a structural and dynamical component of the channel properties in closed and open states, as well as in the sequential motions of the cations, is analyzed using molecular dynamics simulations and ab initio calculations. The polarization and charge transfer effects on the ions' dynamics and kinetics are discussed in terms of partial charge models.
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Affiliation(s)
- Céline Boiteux
- Laboratoire de Physique Moléculaire UMR CNRS 6624, Université de Franche-Comté, La Bouloie, 25030, Besançon Cedex, France
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22
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Renart ML, Barrera FN, Molina ML, Encinar JA, Poveda JA, Fernández AM, Gómez J, González-Ros JM. Effects of conducting and blocking ions on the structure and stability of the potassium channel KcsA. J Biol Chem 2006; 281:29905-15. [PMID: 16815844 DOI: 10.1074/jbc.m602636200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This article reports on the interaction of conducting (K(+)) and blocking (Na(+)) monovalent metal ions with detergent-solubilized and lipid-reconstituted forms of the K(+) channel KcsA. Monitoring of the protein intrinsic fluorescence reveals that the two ions bind competitively to KcsA with distinct affinities (dissociation constants for the KcsA.K(+) and KcsA.Na(+) complexes of approximately 8 and 190 mm, respectively) and induce different conformations of the ion-bound protein. The differences in binding affinity as well as the higher K(+) concentration bathing the intracellular mouth of the channel, through which the cations gain access to the protein binding sites, should favor that only KcsA.K(+) complexes are formed under physiological-like conditions. Nevertheless, despite such prediction, it was also found that concentrations of Na(+) well below its dissociation constant and even in the presence of higher K(+) concentrations, cause a remarkable decrease in the protein thermal stability and facilitate thermal dissociation into subunits of the tetrameric KcsA, as concluded from the temperature dependence of the protein infrared spectra and from gel electrophoresis, respectively. These latter observations cannot be explained based on the occupancy of the binding sites from above and suggest that there must be additional ion binding sites, whose occupancy could not be detected by fluorescence and in which the affinity for Na(+) must be higher or at least similar to that of K(+). Moreover, cation binding as reported by means of fluorescence does not suffice to explain the large differences in free energy of stabilization involved in the formation of the KcsA.Na(+) and KcsA.K(+) complexes, which for the most part should arise from synergistic effects of the ion-mediated intersubunit interactions.
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Affiliation(s)
- María L Renart
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
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23
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Garcia-Martin A, Kwa LG, Strohmann B, Robert B, Holzwarth AR, Braun P. Structural Role of (Bacterio)chlorophyll Ligated in the Energetically Unfavorable β-Position. J Biol Chem 2006; 281:10626-34. [PMID: 16484226 DOI: 10.1074/jbc.m510731200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chlorophyll is attached to apoprotein in diastereotopically distinct ways, by beta- and alpha-ligation. Both the beta- and alpha-ligated chlorophylls of photosystem I are shown to have ample contacts to apoprotein within their proteinaceous binding sites, in particular, at C-13 of the isocyclic ring. The H-bonding patterns for the C-13(1) oxo groups, however, are clearly distinct for the beta-ligated and alpha-ligated chlorophylls. The beta-ligated chlorophylls frequently employ their C-13(1) oxo in H-bonds to neighboring helices and subunits. In contrast, the C-13(1) oxo of alpha-ligated chlorophylls are significantly less involved in H-bonding interactions, particularly to neighboring helices. Remarkably, in the peripheral antenna, light harvesting complex (LH2) from Rhodobacter sphaeroides, a single mutation in the alpha-subunit, introduced to eliminate H-bonding to the beta-bacteriochlorophyll-B850, which is ligated in the "beta-position," results in significant thermal destabilization of the LH2 in the membrane. In addition, in comparison with wild type LH2, the expression level of the LH2 lacking this H-bond is significantly reduced. These findings show that H-bonding to the C-13(1) keto group ofbeta-ligated (bacterio)-chlorophyll is a key structural motif and significantly contributes to the stability of bacteriochlorophyll proteins in the native membrane. Our analysis of photosystem I and II suggests that this hitherto unrecognized motif involving H-bonding to beta-ligated chlorophylls may be equally critical for the stable assembly of the inner core antenna of these multicomponent chlorophyll proteins.
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Chill JH, Louis JM, Miller C, Bax A. NMR study of the tetrameric KcsA potassium channel in detergent micelles. Protein Sci 2006; 15:684-98. [PMID: 16522799 PMCID: PMC2242490 DOI: 10.1110/ps.051954706] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Nuclear magnetic resonance (NMR) studies of large membrane-associated proteins are limited by the difficulties in preparation of stable protein-detergent mixed micelles and by line broadening, which is typical of these macroassemblies. We have used the 68-kDa homotetrameric KcsA, a thermostable N-terminal deletion mutant of a bacterial potassium channel from Streptomyces lividans, as a model system for applying NMR methods to membrane proteins. Optimization of measurement conditions enabled us to perform the backbone assignment of KcsA in SDS micelles and establish its secondary structure, which was found to closely agree with the KcsA crystal structure. The C-terminal cytoplasmic domain, absent in the original structure, contains a 14-residue helix that could participate in tetramerization by forming an intersubunit four-helix bundle. A quantitative estimate of cross- relaxation between detergent and KcsA backbone amide protons, together with relaxation and light scattering data, suggests SDS-KcsA mixed micelles form an oblate spheroid with approximately 180 SDS molecules per channel. K(+) ions bind to the micelle-solubilized channel with a K(D) of 3 +/- 0.5 mM, resulting in chemical shift changes in the selectivity filter. Related pH-induced changes in chemical shift along the "outer" transmembrane helix and the cytoplasmic membrane interface hint at a possible structural explanation for the observed pH-gating of the potassium channel.
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Affiliation(s)
- Jordan H Chill
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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