1
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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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Anishkin A, Adepu KK, Bhandari D, Adams SH, Chintapalli SV. Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane. Biomolecules 2023; 13:1138. [PMID: 37509174 PMCID: PMC10377724 DOI: 10.3390/biom13071138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Myoglobin (Mb) interaction with the outer mitochondrial membrane (OMM) promotes oxygen (O2) release. However, comprehensive molecular details on specific contact regions of the OMM with oxygenated (oxy-) and deoxygenated (deoxy-)Mb are missing. We used molecular dynamics (MD) simulations to explore the interaction of oxy- and deoxy-Mb with the membrane lipids of the OMM in two lipid compositions: (a) a typical whole membrane on average, and (b) specifically the cardiolipin-enriched cristae region (contact site). Unrestrained relaxations showed that on average, both the oxy- and deoxy-Mb established more stable contacts with the lipids typical of the cristae contact site, then with those of the average OMM. However, in steered detachment simulations, deoxy-Mb clung more tightly to the average OMM, and oxy-Mb strongly preferred the contact sites of the OMM. The MD simulation analysis further indicated that a non-specific binding, mediated by local electrostatic interactions, existed between charged or polar groups of Mb and the membrane, for stable interaction. To the best of our knowledge, this is the first computational study providing the molecular details of the direct Mb-mitochondria interaction that assisted in distinguishing the preferred localization of oxy- and deoxy-Mb on the OMM. Our findings support the existing experimental evidence on Mb-mitochondrial association and shed more insights on Mb-mediated O2 transport for cellular bioenergetics.
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Affiliation(s)
- Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Kiran Kumar Adepu
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - Sean H Adams
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA 95616, USA
- Center for Alimentary and Metabolic Science, University of California Davis, Sacramento, CA 95616, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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3
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Nesterov SV, Yaguzhinsky LS, Vasilov RG, Kadantsev VN, Goltsov AN. Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1813. [PMID: 36554218 PMCID: PMC9778164 DOI: 10.3390/e24121813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The results of many experimental and theoretical works indicate that after transport of protons across the mitochondrial inner membrane (MIM) in the oxidative phosphorylation (OXPHOS) system, they are retained on the membrane-water interface in nonequilibrium state with free energy excess due to low proton surface-to-bulk release. This well-established phenomenon suggests that proton trapping on the membrane interface ensures vectorial lateral transport of protons from proton pumps to ATP synthases (proton acceptors). Despite the key role of the proton transport in bioenergetics, the molecular mechanism of proton transfer in the OXPHOS system is not yet completely established. Here, we developed a dynamics model of long-range transport of energized protons along the MIM accompanied by collective excitation of localized waves propagating on the membrane surface. Our model is based on the new data on the macromolecular organization of the OXPHOS system showing the well-ordered structure of respirasomes and ATP synthases on the cristae membrane folds. We developed a two-component dynamics model of the proton transport considering two coupled subsystems: the ordered hydrogen bond (HB) chain of water molecules and lipid headgroups of MIM. We analytically obtained a two-component soliton solution in this model, which describes the motion of the proton kink, corresponding to successive proton hops in the HB chain, and coherent motion of a compression soliton in the chain of lipid headgroups. The local deformation in a soliton range facilitates proton jumps due to water molecules approaching each other in the HB chain. We suggested that the proton-conducting structures formed along the cristae membrane surface promote direct lateral proton transfer in the OXPHOS system. Collective excitations at the water-membrane interface in a form of two-component soliton ensure the coupled non-dissipative transport of charge carriers and elastic energy of MIM deformation to ATP synthases that may be utilized in ATP synthesis providing maximal efficiency in mitochondrial bioenergetics.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Department of Bioenergetics, Institute of Cytochemistry and Molecular Pharmacology, 115404 Moscow, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Raif G. Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
| | - Vasiliy N. Kadantsev
- Institute for Artificial Intelligence, Russian Technological University (MIREA), 119454 Moscow, Russia
| | - Alexey N. Goltsov
- Institute for Artificial Intelligence, Russian Technological University (MIREA), 119454 Moscow, Russia
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4
