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Golla VK, Boyd KJ, May ER. Curvature sensing lipid dynamics in a mitochondrial inner membrane model. Commun Biol 2024; 7:29. [PMID: 38182788 PMCID: PMC10770132 DOI: 10.1038/s42003-023-05657-6] [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: 02/24/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane curvature is essential for many cellular structures and processes, and factors such as leaflet asymmetry, lipid composition, and proteins all play important roles. Cardiolipin is the signature lipid of mitochondrial membranes and is essential for maintaining the highly curved shapes of the inner mitochondrial membrane (IMM) and the spatial arrangement of membrane proteins. In this study, we investigate the partitioning behavior of various lipids present in the IMM using coarse-grained molecular dynamics simulations. This study explores curved bilayer systems containing phosphatidylcholine (PC), phosphatidylethanolamine (PE), and cardiolipin (CDL) in binary and ternary component mixtures. Curvature properties such as mean and Gaussian curvatures, as well as the distribution of lipids into the various curved regions of the cristae models, are quantified. Overall, this work represents an advance beyond previous studies on lipid curvature sensing by simulating these systems in a geometry that has the morphological features and scales of curvature consistent with regions of the IMM. We find that CDL has a stronger preference for accumulating in regions of negative curvature than PE lipids, in agreement with previous results. Furthermore, we find lipid partitioning propensity is dominated by sensitivity to mean curvature, while there is a weaker correlation with Gaussian curvature.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- NVIDIA, 2860 County Hwy G4, Santa Clara, CA, 95051, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
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2
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Loschwitz J, Steffens N, Wang X, Schäffler M, Pfeffer K, Degrandi D, Strodel B. Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2. Sci Rep 2023; 13:679. [PMID: 36639389 PMCID: PMC9839784 DOI: 10.1038/s41598-023-27520-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanylate-binding proteins (GBPs) are a group of GTPases that are induced by interferon-[Formula: see text] and are crucial components of cell-autonomous immunity against intracellular pathogens. Here, we examine murine GBP2 (mGBP2), which we have previously shown to be an essential effector protein for the control of Toxoplasma gondii replication, with its recruitment through the membrane of the parasitophorous vacuole and its involvement in the destruction of this membrane likely playing a role. The overall aim of our work is to provide a molecular-level understanding of the mutual influences of mGBP2 and the parasitophorous vacuole membrane. To this end, we performed lipid-binding assays which revealed that mGBP2 has a particular affinity for cardiolipin. This observation was confirmed by fluorescence microscopy using giant unilamellar vesicles of different lipid compositions. To obtain an understanding of the protein dynamics and how this is affected by GTP binding, mGBP2 dimerization, and membrane binding, assuming that each of these steps are relevant for the function of the protein, we carried out standard as well as replica exchange molecular dynamics simulations with an accumulated simulation time of more than 30 μs. The main findings from these simulations are that mGBP2 features a large-scale hinge motion in its M/E domain, which is present in each of the studied protein states. When bound to a cardiolipin-containing membrane, this hinge motion is particularly pronounced, leading to an up and down motion of the M/E domain on the membrane, which did not occur on a membrane without cardiolipin. Our prognosis is that this up and down motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.
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Affiliation(s)
- Jennifer Loschwitz
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nora Steffens
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xue Wang
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz Schäffler
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Klaus Pfeffer
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany. .,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425, Jülich, Germany.
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3
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Rocha-Roa C, Orjuela JD, Leidy C, Cossio P, Aponte-Santamaría C. Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Lett 2021; 595:2701-2714. [PMID: 34633077 DOI: 10.1002/1873-3468.14206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamic simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolipin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar head and bulky hydrophobic body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.
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Affiliation(s)
- Cristian Rocha-Roa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
| | - Juan David Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los Andes, Bogotá, Colombia
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Chad Leidy
- Biophysics Group, Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
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4
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Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis. Int J Mol Sci 2021; 22:ijms22073793. [PMID: 33917581 PMCID: PMC8038838 DOI: 10.3390/ijms22073793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Bacillus subtilis forms dormant spores upon nutrient depletion. Germinant receptors (GRs) in spore’s inner membrane respond to ligands such as L-alanine, and trigger spore germination. In B. subtilis spores, GerA is the major GR, and has three subunits, GerAA, GerAB, and GerAC. L-Alanine activation of GerA requires all three subunits, but which binds L-alanine is unknown. To date, how GRs trigger germination is unknown, in particular due to lack of detailed structural information about B subunits. Using homology modelling with molecular dynamics (MD) simulations, we present structural predictions for the integral membrane protein GerAB. These predictions indicate that GerAB is an α-helical transmembrane protein containing a water channel. The MD simulations with free L-alanine show that alanine binds transiently to specific sites on GerAB. These results provide a starting point for unraveling the mechanism of L-alanine mediated signaling by GerAB, which may facilitate early events in spore germination.
