1
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Ashrafuzzaman M, Koeppe RE, Andersen OS. Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study. Int J Mol Sci 2024; 25:2758. [PMID: 38474005 PMCID: PMC10931550 DOI: 10.3390/ijms25052758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature.
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Affiliation(s)
- Mohammad Ashrafuzzaman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
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2
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Kwarteng DO, Gangoda M, Kooijman EE. The effect of methylated phosphatidylethanolamine derivatives on the ionization properties of signaling phosphatidic acid. Biophys Chem 2023; 296:107005. [PMID: 36934676 DOI: 10.1016/j.bpc.2023.107005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Phosphatidylethanolamine (PE) and Phosphatidylcholine (PC) are the most abundant glycerophospholipids in eukaryotic membranes. The differences in the physicochemical properties of their headgroups have contrasting modulatory effects on their interaction with intracellular macromolecules. As such, their overall impact on membrane structure and function differs significantly. Enzymatic methylation of PE's amine headgroup produces two methylated derivatives namely monomethyl PE (MMPE) and dimethyl PE (DMPE) which have physicochemical properties that generally range between that of PE and PC. Additionally, their influence on membrane properties differs from both PE and PC. Although variations in headgroup methylation have been reported to affect signaling pathways, the direct influence that these differences exert on the ionization properties of signaling phospholipids have not been investigated. Here, we briefly review membrane function and structure that are mediated by the differences in headgroup methylation between PE, MMPE, DMPE and PC. In addition, using 31P MAS NMR, we investigate the effect of these four phospholipids on the ionization properties of the ubiquitous signaling anionic lipid phosphatidic acid (PA). Our results show that PA's ionization properties are differentially affected by changes in phospholipid headgroup methylation. This could have important implications for PA-protein binding and hence physiological functions in cells where signaling events lead to changes in abundance of methylated PE derivatives in the membrane.
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Affiliation(s)
- Desmond Owusu Kwarteng
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
| | - Mahinda Gangoda
- Department of Chemistry & Biochemistry, Kent State University, P.O. Box 5190, Kent, OH 44242, USA
| | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
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3
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Mukhina T, Pabst G, Ruysschaert JM, Brezesinski G, Schneck E. pH-Dependent physicochemical properties of ornithine lipid in mono- and bilayers. Phys Chem Chem Phys 2022; 24:22778-22791. [PMID: 36111816 DOI: 10.1039/d2cp01045c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In certain bacteria, phosphatidylethanolamine lipids (PEL) get largely replaced by phosphate-free ornithine lipids (OL) under conditions of phosphate starvation. It has so far been unknown how much these two lipid types deviate in their physicochemical properties, and how strongly bacteria thus have to adapt in order to compensate for the difference. Here, we use differential scanning calorimetry, X-ray scattering, and X-ray fluorescence to investigate the properties of OL with saturated C14 alkyl chains in mono- and bilayers. OL is found to have a greater tendency than chain-analogous PEL to form ordered structures and, in contrast to PEL, even a molecular superlattice based on a hydrogen bonding network between the headgroups. This superlattice is virtually electrically uncharged and persists over a wide pH range. Our results indicate that OL and PEL behave very differently in ordered single-component membranes but may behave more similarly in fluid multicomponent membranes.
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Affiliation(s)
- Tetiana Mukhina
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstrase 8, 64289 Darmstadt, Germany.
| | - Georg Pabst
- Insitute of Molecular Biosciences, University of Graz, Universitätsplatz 3, 8010, Graz, Austria
| | - Jean-Marie Ruysschaert
- Laboratoire de Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Gerald Brezesinski
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstrase 8, 64289 Darmstadt, Germany.
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstrase 8, 64289 Darmstadt, Germany.
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4
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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5
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Maer AM, Rusinova R, Providence LL, Ingólfsson HI, Collingwood SA, Lundbæk JA, Andersen OS. Regulation of Gramicidin Channel Function Solely by Changes in Lipid Intrinsic Curvature. Front Physiol 2022; 13:836789. [PMID: 35350699 PMCID: PMC8957996 DOI: 10.3389/fphys.2022.836789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Membrane protein function is regulated by the lipid bilayer composition. In many cases the changes in function correlate with changes in the lipid intrinsic curvature (c 0), and c 0 is considered a determinant of protein function. Yet, water-soluble amphiphiles that cause either negative or positive changes in curvature have similar effects on membrane protein function, showing that changes in lipid bilayer properties other than c 0 are important-and may be dominant. To further investigate the mechanisms underlying the bilayer regulation of protein function, we examined how maneuvers that alter phospholipid head groups effective "size"-and thereby c 0-alter gramicidin (gA) channel function. Using dioleoylphospholipids and planar bilayers, we varied the head groups' physical volume and the electrostatic repulsion among head groups (and thus their effective size). When 1,2-dioleyol-sn-glycero-3-phosphocholine (DOPC), was replaced by 1,2-dioleyol-sn-glycero-3-phosphoethanolamine (DOPE) with a smaller head group (causing a more negative c 0), the channel lifetime (τ) is decreased. When the pH of the solution bathing a 1,2-dioleyol-sn-glycero-3-phosphoserine (DOPS) bilayer is decreased from 7 to 3 (causing decreased head group repulsion and a more negative c 0), τ is decreased. When some DOPS head groups are replaced by zwitterionic head groups, τ is similarly decreased. These effects do not depend on the sign of the change in surface charge. In DOPE:DOPC (3:1) bilayers, pH changes from 5→9 to 5→0 (both increasing head group electrostatic repulsion, thereby causing a less negative c 0) both increase τ. Nor do the effects depend on the use of planar, hydrocarbon-containing bilayers, as similar changes were observed in hydrocarbon-free lipid vesicles. Altering the interactions among phospholipid head groups may alter also other bilayer properties such as thickness or elastic moduli. Such changes could be excluded using capacitance measurements and single channel measurements on gA channels of different lengths. We conclude that changes gA channel function caused by changes in head group effective size can be predicted from the expected changes in c 0.
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Affiliation(s)
| | | | | | | | | | | | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
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6
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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7
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Aragón-Muriel A, Liscano Y, Morales-Morales D, Polo-Cerón D, Oñate-Garzón J. A Study of the Interaction of a New Benzimidazole Schiff Base with Synthetic and Simulated Membrane Models of Bacterial and Mammalian Membranes. MEMBRANES 2021; 11:membranes11060449. [PMID: 34208443 PMCID: PMC8235182 DOI: 10.3390/membranes11060449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022]
Abstract
Biological membranes are complex dynamic systems composed of a great variety of carbohydrates, lipids, and proteins, which together play a pivotal role in the protection of organisms and through which the interchange of different substances is regulated in the cell. Given the complexity of membranes, models mimicking them provide a convenient way to study and better understand their mechanisms of action and their interactions with biologically active compounds. Thus, in the present study, a new Schiff base (Bz-Im) derivative from 2-(m-aminophenyl)benzimidazole and 2,4-dihydroxybenzaldehyde was synthesized and characterized by spectroscopic and spectrometric techniques. Interaction studies of (Bz-Im) with two synthetic membrane models prepared with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and DMPC/1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) 3:1 mixture, imitating eukaryotic and prokaryotic membranes, respectively, were performed by applying differential scanning calorimetry (DSC). Molecular dynamics simulations were also developed to better understand their interactions. In vitro and in silico assays provided approaches to understand the effect of Bz-Im on these lipid systems. The DSC results showed that, at low compound concentrations, the effects were similar in both membrane models. By increasing the concentration of Bz-Im, the DMPC/DMPG membrane exhibited greater fluidity as a result of the interaction with Bz-Im. On the other hand, molecular dynamics studies carried out on the erythrocyte membrane model using the phospholipids POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), SM (N-(15Z-tetracosenoyl)-sphing-4-enine-1-phosphocholine), and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) revealed that after 30 ns of interaction, both hydrophobic interactions and hydrogen bonds were responsible for the affinity of Bz-Im for PE and SM. The interactions of the imine with POPG (1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphoglycerol) in the E. coli membrane model were mainly based on hydrophobic interactions.