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Ge Y, Boopathy S, Nguyen TH, Lugo CM, Chao LH. Absence of Cardiolipin From the Outer Leaflet of a Mitochondrial Inner Membrane Mimic Restricts Opa1-Mediated Fusion. Front Mol Biosci 2022; 8:769135. [PMID: 35004847 PMCID: PMC8728091 DOI: 10.3389/fmolb.2021.769135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Cardiolipin is a tetra-acylated di-phosphatidylglycerol lipid enriched in the matrix-facing (inner) leaflet of the mitochondrial inner membrane. Cardiolipin plays an important role in regulating mitochondria function and dynamics. Yet, the mechanisms connecting cardiolipin distribution and mitochondrial protein function remain indirect. In our previous work, we established an in vitro system reconstituting mitochondrial inner membrane fusion mediated by Opa1. We found that the long form of Opa1 (l-Opa1) works together with the proteolytically processed short form (s-Opa1) to mediate fast and efficient membrane fusion. Here, we extend our reconstitution system to generate supported lipid bilayers with asymmetric cardiolipin distribution. Using this system, we find the presence of cardiolipin on the inter-membrane space-facing (outer) leaflet is important for membrane tethering and fusion. We discuss how the presence of cardiolipin in this leaflet may influence protein and membrane properties, and future applications for this approach.
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Affiliation(s)
- Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Sivakumar Boopathy
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Tran H Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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5
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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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6
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Prunotto A, Bahr G, González LJ, Vila AJ, Dal Peraro M. Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-β-lactamase 1. ACS Infect Dis 2020; 6:2719-2731. [PMID: 32865963 DOI: 10.1021/acsinfecdis.0c00341] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Resistance to last-resort carbapenem antibiotics is an increasing threat to human health, as it critically limits therapeutic options. Metallo-β-lactamases (MBLs) are the largest family of carbapenemases, enzymes that inactivate these drugs. Among MBLs, New Delhi metallo-β-lactamase 1 (NDM-1) has experienced the fastest and largest worldwide dissemination. This success has been attributed to the fact that NDM-1 is a lipidated protein anchored to the outer membrane of bacteria, while all other MBLs are soluble periplasmic enzymes. By means of a combined experimental and computational approach, we show that NDM-1 interacts with the surface of bacterial membranes in a stable, defined conformation, in which the active site is not occluded by the bilayer. Although the lipidation is required for a long-lasting interaction, the globular domain of NDM-1 is tuned to interact specifically with the outer bacterial membrane. In contrast, this affinity is not observed for VIM-2, a natively soluble MBL. Finally, we identify key residues involved in the membrane interaction with NDM-1, which constitute potential targets for developing therapeutic strategies able to combat resistance granted by this enzyme.
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Affiliation(s)
- Alessio Prunotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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7
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Miranda ÉGA, Araujo-Chaves JC, Kawai C, Brito AMM, Dias IWR, Arantes JT, Nantes-Cardoso IL. Cardiolipin Structure and Oxidation Are Affected by Ca 2+ at the Interface of Lipid Bilayers. Front Chem 2020; 7:930. [PMID: 32039150 PMCID: PMC6986261 DOI: 10.3389/fchem.2019.00930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
Ca2+-overload contributes to the oxidation of mitochondrial membrane lipids and associated events such as the permeability transition pore (MPTP) opening. Numerous experimental studies about the Ca2+/cardiolipin (CL) interaction are reported in the literature, but there are few studies in conjunction with theoretical approaches based on ab initio calculations. In the present study, the lipid fraction of the inner mitochondrial membrane was modeled as POPC/CL large unilamellar vesicles (LUVs). POPC/CL and, comparatively, POPC, and CL LUVs were challenged by singlet molecular oxygen using the anionic porphyrin TPPS4 as a photosensitizer and by free radicals produced by Fe2+-citrate. Calcium ion favored both types of lipid oxidation in a lipid composition-dependent manner. In membranes containing predominantly or exclusively POPC, Ca2+ increased the oxidation at later reaction times while the oxidation of CL membranes was exacerbated at the early times of reaction. Considering that Ca2+ interaction affects the lipid structure and packing, density functional theory (DFT) calculations were applied to the Ca2+ association with totally and partially protonated and deprotonated CL, in the presence of water. The interaction of totally and partially protonated CL head groups with Ca2+ decreased the intramolecular P-P distance and increased the hydrophobic volume of the acyl chains. Consistently with the theoretically predicted effect of Ca2+ on CL, in the absence of pro-oxidants, giant unilamellar vesicles (GUVs) challenged by Ca2+ formed buds and many internal vesicles. Therefore, Ca2+ induces changes in CL packing and increases the susceptibility of CL to the oxidation promoted by free radicals and excited species.