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5
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Unraveling the Role of Drug-Lipid Interactions in NSAIDs-Induced Cardiotoxicity. MEMBRANES 2020; 11:membranes11010024. [PMID: 33383697 PMCID: PMC7824678 DOI: 10.3390/membranes11010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023]
Abstract
Cardiovascular (CV) toxicity is nowadays recognized as a class effect of non-aspirin nonsteroidal anti-inflammatory drugs (NSAIDs). However, their mechanisms of cardiotoxicity are not yet well understood, since different compounds with similar action mechanisms exhibit distinct cardiotoxicity. For instance, diclofenac (DIC) is among the most cardiotoxic compounds, while naproxen (NAP) is associated with low CV risk. In this sense, this study aimed to unravel the role of drug-lipid interactions in NSAIDs-induced cardiotoxicity. For that, DIC and NAP interactions with lipid bilayers as model systems of cell and mitochondrial membranes were characterized by derivative spectrophotometry, fluorometric leakage assays, and synchrotron X-ray scattering. Both DIC and NAP were found to have the ability to permeabilize the membrane models, as well as to alter the bilayers’ structure. The NSAIDs-induced modifications were dependent on the lipid composition of the membrane model, the three-dimensional structure of the drug, as well as the drug:lipid molar ratio tested. Altogether, this work supports the hypothesis that NSAIDs-lipid interactions, in particular at the mitochondrial level, may be another key step among the mechanisms underlying NSAIDs-induced cardiotoxicity.
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6
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Wilson BA, Ramanathan A, Lopez CF. Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations. Biophys J 2019; 117:429-444. [PMID: 31349988 PMCID: PMC6697365 DOI: 10.1016/j.bpj.2019.06.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 01/30/2023] Open
Abstract
Cardiolipin is an anionic lipid found in the mitochondrial membranes of eukaryotes ranging from unicellular microorganisms to metazoans. This unique lipid contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion and/or fission dynamics, and apoptosis. However, differences in cardiolipin content between the two mitochondrial membranes, as well as dynamic fluctuations in cardiolipin content in response to stimuli and cellular signaling events, raise questions about how cardiolipin concentration affects mitochondrial membrane structure and dynamics. Although cardiolipin’s structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in higher number lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of cardiolipin in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much-needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
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Affiliation(s)
- Blake A Wilson
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Carlos F Lopez
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University, Nashville, Tennessee.
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7
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Boyd KJ, Alder NN, May ER. Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties. Biophys J 2019; 114:2116-2127. [PMID: 29742405 DOI: 10.1016/j.bpj.2018.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/04/2018] [Accepted: 04/02/2018] [Indexed: 11/29/2022] Open
Abstract
The mitochondrial lipid cardiolipin (CL) contributes to the spatial protein organization and morphological character of the inner mitochondrial membrane. Monolysocardiolipin (MLCL), an intermediate species in the CL remodeling pathway, is enriched in the multisystem disease Barth syndrome. Despite the medical relevance of MLCL, a detailed molecular description that elucidates the structural and dynamic differences between CL and MLCL has not been conducted. To this end, we performed comparative atomistic molecular dynamics studies on bilayers consisting of pure CL or MLCL to elucidate similarities and differences in their molecular and bulk bilayer properties. We describe differential headgroup dynamics and hydrogen bonding patterns between the CL variants and show an increased cohesiveness of MLCL's solvent interfacial region, which may have implications for protein interactions. Finally, using the coarse-grained Martini model, we show that substitution of MLCL for CL in bilayers mimicking mitochondrial composition induces drastic differences in bilayer mechanical properties and curvature-dependent partitioning behavior. Together, the results of this work reveal differences between CL and MLCL at the molecular and mesoscopic levels that may underpin the pathomechanisms of defects in cardiolipin remodeling.