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Affiliation(s)
- Alberto Aragón-Muriel
- Laboratorio de Investigación en Catálisis y Procesos (LICAP), Departamento de Química, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali 760031, Colombia;
| | - Yamil Liscano
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760035, Colombia;
| | - David Morales-Morales
- Instituto de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Circuito Exterior, Coyoacán, Mexico D.F. 04510, Mexico;
| | - Dorian Polo-Cerón
- Laboratorio de Investigación en Catálisis y Procesos (LICAP), Departamento de Química, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali 760031, Colombia;
- Correspondence: (D.P.-C.); (J.O.-G.)
| | - Jose Oñate-Garzón
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760035, Colombia;
- Correspondence: (D.P.-C.); (J.O.-G.)
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8
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Lee AG. Interfacial binding sites for cholesterol on GABA A receptors and competition with neurosteroids. Biophys J 2021; 120:2710-2722. [PMID: 34022235 DOI: 10.1016/j.bpj.2021.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/06/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors in the brain are located in the outer membranes of brain cells where the concentration of cholesterol is high. Of the 25 available high-resolution structures available for GABAA receptors, none were determined in the presence of cholesterol, but four include resolved molecules of cholesterol hemisuccinate (CHS). Here, a molecular docking procedure is used to sweep the transmembrane (TM) surfaces of the receptors for cholesterol binding sites. Cholesterol docking poses determined in this way match 89% of the resolved CHS when CHS molecules deemed unlikely to represent typical bound cholesterols are excluded. The receptors are pentameric, and their TM surfaces consist of a set of five facets, each including pairs of TM helices from two adjacent subunits. Each facet contains hydrophobic hollows running from one side of the membrane to the other, within which are six potential binding sites for cholesterol, three on each side of the membrane. High-resolution structures of GABAA receptors with bound neurosteroids show that neurosteroids bind in these cholesterol binding sites, so the binding of neurosteroids and cholesterol will be competitive.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom.
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9
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Corin K, Bowie JU. How bilayer properties influence membrane protein folding. Protein Sci 2020; 29:2348-2362. [PMID: 33058341 DOI: 10.1002/pro.3973] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/24/2023]
Abstract
The question of how proteins manage to organize into a unique three-dimensional structure has been a major field of study since the first protein structures were determined. For membrane proteins, the question is made more complex because, unlike water-soluble proteins, the solvent is not homogenous or even unique. Each cell and organelle has a distinct lipid composition that can change in response to environmental stimuli. Thus, the study of membrane protein folding requires not only understanding how the unfolded chain navigates its way to the folded state, but also how changes in bilayer properties can affect that search. Here we review what we know so far about the impact of lipid composition on bilayer physical properties and how those properties can affect folding. A better understanding of the lipid bilayer and its effects on membrane protein folding is not only important for a theoretical understanding of the folding process, but can also have a practical impact on our ability to work with and design membrane proteins.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
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10
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Membrane Protein Production in Lactococcus lactis for Structural Studies. Methods Mol Biol 2020. [PMID: 32112313 DOI: 10.1007/978-1-0716-0373-4_3] [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 expression and downstream purification of membrane proteins is the prerequisite for biophysical and structural studies of this major source of therapeutic targets. The gram-positive bacterium Lactococcus lactis is an attractive option for heterologous membrane protein expression and purification thanks to advantageous characteristics such as mild proteolytic activity and small genome size. Vectors designed for gene transcription under the control of inducible promoters are readily available. Specifically, the tightly regulated nisin-inducible gene expression system (NICE) allows to fine-tune the overexpression of different gene products. The expressed protein engineered with a suitable tag can be readily detected and purified from crude membrane extracts. The purpose of this protocol chapter is to detail the procedures of cloning, expression, isolation of the membrane vesicles, and affinity purification of a membrane protein of interest in L. lactis.
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11
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Varandas PAMM, Cobb AJA, Segundo MA, Silva EMP. Emergent Glycerophospholipid Fluorescent Probes: Synthesis and Applications. Bioconjug Chem 2019; 31:417-435. [DOI: 10.1021/acs.bioconjchem.9b00660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pedro A. M. M. Varandas
- LAQV, REQUIMTE, Department of Chemistry Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Alexander J. A. Cobb
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Marcela A. Segundo
- LAQV, REQUIMTE, Department of Chemistry Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Eduarda M. P. Silva
- LAQV, REQUIMTE, Department of Chemistry Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
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12
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Siemers M, Lazaratos M, Karathanou K, Guerra F, Brown LS, Bondar AN. Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins. J Chem Theory Comput 2019; 15:6781-6798. [DOI: 10.1021/acs.jctc.9b00697] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Federico Guerra
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S. Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
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13
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A New Method of Assessing Lipid Mixtures by 31P Magic-Angle Spinning NMR. Biophys J 2019; 114:1368-1376. [PMID: 29590594 DOI: 10.1016/j.bpj.2018.01.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022] Open
Abstract
A variety of lipids that differ by their chains and headgroups are found in biomembranes. In addition to studying the overall membrane phase, determination of the structure, dynamics, and headgroup conformation of individual lipids in the mixture would be of great interest. We have thus developed, to our knowledge, a new approach using solid-state 31P NMR, magic-angle spinning, and chemical-shift anisotropy (CSA) recoupling, using an altered version of the recoupling of chemical shift anisotropy (ROCSA) pulse sequence, here penned PROCSA. The resulting two-dimensional spectra allowed the simultaneous measurement of the isotropic chemical shift and CSA of each lipid headgroup, thus providing a valuable measure of its dynamics and structure. PROCSA was applied to mixtures of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) in various relative proportions, to mimic bacterial membranes and assess the respective roles of lipids in shaping these bilayers. The results were interpreted in terms of membrane topology, lipid propensity to adopt various phases or conformations, and lipid-lipid miscibility. Our results showed that PG dictates the lipid behavior when present in a proportion of 20 mol % or more. A small proportion of PG is thus able to impose a bilayer structure to the hexagonal phase forming PE. We discuss the requirement for lipids, such as PE, to be able to adopt non-bilayer phases in a membrane.