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Affiliation(s)
- Érica G A Miranda
- Laboratory of Nanostructures for Biology and Advanced Materials, NanoBioMAv, Center of Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil
| | - Juliana C Araujo-Chaves
- Laboratory of Nanostructures for Biology and Advanced Materials, NanoBioMAv, Center of Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil
| | - Cintia Kawai
- Laboratory of Nanostructures for Biology and Advanced Materials, NanoBioMAv, Center of Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil
| | - Adrianne M M Brito
- Laboratory of Nanostructures for Biology and Advanced Materials, NanoBioMAv, Center of Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil
| | - Igor W R Dias
- Center of Engineering, Modeling, and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
| | - Jeverson T Arantes
- Center of Engineering, Modeling, and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
| | - Iseli L Nantes-Cardoso
- Laboratory of Nanostructures for Biology and Advanced Materials, NanoBioMAv, Center of Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil
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8
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Gottschalk B, Klec C, Leitinger G, Bernhart E, Rost R, Bischof H, Madreiter-Sokolowski CT, Radulović S, Eroglu E, Sattler W, Waldeck-Weiermair M, Malli R, Graier WF. MICU1 controls cristae junction and spatially anchors mitochondrial Ca 2+ uniporter complex. Nat Commun 2019; 10:3732. [PMID: 31427612 PMCID: PMC6700202 DOI: 10.1038/s41467-019-11692-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Recently identified core proteins (MICU1, MCU, EMRE) forming the mitochondrial Ca2+ uniporter complex propelled investigations into its physiological workings. Here, we apply structured illumination microscopy to visualize and localize these proteins in living cells. Our data show that MICU1 localizes at the inner boundary membrane (IBM) due to electrostatic interaction of its polybasic domain. Moreover, this exclusive localization of MICU1 is important for the stability of cristae junctions (CJ), cytochrome c release and mitochondrial membrane potential. In contrast to MICU1, MCU and EMRE are homogeneously distributed at the inner mitochondrial membrane under resting conditions. However, upon Ca2+ elevation MCU and EMRE dynamically accumulate at the IBM in a MICU1-dependent manner. Eventually, our findings unveil an essential function of MICU1 in CJ stabilization and provide mechanistic insights of how sophistically MICU1 controls the MCU-Complex while maintaining the structural mitochondrial membrane framework.