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Affiliation(s)
- Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
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8
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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9
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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10
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Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity. Biophys J 2017; 113:2311-2315. [PMID: 29056231 PMCID: PMC5722206 DOI: 10.1016/j.bpj.2017.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/12/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022] Open
Abstract
Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.
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Affiliation(s)
- François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Paul Schanda
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Grenoble, France.
| | - Martin S King
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7565, Université de Lorraine, Vandœuvre-lès-Nancy, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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11
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de Souza RM, Siani P, Schmidt TF, Itri R, Dias LG. Methylene Blue Location in (Hydroperoxized) Cardiolipin Monolayer: Implication in Membrane Photodegradation. J Phys Chem B 2017; 121:8512-8522. [DOI: 10.1021/acs.jpcb.7b04824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- R. M. de Souza
- Departamento
de Química, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes 3900, 14040-901, Ribeirão Preto, SP, Brazil
| | - P. Siani
- Departamento
de Química, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes 3900, 14040-901, Ribeirão Preto, SP, Brazil
| | - T. F. Schmidt
- Universidade Federal do ABC (UFABC), Avenida dos Estados 5001, 09210-580, Santo André, SP, Brazil
| | - R. Itri
- Departamento
de Física Aplicada, Instituto de Física, Universidade de São Paulo, Rua do Matão 187, 05508-900, São Paulo, SP, Brazil
| | - L. G. Dias
- Departamento
de Química, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes 3900, 14040-901, Ribeirão Preto, SP, Brazil
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12
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Boyd KJ, Alder NN, May ER. Buckling Under Pressure: Curvature-Based Lipid Segregation and Stability Modulation in Cardiolipin-Containing Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6937-6946. [PMID: 28628337 PMCID: PMC5654595 DOI: 10.1021/acs.langmuir.7b01185] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Mitochondrial metabolic function is affected by the morphology and protein organization of the mitochondrial inner membrane. Cardiolipin (CL) is a unique tetra-acyl lipid that is involved in the maintenance of the highly curved shape of the mitochondrial inner membrane as well as spatial organization of the proteins necessary for respiration and oxidative phosphorylation. Cardiolipin has been suggested to self-organize into lipid domains due to its inverted conical molecular geometry, though the driving forces for this organization are not fully understood. In this work, we use coarse-grained molecular dynamics simulations to study the mechanical properties and lipid dynamics in heterogeneous bilayers both with and without CL, as a function of membrane curvature. We find that incorporation of CL increases bilayer deformability and that CL becomes highly enriched in regions of high negative curvature. We further show that another mitochondrial inverted conical lipid, phosphatidylethanolamine (PE), does not partition or increase the deformability of the membrane in a significant manner. Therefore, CL appears to possess some unique characteristics that cannot be inferred simply from molecular geometry considerations.
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13
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Salazar J, Alarcón M, Huerta J, Navarro B, Aguayo D. Phosphoethanolamine addition to the Heptose I of the Lipopolysaccharide modifies the inner core structure and has an impact on the binding of Polymyxin B to the Escherichia coli outer membrane. Arch Biochem Biophys 2017; 620:28-34. [PMID: 28342805 DOI: 10.1016/j.abb.2017.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/21/2017] [Indexed: 12/21/2022]
Abstract
Phosphoethanolamine (pEtN) decoration of E. coli Lipopolysaccharide (LPS) provides resistance to the antimicrobial Polymyxin B (PolB). While EptA and EptB enzymes catalyze the addition of pEtN to the Lipid A and Kdo (pEtN-Kdo-Lipid A), EptC catalyzes the pEtN addition to the Heptose I (pEtN-HeptI). In this study, we investigated the contribution of pEtN-HeptI to PolB resistance using eptA/eptB and eptC deficient E. coli K12 and its wild-type parent strains. These mutations were shown to decrease the antimicrobial activity of PolB on cells grown under pEtN-addition inducing conditions. Furthermore, the 1-N-phenylnapthylamine uptake assay revealed that in vivo PolB has a reduced OM-permeabilizing activity on the ΔeptA/eptB strain compared with the ΔeptC strain. In vitro, the changes in size and zeta potential of LPS-vesicles indicate that pEtN-HeptI reduce the PolB binding, but in a minor extent than pEtN-Kdo-Lipid A. Molecular dynamics analysis revealed the structural basis of the PolB resistance promoted by pEtN-HeptI, which generate a new hydrogen-bonding networks and a denser inner core region. Altogether, the experimental and theoretical assays shown herein indicate that pEtN-HeptI addition promote an LPS conformational rearrangement, that could act as a shield by hindering the accession of PolB to inner LPS-targets moieties.