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14
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Immadisetty K, Hettige J, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. ACS CENTRAL SCIENCE 2019; 5:43-56. [PMID: 30693324 PMCID: PMC6346382 DOI: 10.1021/acscentsci.8b00480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 06/09/2023]
Abstract
By undergoing conformational changes, active membrane transporters alternate between an inward-facing (IF) and an outward-facing (OF) state to transport their substrates across cellular membrane. The conformational landscape of membrane transporters, however, could be influenced by their environment, and the dependence of the alternating access mechanism on the lipid composition has not been understood at the molecular level. We have performed an extensive set of microsecond-level all-atom molecular dynamics (MD) simulations on bacterial ATP binding cassette (ABC) exporter Sav1866 in six different phosphocholine (PC) and phosphoethanolamine (PE) lipid membrane environments. This study mainly focuses on the energetically downhill OF-to-IF conformational transition of Sav1866 upon the ATP hydrolysis. We observe that the transporter undergoes large-scale conformational changes in the PE environment, particularly in the POPE lipids, resulting in an IF-occluded conformation, a transition that does not occur when the transporter is embedded in any of the PC lipid bilayers. We propose that the PE lipids facilitate the closing of the protein on the periplasmic side due to their highly polar headgroups that mediate the interaction of the two transmembrane (TM) bundles by a network of lipid-lipid and lipid-protein hydrogen bonds. POPE lipids in particular facilitate the closure of periplasmic gate by promoting a hinge formation in TM helices and an interbundle salt bridge formation. This study explains how the alternating access mechanism and the flippase activity in ABC exporters could be lipid-dependent.
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15
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Direct protein-lipid interactions shape the conformational landscape of secondary transporters. Nat Commun 2018; 9:4151. [PMID: 30297844 PMCID: PMC6175955 DOI: 10.1038/s41467-018-06704-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/19/2018] [Indexed: 12/31/2022] Open
Abstract
Secondary transporters undergo structural rearrangements to catalyze substrate translocation across the cell membrane – yet how such conformational changes happen within a lipid environment remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS) with molecular dynamics (MD) simulations to understand how lipids regulate the conformational dynamics of secondary transporters at the molecular level. Using the homologous transporters XylE, LacY and GlpT from Escherichia coli as model systems, we discover that conserved networks of charged residues act as molecular switches that drive the conformational transition between different states. We reveal that these molecular switches are regulated by interactions with surrounding phospholipids and show that phosphatidylethanolamine interferes with the formation of the conserved networks and favors an inward-facing state. Overall, this work provides insights into the importance of lipids in shaping the conformational landscape of an important class of transporters. Secondary transporters catalyse substrate translocation across the cell membrane but the role of lipids during the transport cycle remains unclear. Here authors used hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations to understand how lipids regulate the conformational dynamics of secondary transporters.
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16
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Roth A, Govaerts C. LmrP from Lactoccoccus lactis: a tractable model to understand secondary multidrug transport in MFS. Res Microbiol 2018; 169:468-477. [PMID: 30145366 DOI: 10.1016/j.resmic.2018.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
The secondary transporter LmrP from Lactoccoccus lactis is a remarkable model to study the molecular basis of secondary multidrug transport. This review article addresses more than twenty years of research about transport activity, substrates range, conformational dynamics and mechanistic models of drug export for LmrP. Several studies have shown that the transporter alternates between inward-open and outward-open conformations and that the transition is regulated by the protonation state of key acidic residues and is further modulated by the lipid environment.
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Affiliation(s)
- Aurélie Roth
- SFMB, Université Libre de Bruxelles (ULB) CP206/02, Boulevard du Triomphe, Building BC, B-1050 Brussels, Belgium
| | - Cedric Govaerts
- SFMB, Université Libre de Bruxelles (ULB) CP206/02, Boulevard du Triomphe, Building BC, B-1050 Brussels, Belgium.
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17
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Abstract
Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways. Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways.
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18
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Borrell JH, Domènech Ò. Critical Temperature of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine Monolayers and Its Possible Biological Relevance. J Phys Chem B 2017. [PMID: 28636818 DOI: 10.1021/acs.jpcb.7b04021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because transmembrane proteins (TMPs) can be obtained with sufficient purity for X-ray diffraction studies more frequently than decades ago, their mechanisms of action may now be elucidated. One of the pending issues is the actual interplay between transmembrane proteins and membrane lipids. There is strong evidence of the involvement of specific lipids with some membrane proteins, such as the potassium crystallographically sited activation channel (KcsA) of Streptomyces lividans and the secondary transporter of lactose LacY of Escherichia coli, the activities of which are associated with the presence of anionic phospholipids such as the phosphatidylglycerol (PG) and phosphatidyethanolamine (PE), respectively. Other proteins such as the large conductance mechanosensitive channel (MscL) of E. coli seem to depend on the adaptation of specific phospholipids to the irregular surface of the integral membrane protein. In this work we investigated the lateral compressibility of two homoacid phosphatidylethanolamines (one with both acyl chains unsaturated (DOPE), the other with the acyl chains saturated (DPPE)) and the heteroacid phosphatidyletanolamine (POPE) and their mixtures with POPG. The liquid expanded (LE) to liquid condensed (LC) transition was observed in POPE at a temperature below its critical temperature (Tc = 36 °C). Because Tc lies below the physiological temperature, the occurrence of this phase transition may have something to do with the functioning of LacY. This magnitude is discussed within the context of the experiments carried out at temperatures below the Tc of POPE at which the activity of Lac Y and other TMPs are frequently studied.
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Affiliation(s)
- Jordi H Borrell
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences and ‡Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB) , E-08028 Barcelona, Spain
| | - Òscar Domènech
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences and ‡Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB) , E-08028 Barcelona, Spain
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19
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Gao W, Liu Y, Jing G, Li K, Zhao Y, Sha B, Wang Q, Wu D. Rapid and efficient crossing blood-brain barrier: Hydrophobic drug delivery system based on propionylated amylose helix nanoclusters. Biomaterials 2017; 113:133-144. [DOI: 10.1016/j.biomaterials.2016.10.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
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20
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Lipids modulate the conformational dynamics of a secondary multidrug transporter. Nat Struct Mol Biol 2016; 23:744-51. [PMID: 27399258 DOI: 10.1038/nsmb.3262] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/16/2016] [Indexed: 02/06/2023]
Abstract
Direct interactions with lipids have emerged as key determinants of the folding, structure and function of membrane proteins, but an understanding of how lipids modulate protein dynamics is still lacking. Here, we systematically explored the effects of lipids on the conformational dynamics of the proton-powered multidrug transporter LmrP from Lactococcus lactis, using the pattern of distances between spin-label pairs previously shown to report on alternating access of the protein. We uncovered, at the molecular level, how the lipid headgroups shape the conformational-energy landscape of the transporter. The model emerging from our data suggests a direct interaction between lipid headgroups and a conserved motif of charged residues that control the conformational equilibrium through an interplay of electrostatic interactions within the protein. Together, our data lay the foundation for a comprehensive model of secondary multidrug transport in lipid bilayers.