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Affiliation(s)
- Benjamin Gottschalk
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Christiane Klec
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Gerd Leitinger
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/2, 8010 Graz, Austria
| | - Eva Bernhart
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - René Rost
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Helmut Bischof
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Corina T. Madreiter-Sokolowski
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Snježana Radulović
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria ,0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/2, 8010 Graz, Austria
| | - Emrah Eroglu
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Wolfgang Sattler
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria ,grid.452216.6BioTechMed Graz, Mozartgasse 12/2, Graz, 8010 Austria
| | - Markus Waldeck-Weiermair
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Roland Malli
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria ,grid.452216.6BioTechMed Graz, Mozartgasse 12/2, Graz, 8010 Austria
| | - Wolfgang F. Graier
- 0000 0000 8988 2476grid.11598.34Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria ,grid.452216.6BioTechMed Graz, Mozartgasse 12/2, Graz, 8010 Austria
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9
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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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10
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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: 175] [Impact Index Per Article: 35.0] [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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11
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How cardiolipin peroxidation alters the properties of the inner mitochondrial membrane? Chem Phys Lipids 2018; 214:15-23. [DOI: 10.1016/j.chemphyslip.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/29/2018] [Indexed: 01/16/2023]
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12
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Baheti K, Kale M. Methodologies Related to Computational Models in View of Developing Anti-Alzheimer Drugs: An Overview. Curr Drug Discov Technol 2018; 16:66-73. [PMID: 29663890 DOI: 10.2174/1570163815666180417120833] [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: 07/27/2017] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Since the last two decades, there has been more focus on the development strategies related to Anti-Alzheimer's drug research. This may be attributed to the fact that most of the Alzheimer's cases are still mostly unknown except for a few cases, where genetic differences have been identified. With the progress of the disease, the symptoms involve intellectual deterioration, memory impairment, abnormal personality and behavioural patterns, confusion, aggression, mood swings, irritability Current therapies available for this disease give only symptomatic relief and do not focus on manipulations of biololecular processes. METHODS Nearly all the therapies to treat Alzheimer's disease, target to change the amyloid cascade which is considered to be important in AD pathogenesis. New drug regimens are not able to keep pace with the ever-increasing understanding about dementia at the molecular level. Looking into these aggravated problems, we thought to put forth molecular modeling as a drug discovery approach for developing novel drugs to treat Alzheimer disease. The disease is incurable and it gets worst as it advances and finally causes death. Due to this, the design of drugs to treat this disease has become an utmost priority for research. One of the most important emerging technologies applied for this has been Computer-assisted drug design (CADD). It is a research tool that employs large-scale computing strategies in an attempt to develop a model receptor site which can be used for designing of an anti-Alzheimer drug. RESULTS Various models of amyloid-based calcium channels have been computationally optimized. Docking and De novo evolution are used to design the compounds. They are further subjected to absorption, distribution, metabolism, excretion and toxicity (ADMET) studies to finally bring about active compounds that are able to cross BBB. Many novel compounds have been designed which might be promising ones for the treatment of AD. CONCLUSION The present review describes the research carried out on various heterocyclic scaffolds that can serve as lead compounds to design Anti-Alzheimer's drugs in the future. The molecular modeling methods can thus become a better alternative for the discovery of newer Anti- Alzheimer agents. This methodology is extremely useful to design drugs in minimum time with enhanced activity keeping balanced ethical considerations. Thus, the researchers are opting for this improved process over the conventional methods hoping to achieve a sure shot way out for the sufferings of people affected by Alzheimer besides other diseases.
