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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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2
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Cornelius F, Tsunekawa N, Toyoshima C. Distinct pH dependencies of Na +/K + selectivity at the two faces of Na,K-ATPase. J Biol Chem 2017; 293:2195-2205. [PMID: 29247005 DOI: 10.1074/jbc.ra117.000700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/28/2017] [Indexed: 11/06/2022] Open
Abstract
The sodium pump (Na,K-ATPase) in animal cells is vital for actively maintaining ATP hydrolysis-powered Na+ and K+ electrochemical gradients across the cell membrane. These ion gradients drive co- and countertransport and are critical for establishing the membrane potential. It has been an enigma how Na,K-ATPase discriminates between Na+ and K+, despite the pumped ion on each side being at a lower concentration than the other ion. Recent crystal structures of analogs of the intermediate conformations E2·Pi·2K+ and Na+-bound E1∼P·ADP suggest that the dimensions of the respective binding sites in Na,K-ATPase are crucial in determining its selectivity. Here, we found that the selectivity at each membrane face is pH-dependent and that this dependence is unique for each face. Most notable was a strong increase in the specific affinity for K+ at the extracellular face (i.e. E2 conformation) as the pH is lowered from 7.5 to 5. We also observed a smaller increase in affinity for K+ on the cytoplasmic side (E1 conformation), which reduced the selectivity for Na+ Theoretical analysis of the pKa values of ion-coordinating acidic amino acid residues suggested that the face-specific pH dependences and Na+/K+ selectivities may arise from the protonation or ionization of key residues. The increase in K+ selectivity at low pH on the cytoplasmic face, for instance, appeared to be associated with Asp808 protonation. We conclude that changes in the ionization state of coordinating residues in Na,K-ATPase could contribute to altering face-specific ion selectivity.
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Affiliation(s)
- Flemming Cornelius
- From the Department of Biomedicine, University of Aarhus, Ole Worms Allé 6, 8000 Aarhus C, Denmark and
| | - Naoki Tsunekawa
- the Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032
| | - Chikashi Toyoshima
- the Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032
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4
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Gonzalez MA, Barriga HMG, Richens JL, Law RV, O'Shea P, Bresme F. How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study. Phys Chem Chem Phys 2017; 19:9199-9209. [DOI: 10.1039/c7cp01400g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems.
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Affiliation(s)
| | | | | | - Robert V. Law
- Department of Chemistry
- Imperial College London
- London
- UK
| | - Paul O'Shea
- Department of Chemistry
- Imperial College London
- London
- UK
- School of Life Sciences
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5
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Komuro Y, Re S, Kobayashi C, Muneyuki E, Sugita Y. CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase. J Chem Theory Comput 2015; 10:4133-42. [PMID: 26588553 DOI: 10.1021/ct5004143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Adenosine triphosphate (ATP) is an indispensable energy source in cells. In a wide variety of biological phenomena like glycolysis, muscle contraction/relaxation, and active ion transport, chemical energy released from ATP hydrolysis is converted to mechanical forces to bring about large-scale conformational changes in proteins. Investigation of structure-function relationships in these proteins by molecular dynamics (MD) simulations requires modeling of ATP in solution and ATP bound to proteins with accurate force-field parameters. In this study, we derived new force-field parameters for the triphosphate moiety of ATP based on the high-precision quantum calculations of methyl triphosphate. We tested our new parameters on membrane-embedded sarcoplasmic reticulum Ca(2+)-ATPase and four soluble proteins. The ATP-bound structure of Ca(2+)-ATPase remains stable during MD simulations, contrary to the outcome in shorter simulations using original parameters. Similar results were obtained with the four ATP-bound soluble proteins. The new force-field parameters were also tested by investigating the range of conformations sampled during replica-exchange MD simulations of ATP in explicit water. Modified parameters allowed a much wider range of conformational sampling compared with the bias toward extended forms with original parameters. A diverse range of structures agrees with the broad distribution of ATP conformations in proteins deposited in the Protein Data Bank. These simulations suggest that the modified parameters will be useful in studies of ATP in solution and of the many ATP-utilizing proteins.