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21
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Hresko RC, Kraft TE, Quigley A, Carpenter EP, Hruz PW. Mammalian Glucose Transporter Activity Is Dependent upon Anionic and Conical Phospholipids. J Biol Chem 2016; 291:17271-82. [PMID: 27302065 PMCID: PMC5016126 DOI: 10.1074/jbc.m116.730168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 01/05/2023] Open
Abstract
The regulated movement of glucose across mammalian cell membranes is mediated by facilitative glucose transporters (GLUTs) embedded in lipid bilayers. Despite the known importance of phospholipids in regulating protein structure and activity, the lipid-induced effects on the GLUTs remain poorly understood. We systematically examined the effects of physiologically relevant phospholipids on glucose transport in liposomes containing purified GLUT4 and GLUT3. The anionic phospholipids, phosphatidic acid, phosphatidylserine, phosphatidylglycerol, and phosphatidylinositol, were found to be essential for transporter function by activating it and stabilizing its structure. Conical lipids, phosphatidylethanolamine and diacylglycerol, enhanced transporter activity up to 3-fold in the presence of anionic phospholipids but did not stabilize protein structure. Kinetic analyses revealed that both lipids increase the kcat of transport without changing the Km values. These results allowed us to elucidate the activation of GLUT by plasma membrane phospholipids and to extend the field of membrane protein-lipid interactions to the family of structurally and functionally related human solute carriers.
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Affiliation(s)
| | | | - Andrew Quigley
- the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Elisabeth P Carpenter
- the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Paul W Hruz
- From the Departments of Pediatrics and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110 and
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22
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Zhang XC, Zhao Y, Heng J, Jiang D. Energy coupling mechanisms of MFS transporters. Protein Sci 2015; 24:1560-79. [PMID: 26234418 DOI: 10.1002/pro.2759] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 01/01/2023]
Abstract
Major facilitator superfamily (MFS) is a large class of secondary active transporters widely expressed across all life kingdoms. Although a common 12-transmembrane helix-bundle architecture is found in most MFS crystal structures available, a common mechanism of energy coupling remains to be elucidated. Here, we discuss several models for energy-coupling in the transport process of the transporters, largely based on currently available structures and the results of their biochemical analyses. Special attention is paid to the interaction between protonation and the negative-inside membrane potential. Also, functional roles of the conserved sequence motifs are discussed in the context of the 3D structures. We anticipate that in the near future, a unified picture of the functions of MFS transporters will emerge from the insights gained from studies of the common architectures and conserved motifs.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Jie Heng
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Daohua Jiang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
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23
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Paran CW, Zou K, Ferrara PJ, Song H, Turk J, Funai K. Lipogenesis mitigates dysregulated sarcoplasmic reticulum calcium uptake in muscular dystrophy. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1530-8. [PMID: 26361872 DOI: 10.1016/j.bbalip.2015.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/27/2015] [Accepted: 09/06/2015] [Indexed: 01/07/2023]
Abstract
Muscular dystrophy is accompanied by a reduction in activity of sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) that contributes to abnormal Ca(2+) homeostasis in sarco/endoplasmic reticulum (SR/ER). Recent findings suggest that skeletal muscle fatty acid synthase (FAS) modulates SERCA activity and muscle function via its effects on SR membrane phospholipids. In this study, we examined muscle's lipid metabolism in mdx mice, a mouse model for Duchenne muscular dystrophy (DMD). De novo lipogenesis was ~50% reduced in mdx muscles compared to wildtype (WT) muscles. Gene expressions of lipogenic and other ER lipid-modifying enzymes were found to be differentially expressed between wildtype (WT) and mdx muscles. A comprehensive examination of muscles' SR phospholipidome revealed elevated phosphatidylcholine (PC) and PC/phosphatidylethanolamine (PE) ratio in mdx compared to WT mice. Studies in primary myocytes suggested that defects in key lipogenic enzymes including FAS, stearoyl-CoA desaturase-1 (SCD1), and Lipin1 are likely contributing to reduced SERCA activity in mdx mice. Triple transgenic expression of FAS, SCD1, and Lipin1 (3TG) in mdx myocytes partly rescued SERCA activity, which coincided with an increase in SR PE that normalized PC/PE ratio. These findings implicate a defect in lipogenesis to be a contributing factor for SERCA dysfunction in muscular dystrophy. Restoration of muscle's lipogenic pathway appears to mitigate SERCA function through its effects on SR membrane composition.
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Affiliation(s)
- Christopher W Paran
- Department of Kinesiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; Department of Physiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA
| | - Kai Zou
- Department of Kinesiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA
| | - Patrick J Ferrara
- Department of Kinesiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA
| | - Haowei Song
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA
| | - John Turk
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA
| | - Katsuhiko Funai
- Department of Kinesiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; Department of Physiology, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA; East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, North Carolina 27834, USA.
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24
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Borrell JH, Montero MT, Morros A, Domènech Ò. Unspecific membrane protein-lipid recognition: combination of AFM imaging, force spectroscopy, DSC and FRET measurements. J Mol Recognit 2015; 28:679-86. [DOI: 10.1002/jmr.2483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/31/2015] [Accepted: 04/19/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Jordi H. Borrell
- Departament de Fisicoquímica; Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia IN UB; Barcelona Catalonia 08028 Spain
| | - M. Teresa Montero
- Departament de Fisicoquímica; Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia IN UB; Barcelona Catalonia 08028 Spain
| | - Antoni Morros
- Unitat de Biofísica; Departament de Bioquímica i Biología Molecular, Facultat de Medicina UAB; Bellaterra (Barcelona) 08193 Spain
| | - Òscar Domènech
- Departament de Fisicoquímica; Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia IN UB; Barcelona Catalonia 08028 Spain
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25
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McIlwain BC, Vandenberg RJ, Ryan RM. Transport rates of a glutamate transporter homologue are influenced by the lipid bilayer. J Biol Chem 2015; 290:9780-8. [PMID: 25713135 DOI: 10.1074/jbc.m114.630590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/06/2022] Open
Abstract
The aspartate transporter from Pyrococcus horikoshii (GltPh) is a model for the structure of the SLC1 family of amino acid transporters. Crystal structures of GltPh provide insight into mechanisms of ion coupling and substrate transport; however, structures have been solved in the absence of a lipid bilayer so they provide limited information regarding interactions that occur between the protein and lipids of the membrane. Here, we investigated the effect of the lipid environment on aspartate transport by reconstituting GltPh into liposomes of defined lipid composition where the primary lipid is phosphatidylethanolamine (PE) or its methyl derivatives. We showed that the rate of aspartate transport and the transmembrane orientation of GltPh were influenced by the primary lipid in the liposomes. In PE liposomes, we observed the highest transport rate and showed that 85% of the transporters were orientated right-side out, whereas in trimethyl PE liposomes, 50% of transporters were right-side out, and we observed a 4-fold reduction in transport rate. Differences in orientation can only partially explain the lipid composition effect on transport rate. Crystal structures of GltPh revealed a tyrosine residue (Tyr-33) that we propose interacts with lipid headgroups during the transport cycle. Based on site-directed mutagenesis, we propose that a cation-π interaction between Tyr-33 and the lipid headgroups can influence conformational flexibility of the trimerization domain and thus the rate of transport. These results provide a specific example of how interactions between membrane lipids and membrane-bound proteins can influence function and highlight the importance of the role of the membrane in transporter function.