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Affiliation(s)
- Javier Salazar
- Universidad Andres Bello, Facultad de Ciencias Biológicas, Molecular Biophysics & Bioinformatics Group, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago, Chile
| | - Mackarenna Alarcón
- Universidad Andres Bello, Facultad de Ciencias Biológicas, Molecular Biophysics & Bioinformatics Group, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago, Chile
| | - Jaime Huerta
- Universidad Andres Bello, Facultad de Ciencias Biológicas, Molecular Biophysics & Bioinformatics Group, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago, Chile
| | - Belén Navarro
- Universidad Andres Bello, Facultad de Ciencias Biológicas, Molecular Biophysics & Bioinformatics Group, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago, Chile
| | - Daniel Aguayo
- Universidad Andres Bello, Facultad de Ciencias Biológicas, Molecular Biophysics & Bioinformatics Group, Center for Bioinformatics and Integrative Biology (CBIB), República 239, Santiago, Chile; Centro Interdisciplinario de Neurociencia de Valparaíso, Valparaíso, Chile.
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14
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Husen P, Solov'yov IA. Mutations at the Q o Site of the Cytochrome bc 1 Complex Strongly Affect Oxygen Binding. J Phys Chem B 2016; 121:3308-3317. [PMID: 27748117 DOI: 10.1021/acs.jpcb.6b08226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The homodimeric bc1 protein complex is embedded in membranes of mitochondria and photosynthetic bacteria, where it transports protons across the membrane to maintain an electrostatic potential used to drive ATP synthesis as part of the respiratory or photosynthetic pathways. The reaction cycle of the bc1 complex is driven by series of redox processes involving substrate molecules from the membrane, but occasional side reactions between an intermediate semiquinone substrate and molecular oxygen are suspected to be a source of toxic superoxide, which is believed to be a factor in aging. The present investigation employs molecular dynamics simulations to study the effect of mutations in the Qo binding sites of the bc1 complex on the ability of oxygen molecules to migrate to and bind at various locations within the complex. It is found that the mutations strongly affect the ability of oxygen to bind at the Qo sites, and moreover, different behavior of the two monomers of the bc1 complex is observed. The conformational differences at the Qo sites of the two monomers are studied in detail and discussed. The anionic form of semiquinone was identified as leading to the greatest opportunity for side reactions with oxygen.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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15
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Barragan AM, Schulten K, Solov'yov IA. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc 1 Complex. J Phys Chem B 2016; 120:11369-11380. [PMID: 27661199 DOI: 10.1021/acs.jpcb.6b07394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bc1 complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc1 complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc1 complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Qo-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Qo-site has further supported the conclusion. Finally, key structural elements of the bc1 complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
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16
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Husen P, Solov'yov IA. Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation. J Am Chem Soc 2016; 138:12150-8. [PMID: 27447781 DOI: 10.1021/jacs.6b04849] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
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17
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Pöyry S, Vattulainen I. Role of charged lipids in membrane structures - Insight given by simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2322-2333. [PMID: 27003126 DOI: 10.1016/j.bbamem.2016.03.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 01/28/2023]
Abstract
Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sanja Pöyry
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark; Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.