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Affiliation(s)
- Kirtee Baheti
- Department of Pharmaceutical Chemistry, Government College of Pharmacy, Aurangabad-431005, Maharashtra, India
| | - Mayura Kale
- Department of Pharmaceutical Chemistry, Government College of Pharmacy, Aurangabad-431005, Maharashtra, India
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13
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Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1035-1045. [PMID: 29366674 PMCID: PMC5988563 DOI: 10.1016/j.bbamem.2018.01.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/24/2022]
Abstract
Cardiolipin in eukaryotes is found in the mitochondrial inner membrane, where it interacts with membrane proteins and, although not essential, is necessary for the optimal activity of a number of proteins. One of them is the mitochondrial ADP/ATP carrier, which imports ADP into the mitochondrion and exports ATP. In the crystal structures, cardiolipin is bound to three equivalent sites of the ADP/ATP carrier, but its role is unresolved. Conservation of residues at these cardiolipin binding sites across other members of the mitochondrial carrier superfamily indicates cardiolipin binding is likely to be important for the function of all mitochondrial carriers. Multiscale simulations were performed in a cardiolipin-containing membrane to investigate the dynamics of cardiolipin around the yeast and bovine ADP/ATP carriers in a lipid bilayer and the properties of the cardiolipin-binding sites. In coarse-grain simulations, cardiolipin molecules bound to the carriers for longer periods of time than phosphatidylcholine and phosphatidylethanolamine lipids—with timescales in the tens of microseconds. Three long-lived cardiolipin binding sites overlapped with those in the crystal structures of the carriers. Other shorter-lived cardiolipin interaction sites were identified in both membrane leaflets. However, the timescales of the interactions were of the same order as phosphatidylcholine and phosphatidylethanolamine, suggesting that these sites are not specific for cardiolipin binding. The calculation of lipid binding times and the overlap of the cardiolipin binding sites between the structures and simulations demonstrate the potential of multiscale simulations to investigate the dynamics and behavior of lipids interacting with membrane proteins. Coarse-grained models of AAC in mixed lipid bilayers were simulated. Three long-lived cardiolipin sites correspond to those in the crystal structures. No other long-lived binding sites were observed for cardiolipin or other phospholipids. Trimethylation of Lys-51 of AAC had no effect on cardiolipin interactions.
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Murcar-Evans BI, Cabral AD, Toutah K, de Araujo ED, Lai A, Macdonald PM, Berger-Becvar A, Kraskouskaya D, Gunning PT. ProxyPhos sensors for the detection of negatively charged membranes. Analyst 2017; 142:4511-4521. [DOI: 10.1039/c7an00568g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
ProxyPhos sensors selectively detect negatively charged phospholipid membranes.
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Affiliation(s)
- Bronte I. Murcar-Evans
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Aaron D. Cabral
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Krimo Toutah
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Elvin D. de Araujo
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Angel Lai
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Peter M. Macdonald
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Angelika Berger-Becvar
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Dziyana Kraskouskaya
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Patrick T. Gunning
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
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15
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Antón Z, Landajuela A, Hervás JH, Montes LR, Hernández-Tiedra S, Velasco G, Goñi FM, Alonso A. Human Atg8-cardiolipin interactions in mitophagy: Specific properties of LC3B, GABARAPL2 and GABARAP. Autophagy 2016; 12:2386-2403. [PMID: 27764541 DOI: 10.1080/15548627.2016.1240856] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The phospholipid cardiolipin (CL) has been proposed to play a role in selective mitochondrial autophagy, or mitophagy. CL externalization to the outer mitochondrial membrane would act as a signal for the human Atg8 ortholog subfamily, MAP1LC3 (LC3). The latter would mediate both mitochondrial recognition and autophagosome formation, ultimately leading to removal of damaged mitochondria. We have applied quantitative biophysical techniques to the study of CL interaction with various Atg8 human orthologs, namely LC3B, GABARAPL2 and GABARAP. We have found that LC3B interacts preferentially with CL over other di-anionic lipids, that CL-LC3B binding occurs with positive cooperativity, and that the CL-LC3B interaction relies only partially on electrostatic forces. CL-induced increased membrane fluidity appears also as an important factor helping LC3B to bind CL. The LC3B C terminus remains exposed to the hydrophilic environment after protein binding to CL-enriched membranes. In intact U87MG human glioblastoma cells rotenone-induced autophagy leads to LC3B translocation to mitochondria and subsequent delivery of mitochondria to lysosomes. We have also observed that GABARAP, but not GABARAPL2, interacts with CL in vitro. However neither GABARAP nor GABARAPL2 were translocated to mitochondria in rotenone-treated U87MG cells. Thus the various human Atg8 orthologs might play specific roles in different autophagic processes.