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Affiliation(s)
- Benjamin C McIlwain
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Robert J Vandenberg
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Renae M Ryan
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
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26
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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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27
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Suárez-Germà C, Hernández-Borrell J, Prieto M, Loura LMS. Modeling FRET to investigate the selectivity of lactose permease ofEscherichia colifor lipids. Mol Membr Biol 2014; 31:120-30. [DOI: 10.3109/09687688.2014.915351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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van der Post ST, Hunger J, Bonn M, Bakker HJ. Observation of Water Separated Ion-Pairs between Cations and Phospholipid Headgroups. J Phys Chem B 2014; 118:4397-403. [DOI: 10.1021/jp411458z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Johannes Hunger
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Huib J. Bakker
- FOM Institute AMOLF, Science
Park 104, Amsterdam, The Netherlands
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29
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Masureel M, Martens C, Stein RA, Mishra S, Ruysschaert JM, Mchaourab HS, Govaerts C. Protonation drives the conformational switch in the multidrug transporter LmrP. Nat Chem Biol 2014; 10:149-55. [PMID: 24316739 PMCID: PMC4749020 DOI: 10.1038/nchembio.1408] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/18/2013] [Indexed: 02/07/2023]
Abstract
Multidrug antiporters of the major facilitator superfamily couple proton translocation to the extrusion of cytotoxic molecules. The conformational changes that underlie the transport cycle and the structural basis of coupling of these transporters have not been elucidated. Here we used extensive double electron-electron resonance measurements to uncover the conformational equilibrium of LmrP, a multidrug transporter from Lactococcus lactis, and to investigate how protons and ligands shift this equilibrium to enable transport. We find that the transporter switches between outward-open and outward-closed conformations, depending on the protonation states of specific acidic residues forming a transmembrane protonation relay. Our data can be framed in a model of transport wherein substrate binding initiates the transport cycle by opening the extracellular side. Subsequent protonation of membrane-embedded acidic residues induces substrate release to the extracellular side and triggers a cascade of conformational changes that concludes in proton release to the intracellular side.
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Affiliation(s)
- Matthieu Masureel
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
| | - Chloé Martens
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean-Marie Ruysschaert
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Hassane S Mchaourab
- 1] Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2]
| | - Cédric Govaerts
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
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30
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Steed PR, Zou P, Trone KE, Mchaourab HS. Structure and pH-induced structural rearrangements of the putative multidrug efflux pump EmrD in liposomes probed by site-directed spin labeling. Biochemistry 2013; 52:7964-74. [PMID: 24148002 DOI: 10.1021/bi4012385] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
EmrD is the only structurally characterized drug/H(+) antiporter of the major facilitator superfamily (MFS). It has been crystallized in a doubly occluded conformation that is considered representative of an intermediate state in the transport cycle of MFS transporters. However, unexpected features of the crystal structure and the lack of functional information available for EmrD limit the utility of the structural data. To assess whether the crystal structure represents a stable state in a native-like environment, we used electron paramagnetic resonance (EPR) spectroscopy to determine the mobility and accessibility of spin labels at 76 positions in six transmembrane (TM) helices of EmrD reconstituted in liposomes. While the EPR data were mostly consistent with the crystal structure, they also revealed significant deviations from the predicted orientation and topology of TM helices at several locations. Additionally, we were unable to reproduce EmrD-dependent multidrug resistance phenotypes in vitro and in cell-based assays of drug transport. In spite of structural and functional discrepancies, we mapped a pH-dependent conformational change in which the cytoplasmic side of the N-terminal half opened locally in response to protonation. This conformational switch is consistent with the expected pH-dependent behavior of MFS H(+)-coupled antiporters.
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Affiliation(s)
- P Ryan Steed
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | - Ping Zou
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | - Kristin E Trone
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
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31
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Influence of lipids on protein-mediated transmembrane transport. Chem Phys Lipids 2013; 169:57-71. [PMID: 23473882 DOI: 10.1016/j.chemphyslip.2013.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins are responsible for transporting ions and small molecules across the hydrophobic region of the cell membrane. We are reviewing the evidence for regulation of these transport processes by interactions with the lipids of the membrane. We focus on ion channels, including potassium channels, mechanosensitive and pentameric ligand gated ion channels, and active transporters, including pumps, sodium or proton driven secondary transporters and ABC transporters. For ion channels it has been convincingly shown that specific lipid-protein interactions can directly affect their function. In some cases, a combined approach of molecular and structural biology together with computer simulations has revealed the molecular mechanisms. There are also many transporters whose activity depends on lipids but understanding of the molecular mechanisms is only beginning.
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32
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Vitrac H, Bogdanov M, Dowhan W. Proper fatty acid composition rather than an ionizable lipid amine is required for full transport function of lactose permease from Escherichia coli. J Biol Chem 2013; 288:5873-85. [PMID: 23322771 DOI: 10.1074/jbc.m112.442988] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Energy-dependent uphill transport but not energy-independent downhill transport by lactose permease (LacY) is impaired when expressed in Escherichia coli cells or reconstituted in liposomes lacking phosphatidylethanolamine (PE) and containing only anionic phospholipids. The absence of PE results in inversion of the N-terminal half and misfolding of periplasmic domain P7, which are required for uphill transport of substrates. Replacement of PE in vitro by lipids with no net charge (phosphatidylcholine (PC), monoglucosyl diacylglycerol (GlcDAG), or diglucosyl diacylglycerol (GlcGlcDAG)) supported wild type transmembrane topology of the N-terminal half of LacY. The restoration of uphill transport in vitro was dependent on LacY native topology and proper folding of P7. Support of uphill transport by net neutral lipids in vitro (PE > PC ≫ GlcDAG ≠ GlcGlcDAG provided that PE or PC contained one saturated fatty acid) paralleled the results observed previously in vivo (PE = PC > GlcDAG ≠ GlcGlcDAG). Therefore, a free amino group is not required for uphill transport as previously concluded based on the lack of in vitro uphill transport when fully unsaturated PC replaced E. coli-derived PE. A close correlation was observed in vivo and in vitro between the ability of LacY to carry out uphill transport, the native conformation of P7, and the lipid headgroup and fatty acid composition. Therefore, the headgroup and the fatty acid composition of lipids are important for defining LacY topological organization and catalytically important structural features, further illustrating the direct role of lipids, independent of other cellular factors, in defining membrane protein structure/function.