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18
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Sathappa M, Alder NN. The ionization properties of cardiolipin and its variants in model bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1362-72. [PMID: 26965987 DOI: 10.1016/j.bbamem.2016.03.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 01/01/2023]
Abstract
The anionic phospholipid cardiolipin has an unusual dimeric structure with a two-phosphate headgroup and four acyl chains. Cardiolipin is present in energy-transducing membranes that maintain electrochemical gradients, including most bacterial plasma membranes and the mitochondrial inner membrane, where it mediates respiratory complex assembly and activation, among many other roles. Dysfunctional biogenesis of cardiolipin is implicated in the pathogenesis of several diseases including Barth syndrome. Because cardiolipin is a dominant anionic lipid in energy-conserving membranes, its headgroup is a major contributor to surface charge density and the bilayer electrostatic profile. However, the proton dissociation behavior of its headgroup remains controversial. In one model, the pKa values of the phosphates differ by several units and the headgroup exists as a monoanion at physiological pH. In another model, both phosphates ionize as strong acids with low pKa values and the headgroup exists in dianionic form at physiological pH. Using independent electrokinetic and spectroscopic approaches, coupled with analysis using Gouy-Chapman-Stern formalism, we have analyzed the ionization properties of cardiolipin within biologically relevant lipid bilayer model systems. We show that both phosphates of the cardiolipin headgroup show strong ionization behavior with low pKa values. Moreover, cardiolipin variants lacking structural features proposed to be required to maintain disparate pKa values--namely the secondary hydroxyl on the central glycerol or a full complement of four acyl chains--were shown to have ionization behavior identical to intact cardiolipin. Hence, these results indicate that within the physiological pH range, the cardiolipin headgroup is fully ionized as a dianion. We discuss the implications of these results with respect to the role of cardiolipin in defining membrane surface potential, activating respiratory complexes, and modulating membrane curvature.
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Affiliation(s)
- Murugappan Sathappa
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States.
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19
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Schmidt TF, Caseli L, Oliveira ON, Itri R. Binding of methylene blue onto Langmuir monolayers representing cell membranes may explain its efficiency as photosensitizer in photodynamic therapy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4205-12. [PMID: 25798992 DOI: 10.1021/acs.langmuir.5b00166] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We provide evidence for the electrostatic interactions between the cationic photosensitizer methylene blue (MB) and cell membrane models represented by neat and mixed Langmuir monolayers of dioleylphosphatidylcholine (DOPC) and 1,1',2,2'-tetraoleoylcardiolipin (CL). From surface pressure measurements, MB was found to adsorb strongly and expand CL-containing monolayers, while it caused an apparent decreasing in molecular area on neat DOPC monolayer. The binding site of MB could be inferred from data with the surface-specific polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS) technique, where changes induced by MB were observed in the vibrational modes of the phosphate groups of both CL and DOPC. The incorporation of MB also affected the carbonyl groups and the packing of the alkyl chains, thus indicating that MB binding site favors singlet oxygen generation close to the double bonds in the alkyl chains, an important requirement for photodynamic efficiency. Significantly, the data presented here demonstrate that MB may act in membranes composed by PCs, such as mammalian plasma membranes, and in those containing CL, as in bacterial and inner mitochondrial membranes.
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Affiliation(s)
- Thaís F Schmidt
- †Federal University of ABC (UFABC), Santo André, SP 09210-580, Brazil
| | - Luciano Caseli
- ‡Institute of Environmental, Chemical, and Pharmaceutical Sciences, Federal University of São Paulo, Diadema, SP 09913-030, Brazil
| | - Osvaldo N Oliveira
- §São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil
| | - Rosangela Itri
- ∥Institute of Physics, University of São Paulo, São Paulo, SP 05508-090, Brazil
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20
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Rhéault JF, Gagné È, Guertin M, Lamoureux G, Auger M, Lagüe P. Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study. Biochemistry 2015; 54:2073-84. [DOI: 10.1021/bi5010624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jean-François Rhéault
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
| | | | - Michel Guertin
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
| | - Guillaume Lamoureux
- Centre for Research
in Molecular Modeling (CERMM), Concordia University, Montréal, Québec, Canada
| | | | - Patrick Lagüe
- Department
of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Québec, Canada
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21
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Pan J, Cheng X, Sharp M, Ho CS, Khadka N, Katsaras J. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations. SOFT MATTER 2015; 11:130-138. [PMID: 25369786 DOI: 10.1039/c4sm02227k] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density. Of note, the distance between electron density maxima DHH (39.4 Å) and the hydrocarbon chain thickness 2DC (29.1 Å) of TOCL bilayers were both found to be larger than the corresponding values for dioleoyl phosphatidylcholine (DOPC) bilayers. Conversely, TOCL bilayers have a smaller overall bilayer thickness DB (36.7 Å), primarily due to their smaller headgroup volume per phosphate. SDP analysis yielded a lipid area of 129.8 Å(2), indicating that the cross-sectional area per oleoyl chain in TOCL bilayers (i.e., 32.5 Å(2)) is smaller than that for DOPC bilayers. Multiple sets of MD simulations were performed with the lipid area constrained at different values. The calculated surface tension versus lipid area resulted in a lateral area compressibility modulus KA of 342 mN m(-1), which is slightly larger compared to DOPC bilayers. Model free comparison to experimental scattering data revealed the best simulated TOCL bilayer from which detailed molecular interactions were determined. Specifically, Na(+) cations were found to interact most strongly with the glycerol hydroxyl linkage, followed by the phosphate and backbone carbonyl oxygens. Inter- and intra-lipid interactions were facilitated by hydrogen bonding between the glycerol hydroxyl and phosphate oxygen, but not with the backbone carbonyl. Finally, analysis of the intermediate scattering functions from NSE spectroscopy measurements of TOCL bilayers yielded a bending modulus KC of 1.06 × 10(-19) J, which was larger than that observed in DOPC bilayers. Our results show the physicochemical properties of cardiolin bilayers that may be important in explaining their functionality in the inner mitochondrial membrane.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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22
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Barragan AM, Crofts AR, Schulten K, Solov'yov IA. Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. J Phys Chem B 2014; 119:433-47. [PMID: 25372183 PMCID: PMC4297238 DOI: 10.1021/jp510022w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Enzymes of the bc1 complex family power
the biosphere through their central role in respiration and photosynthesis.