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Affiliation(s)
- Zuriñe Antón
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
| | - Ane Landajuela
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
| | - Javier H Hervás
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
| | - L Ruth Montes
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
| | - Sonia Hernández-Tiedra
- b Departamento de Bioquímica y Biología Molecular I , Universidad Complutense , Madrid , Spain.,c Instituto de Investigaciones Sanitarias San Carlos (IdISSC) , Madrid , Spain
| | - Guillermo Velasco
- b Departamento de Bioquímica y Biología Molecular I , Universidad Complutense , Madrid , Spain.,c Instituto de Investigaciones Sanitarias San Carlos (IdISSC) , Madrid , Spain
| | - Felix M Goñi
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
| | - Alicia Alonso
- a Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica y Biología Molecular , Universidad del País Vasco , Bilbao , Spain
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16
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Audagnotto M, Lemmin T, Barducci A, Dal Peraro M. Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer. J Phys Chem Lett 2016; 7:3572-3578. [PMID: 27518597 DOI: 10.1021/acs.jpclett.6b01721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The proteolytic cleavage of the transmembrane (TM) domain of the amyloid precursor protein (APP) releases amyloid-β (Aβ) peptides, which accumulation in the brain tissue is an early indicator of Alzheimer's disease. We used multiscale molecular dynamics simulations to investigate the stability of APP-TM dimer in realistic models of the synaptic plasma membrane (SPM). Between the two possible dimerization motifs proposed by NMR and EPR, namely G709XXXA713 and G700XXXG704XXXG708, our study revealed that the dimer promoted by the G709XXXA713 motif is not stable in the SPM due to the competition with highly unsaturated lipids that constitute the SPM. Under the same conditions, the dimer promoted by the G700XXXG704XXXG708 motif is instead the most stable species and likely the most biologically relevant. Independently of the dimerization state, both these motifs can be involved in the recruitment of cholesterol molecules.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California-San Francisco , San Francisco, California 94143, United States
| | - Alessandro Barducci
- Inserm, U1054 Montpellier, France
- Université de Montpellier, CNRS, UMR 5048 , Centre de Biochimie Structurale, U1054 Montpellier, France
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
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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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Graef F, Gordon S, Lehr CM. Anti-infectives in Drug Delivery-Overcoming the Gram-Negative Bacterial Cell Envelope. Curr Top Microbiol Immunol 2016; 398:475-496. [PMID: 26942419 DOI: 10.1007/82_2016_491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Infectious diseases are becoming a major menace to the state of health worldwide, with difficulties in effective treatment especially of nosocomial infections caused by Gram-negative bacteria being increasingly reported. Inadequate permeation of anti-infectives into or across the Gram-negative bacterial cell envelope, due to its intrinsic barrier function as well as barrier enhancement mediated by resistance mechanisms, can be identified as one of the major reasons for insufficient therapeutic effects. Several in vitro, in silico, and in cellulo models are currently employed to increase the knowledge of anti-infective transport processes into or across the bacterial cell envelope; however, all such models exhibit drawbacks or have limitations with respect to the information they are able to provide. Thus, new approaches which allow for more comprehensive characterization of anti-infective permeation processes (and as such, would be usable as screening methods in early drug discovery and development) are desperately needed. Furthermore, delivery methods or technologies capable of enhancing anti-infective permeation into or across the bacterial cell envelope are required. In this respect, particle-based carrier systems have already been shown to provide the opportunity to overcome compound-related difficulties and allow for targeted delivery. In addition, formulations combining efflux pump inhibitors or antimicrobial peptides with anti-infectives show promise in the restoration of antibiotic activity in resistant bacterial strains. Despite considerable progress in this field however, the design of carriers to specifically enhance transport across the bacterial envelope or to target difficult-to-treat (e.g., intracellular) infections remains an urgently needed area of improvement. What follows is a summary and evaluation of the state of the art of both bacterial permeation models and advanced anti-infective formulation strategies, together with an outlook for future directions in these fields.
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Affiliation(s)
- Florian Graef
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany
| | - Sarah Gordon
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany. .,Department of Pharmacy, Saarland University, Saarbrücken, Germany.