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Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, USA
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33
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Suárez-Germà C, Loura LMS, Domènech O, Montero MT, Vázquez-Ibar JL, Hernández-Borrell J. Phosphatidylethanolamine-lactose permease interaction: a comparative study based on FRET. J Phys Chem B 2012; 116:14023-8. [PMID: 23137163 DOI: 10.1021/jp309726v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work we have investigated the selectivity of lactose permease (LacY) of Escherichia coli (E. coli) for its surrounding phospholipids when reconstituted in binary mixtures of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), 1,2-Palmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), or 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) with 1-palmitoyl-2-oleoyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (POPG). Förster resonance energy transfer (FRET) measurements have been performed to investigate the selectivity between a single tryptophan mutant of LacY used as donor (D), and two analogues of POPE and POPG labeled with pyrene in the acyl chains (Pyr-PE and Pyr-PG) used as acceptors. As a difference from previous works, now the donor has been single-W151/C154G/D68C LacY. It has been reported that the replacement of the aspartic acid in position 68 by cysteine inhibits active transport in LacY. The objectives of this work were to elucidate the phospholipid composition of the annular region of this mutant and to determine whether the mutation performed, D68C, induced changes in the protein-lipid selectivity. FRET efficiencies for Pyr-PE were always higher than for Pyr-PG. The values of the probability of each site in the annular ring being occupied by a label (μ) were similar at the studied temperatures (24 °C and 37 °C), suggesting that the lipid environment is not significantly affected when increasing the temperature. By comparing the results with those obtained for single-W151/C154G LacY, we observe that the mutation in the 68 residue indeed changes the selectivity of the protein for the phospholipids. This might be probably due to a change in the conformational dynamics of LacY.
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Affiliation(s)
- Carme Suárez-Germà
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Spain
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34
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Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J 2012; 103:1698-705. [PMID: 23083713 DOI: 10.1016/j.bpj.2012.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022] Open
Abstract
Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability.
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35
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Wang W, van Veen HW. Basic residues R260 and K357 affect the conformational dynamics of the major facilitator superfamily multidrug transporter LmrP. PLoS One 2012; 7:e38715. [PMID: 22761697 PMCID: PMC3380022 DOI: 10.1371/journal.pone.0038715] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/11/2012] [Indexed: 11/19/2022] Open
Abstract
Secondary-active multidrug transporters can confer resistance on cells to pharmaceuticals by mediating their extrusion away from intracellular targets via substrate/H(+)(Na(+)) antiport. While the interactions of catalytic carboxylates in these transporters with coupling ions and substrates (drugs) have been studied in some detail, the functional importance of basic residues has received much less attention. The only two basic residues R260 and K357 in transmembrane helices in the Major Facilitator Superfamily transporter LmrP from Lactococcus lactis are present on the outer surface of the protein, where they are exposed to the phospholipid head group region of the outer leaflet (R260) and inner leaflet (K357) of the cytoplasmic membrane. Although our observations on the proton-motive force dependence and kinetics of substrate transport, and substrate-dependent proton transport demonstrate that K357A and R260A mutants are affected in ethidium-proton and benzalkonium-proton antiport compared to wildtype LmrP, our findings suggest that R260 and K357 are not directly involved in the binding of substrates or the translocation of protons. Secondary-active multidrug transporters are thought to operate by a mechanism in which binding sites for substrates are alternately exposed to each face of the membrane. Disulfide crosslinking experiments were performed with a double cysteine mutant of LmrP that reports the substrate-stimulated transition from the outward-facing state to the inward-facing state with high substrate-binding affinity. In the experiments, the R260A and K357A mutations were found to influence the dynamics of these major protein conformations in the transport cycle, potentially by removing the interactions of R260 and K357 with phospholipids and/or other residues in LmrP. The R260A and K357A mutations therefore modify the maximum rate at which the transport cycle can operate and, as the transitions between conformational states are differently affected by components of the proton-motive force, the mutations also influence the energetics of transport.
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Affiliation(s)
- Wei Wang
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Hendrik W. van Veen
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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36
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Tajparast M, Glavinović M. Strain, stress and energy in lipid bilayer induced by electrostatic/electrokinetic forces. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:829-38. [DOI: 10.1016/j.bbamem.2011.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 09/14/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
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37
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Suárez-Germà C, Loura LMS, Prieto M, Domènech Ò, Montero MT, Rodríguez-Banqueri A, Vázquez-Ibar JL, Hernández-Borrell J. Membrane Protein–Lipid Selectivity: Enhancing Sensitivity for Modeling FRET Data. J Phys Chem B 2012; 116:2438-45. [DOI: 10.1021/jp2105665] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Luís M. S. Loura
- Faculdade de Farmácia, Universidade de Coimbra, Azinhaga de Santa Comba, 3000-548
Coimbra, Portugal and Centro de Química de Coimbra, 3004-535 Coimbra, Portugal
| | - Manuel Prieto
- Centro de Química-Física Molecular and IN, IST, 1049-001, Lisboa, Portugal
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38
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Bondar AN, White SH. Hydrogen bond dynamics in membrane protein function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:942-50. [PMID: 22178866 DOI: 10.1016/j.bbamem.2011.11.035] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 11/30/2022]
Abstract
Changes in inter-helical hydrogen bonding are associated with the conformational dynamics of membrane proteins. The function of the protein depends on the surrounding lipid membrane. Here we review through specific examples how dynamical hydrogen bonds can ensure an elegant and efficient mechanism of long-distance intra-protein and protein-lipid coupling, contributing to the stability of discrete protein conformational substates and to rapid propagation of structural perturbations. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195 Berlin, Germany.
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39
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Harris NJ, Booth PJ. Folding and stability of membrane transport proteins in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1055-66. [PMID: 22100867 DOI: 10.1016/j.bbamem.2011.11.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/26/2011] [Accepted: 11/03/2011] [Indexed: 10/15/2022]
Abstract
Transmembrane transporters are responsible for maintaining a correct internal cellular environment. The inherent flexibility of transporters together with their hydrophobic environment means that they are challenging to study in vitro, but recently significant progress been made. This review will focus on in vitro stability and folding studies of transmembrane alpha helical transporters, including reversible folding systems and thermal denaturation. The successful re-assembly of a small number of ATP binding cassette transporters is also described as this is a significant step forward in terms of understanding the folding and assembly of these more complex, multi-subunit proteins. The studies on transporters discussed here represent substantial advances for membrane protein studies as well as for research into protein folding. The work demonstrates that large flexible hydrophobic proteins are within reach of in vitro folding studies, thus holding promise for furthering knowledge on the structure, function and biogenesis of ubiquitous membrane transporter families. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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40
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Gustavsson M, Traaseth NJ, Veglia G. Activating and deactivating roles of lipid bilayers on the Ca(2+)-ATPase/phospholamban complex. Biochemistry 2011; 50:10367-74. [PMID: 21992175 DOI: 10.1021/bi200759y] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physicochemical properties of the lipid bilayer shape the structure and topology of membrane proteins and regulate their biological function. Here, we investigated the functional effects of various lipid bilayer compositions on the sarcoplasmic reticulum (SR) Ca(2+)-ATPase (SERCA) in the presence and absence of its endogenous regulator, phospholamban (PLN). In the cardiac muscle, SERCA hydrolyzes one ATP molecule to translocate two Ca(2+) ions into the SR membrane per enzymatic cycle. Unphosphorylated PLN reduces SERCA's affinity for Ca(2+) and affects the enzymatic turnover. We varied bilayer thickness, headgroup, and fluidity and found that both the maximal velocity (V(max)) of the enzyme and its apparent affinity for Ca(2+) (K(Ca)) are strongly affected. Our results show that (a) SERCA's V(max) has a biphasic dependence on bilayer thickness, reaching maximum activity with 22-carbon lipid chain length, (b) phosphatidylethanolamine (PE) and phosphatidylserine (PS) increase Ca(2+) affinity, and (c) monounsaturated lipids afford higher SERCA V(max) and Ca(2+) affinity than diunsaturated lipids. The presence of PLN removes the activating effect of PE and shifts SERCA's activity profile, with a maximal activity reached in bilayers with 20-carbon lipid chain length. Our results in synthetic lipid systems compare well with those carried out in native SR lipids. Importantly, we found that specific membrane compositions closely reproduce PLN effects (V(max) and K(Ca)) found in living cells, reconciling an ongoing controversy regarding the regulatory role of PLN on SERCA function. Taken with the physiological changes occurring in the SR membrane composition, these studies underscore a possible allosteric role of the lipid bilayers on the SERCA/PLN complex.