These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate
a proton-motive force that drives ATP synthesis. Key for the function
of the bc1 complex is the initial redox
process that involves a bifurcated electron transfer in which the
two electrons from a quinol substrate are passed to different electron
acceptors in the bc1 complex. The electron
transfer is coupled to proton transfer. The overall mechanism of quinol
oxidation by the bc1 complex is well enough
characterized to allow exploration at the atomistic level, but details
are still highly controversial. The controversy stems from the uncertain
binding motifs of quinol at the so-called Qo active site of the bc1 complex.
Here we employ a combination of classical all atom molecular dynamics
and quantum chemical calculations to reveal the binding modes of quinol
at the Qo-site of the bc1 complex from Rhodobacter capsulatus. The calculations suggest a novel configuration of amino acid residues
responsible for quinol binding and support a mechanism for proton-coupled
electron transfer from quinol to iron–sulfur cluster through
a bridging hydrogen bond from histidine that stabilizes the reaction
complex.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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23
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Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 2014; 35:1997-2004. [PMID: 25130509 DOI: 10.1002/jcc.23702] [Citation(s) in RCA: 1619] [Impact Index Per Article: 161.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 01/12/2023]
Abstract
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas, 66047
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24
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Song DH, Park J, Maurer LL, Lu W, Philbert MA, Sastry AM. Biophysical significance of the inner mitochondrial membrane structure on the electrochemical potential of mitochondria. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:062723. [PMID: 24483502 PMCID: PMC4315510 DOI: 10.1103/physreve.88.062723] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Indexed: 05/29/2023]
Abstract
The available literature supports the hypothesis that the morphology of the inner mitochondrial membrane is regulated by different energy states, that the three-dimensional morphology of cristae is dynamic, and that both are related to biochemical function. Examination of the correlation between the inner mitochondrial membrane (IMM) structure and mitochondrial energetic function is critical to an understanding of the links between mesoscale morphology and function in progressive mitochondrial dysfunction such as aging, neurodegeneration, and disease. To investigate this relationship, we develop a model to examine the effects of three-dimensional IMM morphology on the electrochemical potential of mitochondria. The two-dimensional axisymmetric finite element method is used to simulate mitochondrial electric potential and proton concentration distribution. This simulation model demonstrates that the proton motive force (Δp) produced on the membranes of cristae can be higher than that on the inner boundary membrane. The model also shows that high proton concentration in cristae can be induced by the morphology-dependent electric potential gradient along the outer side of the IMM. Furthermore, simulation results show that a high Δp is induced by the large surface-to-volume ratio of an individual crista, whereas a high capacity for ATP synthesis can primarily be achieved by increasing the surface area of an individual crista. The mathematical model presented here provides compelling support for the idea that morphology at the mesoscale is a significant driver of mitochondrial function.
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Affiliation(s)
- Dong Hoon Song
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jonghyun Park
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Laura L Maurer
- Toxicology Program, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wei Lu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Martin A Philbert
- Toxicology Program, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
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25
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Pöyry S, Cramariuc O, Postila PA, Kaszuba K, Sarewicz M, Osyczka A, Vattulainen I, Róg T. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:769-78. [DOI: 10.1016/j.bbabio.2013.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/05/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
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