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20
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Bovigny C, Tamò G, Lemmin T, Maïno N, Dal Peraro M. LipidBuilder: A Framework To Build Realistic Models for Biological Membranes. J Chem Inf Model 2015; 55:2491-9. [PMID: 26606666 DOI: 10.1021/acs.jcim.5b00501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physical and chemical characterization of biological membranes is of fundamental importance for understanding the functional role of lipid bilayers in shaping cells and organelles, steering vesicle trafficking and promoting membrane-protein signaling. Molecular dynamics simulations stand as a powerful tool to probe the properties of membranes at atomistic level. However, the biological membrane is highly complex, and closely mimicking its physiological constitution in silico is not a straightforward task. Here, we present LipidBuilder, a framework for creating and storing models of biologically relevant phospholipid species with acyl tails of heterogeneous composition. LipidBuilder also enables the assembly of these database-stored lipids into realistic bilayers featuring asymmetric distribution on layer leaflets and concentration of given membrane constituents as defined, for example, by lipidomics experiments. The ability of LipidBuilder to assemble robust membrane models was validated by simulating membranes of homogeneous lipid composition for which experimental data are available. Furthermore, taking advantage of the extensive lipid headgroup repertoire, we assembled models of membranes of heterogeneous nature as naturally found in viral (phage PRD1), bacterial (Salmonella enterica, Laurinavicius , S. ; Kakela , R. ; Somerharju , P. ; Bamford , D. H. ; Virology 2004 , 322 , 328 - 336 ) and plant (Chlorella kessleri, Rezanka , T. ; Podojil , M. ; J. Chromatogr. 1989 , 463 , 397 - 408 ) organisms. These realistic membrane models were built using a near-exact lipid composition revealed from analytical chemistry experiments. We suggest LipidBuilder as a useful tool to model biological membranes of near-biological complexity, and as a robust complement to the current efforts to characterize the biophysical properties of biological membrane using molecular simulation.
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Affiliation(s)
- Christophe Bovigny
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
| | - Giorgio Tamò
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
| | - Thomas Lemmin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Nicolas Maïno
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB) , CH-1015 Lausanne, Switzerland
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21
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Gorczyca M, Korchowiec B, Korchowiec J, Trojan S, Rubio-Magnieto J, Luis SV, Rogalska E. A Study of the Interaction between a Family of Gemini Amphiphilic Pseudopeptides and Model Monomolecular Film Membranes Formed with a Cardiolipin. J Phys Chem B 2015; 119:6668-79. [PMID: 25959677 DOI: 10.1021/acs.jpcb.5b02575] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between five gemini amphiphilic pseudopeptides (GAPs) differing by the length of the central spacer and a model membrane lipid, 1,3-bis[1,2-dimyristoyl-sn-glycero-3-phospho]-sn-glycerol (cardiolipin) were studied with the aim to evaluate their possible antimicrobial properties. To this end, monomolecular films were formed at the air/water interface with pure cardiolipin or cardiolipin/GAPs mixtures; film properties were determined using surface pressure and surface potential measurements, as well as polarization-modulation infrared reflection-absorption spectroscopy. Moreover, to better understand the GAPs-phospholipid interaction at the molecular level, molecular dynamics simulations were performed. The results obtained indicate that the length of the central spacer has an effect on the interaction of GAPs with cardiolipin and on the properties of the lipid film. The GAPs with the longer linkers can be expected to be useful for biological membrane modification and for possible antimicrobial applications.
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Affiliation(s)
- Marcelina Gorczyca
- †Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | - Beata Korchowiec
- ‡Department of Physical Chemistry and Electrochemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | - Jacek Korchowiec
- †Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | - Sonia Trojan
- †Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | - Jenifer Rubio-Magnieto
- §Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat, s/n, 12071 Castellón, Spain
| | - Santiago V Luis
- §Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat, s/n, 12071 Castellón, Spain
| | - Ewa Rogalska
- ∥Structure et Réactivité des Systèmes Moléculaires Complexes, BP 239, CNRS/Université de Lorraine, 54506 Vandoeuvre-lès-Nancy cedex, France
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22
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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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