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Affiliation(s)
- Martin Gustavsson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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41
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Suárez-Germà C, Montero M, Ignés-Mullol J, Hernández-Borrell J, Domènech Ò. Acyl Chain Differences in Phosphatidylethanolamine Determine Domain Formation and LacY Distribution in Biomimetic Model Membranes. J Phys Chem B 2011; 115:12778-84. [DOI: 10.1021/jp206369k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Carme Suárez-Germà
- Department of Physical Chemistry, Faculty of Pharmacy, and ‡Faculty of Chemistry, IN2UB, University of Barcelona, E-08028-Barcelona, Spain
| | - M.Teresa Montero
- Department of Physical Chemistry, Faculty of Pharmacy, and ‡Faculty of Chemistry, IN2UB, University of Barcelona, E-08028-Barcelona, Spain
| | - Jordi Ignés-Mullol
- Department of Physical Chemistry, Faculty of Pharmacy, and ‡Faculty of Chemistry, IN2UB, University of Barcelona, E-08028-Barcelona, Spain
| | - Jordi Hernández-Borrell
- Department of Physical Chemistry, Faculty of Pharmacy, and ‡Faculty of Chemistry, IN2UB, University of Barcelona, E-08028-Barcelona, Spain
| | - Òscar Domènech
- Department of Physical Chemistry, Faculty of Pharmacy, and ‡Faculty of Chemistry, IN2UB, University of Barcelona, E-08028-Barcelona, Spain
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42
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Molecular genetic and biochemical approaches for defining lipid-dependent membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1097-107. [PMID: 21945882 DOI: 10.1016/j.bbamem.2011.09.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 08/30/2011] [Accepted: 09/12/2011] [Indexed: 12/12/2022]
Abstract
We provide an overview of lipid-dependent polytopic membrane protein folding and topogenesis. Lipid dependence of this process was determined by employing Escherichia coli cells in which specific lipids can be eliminated, substituted, tightly titrated or controlled temporally during membrane protein synthesis and assembly. The secondary transport protein lactose permease (LacY) was used to establish general principles underlying the molecular basis of lipid-dependent effects on protein domain folding, protein transmembrane domain (TM) orientation, and function. These principles were then extended to several other secondary transport proteins of E. coli. The methods used to follow proper conformational organization of protein domains and the topological organization of protein TMs in whole cells and membranes are described. The proper folding of an extramembrane domain of LacY that is crucial for energy dependent uphill transport function depends on specific lipids acting as non-protein molecular chaperones. Correct TM topogenesis is dependent on charge interactions between the cytoplasmic surface of membrane proteins and a proper balance of the membrane surface net charge defined by the lipid head groups. Short-range interactions between the nascent protein chain and the translocon are necessary but not sufficient for establishment of final topology. After release from the translocon short-range interactions between lipid head groups and the nascent protein chain, partitioning of protein hydrophobic domains into the membrane bilayer, and long-range interactions within the protein thermodynamically drive final membrane protein organization. Given the diversity of membrane lipid compositions throughout nature, it is tempting to speculate that during the course of evolution the physical and chemical properties of proteins and lipids have co-evolved in the context of the lipid environment of membrane systems in which both are mutually dependent on each other for functional organization of proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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43
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Lee AG. Biological membranes: the importance of molecular detail. Trends Biochem Sci 2011; 36:493-500. [PMID: 21855348 DOI: 10.1016/j.tibs.2011.06.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/21/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Are lipid interactions with membrane proteins best described in terms of the physical properties of the lipid bilayer or in terms of direct molecular interactions between particular lipid molecules and particular sites on a protein? A molecular interpretation is more challenging because it requires detailed knowledge of the 3D structure of a membrane protein, but recent studies have suggested that a molecular interpretation is necessary. Here, the idea is explored that lipid molecules modify the ways that transmembrane α-helices pack into bundles, by penetrating between the helices and by binding into clefts between the helices, and that these effects on helix packing will modulate the activity of a membrane protein.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton, SO17 1BJ, UK.
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44
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Soubias O, Teague WE, Hines KG, Mitchell DC, Gawrisch K. Contribution of membrane elastic energy to rhodopsin function. Biophys J 2010; 99:817-24. [PMID: 20682259 DOI: 10.1016/j.bpj.2010.04.068] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 04/16/2010] [Accepted: 04/23/2010] [Indexed: 11/16/2022] Open
Abstract
We considered the issue of whether shifts in the metarhodopsin I (MI)-metarhodopsin II (MII) equilibrium from lipid composition are fully explicable by differences in bilayer curvature elastic stress. A series of six lipids with known spontaneous radii of monolayer curvature and bending elastic moduli were added at increasing concentrations to the matrix lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the MI-MII equilibrium measured by flash photolysis followed by recording UV-vis spectra. The average area-per-lipid molecule and the membrane hydrophobic thickness were derived from measurements of the (2)H NMR order parameter profile of the palmitic acid chain in POPC. For the series of ethanolamines with different levels of headgroup methylation, shifts in the MI-MII equilibrium correlated with changes in membrane elastic properties as expressed by the product of spontaneous radius of monolayer curvature, bending elastic modulus, and lateral area per molecule. However, for the entire series of lipids, elastic energy explained the shifts only partially. Additional contributions correlated with the capability of the ethanolamine headgroups to engage in hydrogen bonding with the protein, independent of the state of ethanolamine methylation, with introduction of polyunsaturated sn-2 hydrocarbon chains, and with replacement of the palmitic acid sn-1 chains by oleic acid. The experiments point to the importance of interactions of rhodopsin with particular lipid species in the first layer of lipids surrounding the protein as well as to membrane elastic stress in the lipid-protein domain.