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Affiliation(s)
- Yasuaki Komuro
- Graduate School of Science and Engineering, Chuo University , 1-13-27, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.,RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.,RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Chigusa Kobayashi
- RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University , 1-13-27, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.,RIKEN Advanced Institute for Computational Science, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F , 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN iTHES , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan
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6
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Davoudi S, Amjad‐Iranagh S, Zaeifi Yamchi M. Molecular dynamic simulation of Ca
2+
‐ATPase interacting with lipid bilayer membrane. IET Nanobiotechnol 2015; 9:85-94. [DOI: 10.1049/iet-nbt.2013.0073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Samaneh Davoudi
- Chemical Engineering DepartmentAmirkabir University of TechnologyTehranIran
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7
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A coarse-grained molecular dynamics investigation of the phase behavior of DPPC/cholesterol mixtures. Chem Phys Lipids 2015; 185:88-98. [DOI: 10.1016/j.chemphyslip.2014.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 11/21/2022]
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8
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Vincent PE, Weinberg PD. Flow-dependent concentration polarization and the endothelial glycocalyx layer: multi-scale aspects of arterial mass transport and their implications for atherosclerosis. Biomech Model Mechanobiol 2013; 13:313-26. [DOI: 10.1007/s10237-013-0512-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 06/26/2013] [Indexed: 10/26/2022]
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9
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Chen Y, Xu G. Improvement of Ca2+-tolerance by the introduction of EO groups for the anionic surfactants: Molecular dynamics simulation. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2013.02.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Kekenes-Huskey PM, Metzger VT, Grant BJ, Andrew McCammon J. Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca²+ ATPase. Protein Sci 2013; 21:1429-43. [PMID: 22821874 DOI: 10.1002/pro.2129] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sarcoplasmic reticulum Ca²⁺ ATPase (SERCA) is a membrane-bound pump that utilizes ATP to drive calcium ions from the myocyte cytosol against the higher calcium concentration in the sarcoplasmic reticulum. Conformational transitions associated with Ca²⁺-binding are important to its catalytic function. We have identified collective motions that partition SERCA crystallographic structures into multiple catalytically-distinct states using principal component analysis. Using Brownian dynamics simulations, we demonstrate the important contribution of surface-exposed, polar residues in the diffusional encounter of Ca²⁺. Molecular dynamics simulations indicate the role of Glu309 gating in binding Ca²⁺, as well as subsequent changes in the dynamics of SERCA's cytosolic domains. Together these data provide structural and dynamical insights into a multistep process involving Ca²⁺ binding and catalytic transitions.
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Affiliation(s)
- Peter M Kekenes-Huskey
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA.
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11
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Lervik A, Bresme F, Kjelstrup S, Rubí JM. On the thermodynamic efficiency of Ca²⁺-ATPase molecular machines. Biophys J 2013; 103:1218-26. [PMID: 22995494 DOI: 10.1016/j.bpj.2012.07.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/05/2012] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
Experimental studies have shown that the activity of the reconstituted molecular pump Ca(2+)-ATPase strongly depends on the thickness of the supporting bilayer. It is thus expected that the bilayer structure will have an impact on the thermodynamic efficiency of this nanomachine. Here, we introduce a nonequilibrium-thermodynamics theoretical approach to estimate the thermodynamic efficiency of the Ca(2+)-ATPase from analysis of available experimental data about ATP hydrolysis and Ca(2+) transport. We find that the entropy production, i.e., the heat released to the surroundings under working conditions, is approximately constant for bilayers containing phospholipids with hydrocarbon chains of 18-22 carbon atoms. Our estimates for the heat released during the pump operation agree with results obtained from separate calorimetric experiments on the Ca(2+)-ATPase derived from sarcoplasmic reticulum. We show that the thermodynamic efficiency of the reconstituted Ca(2+)-ATPase reaches a maximum for bilayer thicknesses corresponding to maximum activity. Surprisingly, the estimated thermodynamic efficiency is very low, ∼12%. We discuss the significance of this result as representative of the efficiency of other nanomachines, and we address the influence of the experimental set-up on such a low efficiency. Overall, our approach provides a general route to estimate thermodynamic efficiencies and heat dissipation in experimental studies of nanomachines.
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Affiliation(s)
- Anders Lervik
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway.
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12
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Kekenes-Huskey PM, Gillette A, Hake J, McCammon JA. Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA. ACTA ACUST UNITED AC 2012; 5. [PMID: 23293662 DOI: 10.1088/1749-4699/5/1/014015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca(2+) ATPase (SERCA). We find that a combination of diffusional encounter and internal 'buried channel' descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude.
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Affiliation(s)
- P M Kekenes-Huskey
- Department of Pharmacology, University of California San Diego, La Jolla CA 92093
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13
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Thøgersen L, Nissen P. Flexible P-type ATPases interacting with the membrane. Curr Opin Struct Biol 2012; 22:491-9. [PMID: 22749193 DOI: 10.1016/j.sbi.2012.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 01/13/2023]
Abstract
Cation pumps and lipid flippases of the P-type ATPase family maintain electrochemical gradients and asymmetric lipid distributions across membranes, and offer significant insight of protein:membrane interactions. The sarcoplasmic reticulum Ca(2+)-ATPase features flexible and adaptive interactions with the surrounding membrane, while the Na(+),K(+)-ATPase complex is modulated by membrane components and a role for the γ-subunit as a stabilizer of a specific lipid interaction with the α-subunit has been proposed. The first crystal structure of a heavy-metal transporting ATPase shows a markedly amphipathic helix at the cytoplasmic membrane surface, highlighting this structure as a general motif of all P-type ATPases although with specialization to different membranes. Residues of central importance for the lipid flippase activity of the P4-type ATPase subfamily have been pinpointed by mutational studies, but the transport pathway and mechanism remain unknown.
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Affiliation(s)
- Lea Thøgersen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, DK-8000 Aarhus C, Denmark
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