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Affiliation(s)
- Olivier Soubias
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
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45
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Lactose permease lipid selectivity using Förster resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1707-13. [DOI: 10.1016/j.bbamem.2010.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 05/09/2010] [Accepted: 05/12/2010] [Indexed: 11/23/2022]
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46
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Plasticity of lipid-protein interactions in the function and topogenesis of the membrane protein lactose permease from Escherichia coli. Proc Natl Acad Sci U S A 2010; 107:15057-62. [PMID: 20696931 DOI: 10.1073/pnas.1006286107] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphatidylcholine (PC) has been widely used in place of naturally occurring phosphatidylethanolamine (PE) in reconstitution of bacterial membrane proteins. However, PC does not support native structure or function for several reconstituted transport proteins. Lactose permease (LacY) of Escherichia coli, when reconstituted in E. coli phospholipids, exhibits energy-dependent uphill and energy-independent downhill transport function and proper conformation of periplasmic domain P7, which is tightly linked to uphill transport function. LacY expressed in cells lacking PE and containing only anionic phospholipids exhibits only downhill transport and lacks native P7 conformation. Reconstitution of LacY in the presence of E. coli-derived PE, but not dioleoyl-PC, results in uphill transport. We now show that LacY exhibits uphill transport and native conformation of P7 when expressed in a mutant of E. coli in which PC completely replaces PE even though the structure is not completely native. E. coli-derived PC and synthetic PC species containing at least one saturated fatty acid also support the native conformation of P7 dependent on the presence of anionic phospholipids. Our results demonstrate that the different effects of PE and PC species on LacY structure and function cannot be explained by differences in the direct interaction of the lipid head groups with specific amino acid residues alone but are due to more complex effects of the physical and chemical properties of the lipid environment on protein structure. This conclusion is supported by the effect of different lipids on the proper folding of domain P7, which indirectly influences uphill transport function.
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47
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Gustot A, Smriti, Ruysschaert JM, McHaourab H, Govaerts C. Lipid composition regulates the orientation of transmembrane helices in HorA, an ABC multidrug transporter. J Biol Chem 2010; 285:14144-51. [PMID: 20223819 DOI: 10.1074/jbc.m109.079673] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette (ABC) transporters constitute a large class of molecular pumps whose central role in chemotherapy resistance has highlighted their clinical relevance. We investigated whether the lipid composition of the membrane affects the function and structure of HorA, a bacterial ABC multidrug transporter. When the transporter was reconstituted in a bilayer where phosphatidylethanolamine (PE), the main lipid of the bacterial membrane, was replaced with phosphatidylcholine (PC), ATP hydrolysis and substrate transport became uncoupled. Although ATPase activity was maintained, HorA lost its ability to extrude the prototypical substrate Hoechst33342. Attenuated Total Reflection-Fourier Transform Infrared spectroscopy (ATR-FTIR) revealed that, although the secondary structure of the protein was unaffected, the orientation of the transmembrane helices (TM) was modified by the change in lipid composition. The orientation of the backbone carbonyls indicated that the helices opened wider in PE versus PC-containing liposomes, with 10 degrees difference. This was supported by hydrogen/deuterium exchange studies showing increased protection of the backbone from the solvent in PC-containing liposomes. Electron Paramagnetic Resonance was used to further probe the structural change. In the PC-containing liposomes we observed increased mobility of the spin label in TM4, along with increased exposure to molecular oxygen, used as a hydrophobic quencher. This indicates that the lipid change induced modification of the orientation of TM4, exposing Cys-180 to the lipid phase. The lipid composition of the bilayer thus modulates the structure of HorA, and in turn its ability to extrude its substrates.
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Affiliation(s)
- Adelin Gustot
- Department of Structure and Function of Biological Membranes, Structural Biology and Bioinformatics Center, Université Libre de Bruxelles, CP206/2, Boulevard du Triomphe, 1050 Brussels, Belgium
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48
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Dielectric relaxation dynamics of water in model membranes probed by terahertz spectroscopy. Biophys J 2010; 97:2484-92. [PMID: 19883591 DOI: 10.1016/j.bpj.2009.08.024] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/10/2009] [Accepted: 08/17/2009] [Indexed: 11/22/2022] Open
Abstract
We study hydrated model membranes, consisting of stacked bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids, using terahertz time-domain spectroscopy and infrared spectroscopy. Terahertz spectroscopy enables the investigation of water dynamics, owing to its sensitivity to dielectric relaxation processes associated with water reorientation. By controlling the number of water molecules per lipid molecule in the system, we elucidate how the interplay between the model membrane and water molecules results in different water dynamics. For decreasing hydration levels, we observe the appearance of new types of water dynamics: the collective bulklike dynamics become less pronounced, whereas an increased amount of both very slowly reorienting (i.e., irrotational) and very rapidly reorienting (i.e., fast) water molecules appear. Temperature-dependent measurements reveal the interconversion between the three distinct types of water present in the system.
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49
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Seeger HM, Bortolotti CA, Alessandrini A, Facci P. Phase-transition-induced protein redistribution in lipid bilayers. J Phys Chem B 2010; 113:16654-9. [PMID: 19928819 DOI: 10.1021/jp907505m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report an atomic force microscopy study on the lateral spatial redistribution of an integral membrane protein reconstituted in supported lipid bilayers (SLBs) subjected to a thermally induced phase transition. KcsA proteins were reconstituted in proteoliposomes of POPE/POPG (3:1, mol/mol), and SLBs, including the proteins, were then obtained by the vesicle fusion technique on mica. By decreasing the temperature, the lipid bilayer passed from a liquid disordered (l(d)) phase in which the proteins are homogeneously distributed to a coexistence of solid ordered (s(o)) and l(d) domains with the proteins preferentially distributed in the l(d) domains. The inhomogeneous distribution eventually led to protein clustering. The obtained results are discussed in light of the role that the lipid/protein interaction can have in determining the function of integral membrane proteins.
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Affiliation(s)
- Heiko M Seeger
- CNR-INFM-S3 National Center on nanoStructures and bioSystems at Surfaces, Via Campi 213/A, 41125 Modena, Italy
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50
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Lensink MF, Govaerts C, Ruysschaert JM. Identification of specific lipid-binding sites in integral membrane proteins. J Biol Chem 2010; 285:10519-26. [PMID: 20139086 DOI: 10.1074/jbc.m109.068890] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-lipid interactions are increasingly recognized as central to the structure and function of membrane proteins. However, with the exception of simplified models, specific protein-lipid interactions are particularly difficult to highlight experimentally. Here, we used molecular dynamics simulations to identify a specific protein-lipid interaction in lactose permease, a prototypical model for transmembrane proteins. The interactions can be correlated with the functional dependence of the protein to specific lipid species. The technique is simple and widely applicable to other membrane proteins, and a variety of lipid matrices can be used.
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Affiliation(s)
- Marc F Lensink
- Structure and Function of Biological Membranes, Université Libre de Bruxelles, Boulevard du Triomphe-CP 263, B-1050 Brussels, Belgium.
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