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Bigotti MG, Brancaccio A. High degree of conservation of the enzymes synthesizing the laminin-binding glycoepitope of α-dystroglycan. Open Biol 2021; 11:210104. [PMID: 34582712 PMCID: PMC8478517 DOI: 10.1098/rsob.210104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The dystroglycan (DG) complex plays a pivotal role for the stabilization of muscles in Metazoa. It is formed by two subunits, extracellular α-DG and transmembrane β-DG, originating from a unique precursor via a complex post-translational maturation process. The α-DG subunit is extensively glycosylated in sequential steps by several specific enzymes and employs such glycan scaffold to tightly bind basement membrane molecules. Mutations of several of these enzymes cause an alteration of the carbohydrate structure of α-DG, resulting in severe neuromuscular disorders collectively named dystroglycanopathies. Given the fundamental role played by DG in muscle stability, it is biochemically and clinically relevant to investigate these post-translational modifying enzymes from an evolutionary perspective. A first phylogenetic history of the thirteen enzymes involved in the fabrication of the so-called 'M3 core' laminin-binding epitope has been traced by an overall sequence comparison approach, and interesting details on the primordial enzyme set have emerged, as well as substantial conservation in Metazoa. The optimization along with the evolution of a well-conserved enzymatic set responsible for the glycosylation of α-DG indicate the importance of the glycosylation shell in modulating the connection between sarcolemma and surrounding basement membranes to increase skeletal muscle stability, and eventually support movement and locomotion.
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Affiliation(s)
- Maria Giulia Bigotti
- School of Translational Health Sciences, Research Floor Level 7, Bristol Royal Infirmary, Upper Maudlin Street, Bristol BS2 8HW, UK,School of Biochemistry, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Andrea Brancaccio
- School of Biochemistry, University Walk, University of Bristol, Bristol BS8 1TD, UK,Institute of Chemical Sciences and Technologies ‘Giulio Natta’ (SCITEC) - CNR, Largo F.Vito 1, 00168, Rome, Italy
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2
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Evans LS, Hussain R, Siligardi G, Williamson PT. Magnetically aligned membrane mimetics enabling comparable chiroptical and magnetic resonance spectroscopy studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183343. [DOI: 10.1016/j.bbamem.2020.183343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
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3
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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4
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Irvine WA, Flanagan JU, Allison JR. Computational Prediction of Amino Acids Governing Protein-Membrane Interaction for the PIP3 Cell Signaling System. Structure 2019; 27:371-380.e3. [DOI: 10.1016/j.str.2018.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/13/2018] [Accepted: 10/18/2018] [Indexed: 10/27/2022]
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5
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TPC2 polymorphisms associated with a hair pigmentation phenotype in humans result in gain of channel function by independent mechanisms. Proc Natl Acad Sci U S A 2017; 114:E8595-E8602. [PMID: 28923947 DOI: 10.1073/pnas.1705739114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Two-pore channels (TPCs) are endolysosomal cation channels. Two members exist in humans, TPC1 and TPC2. Functional roles associated with the ubiquitously expressed TPCs include VEGF-induced neoangiogenesis, LDL-cholesterol trafficking and degradation, physical endurance under fasting conditions, autophagy regulation, the acrosome reaction in sperm, cancer cell migration, and intracellular trafficking of pathogens such as Ebola virus or bacterial toxins (e.g., cholera toxin). In a genome-wide association study for variants associated with human pigmentation characteristics two coding variants of TPC2, rs35264875 (encoding M484L) and rs3829241 (encoding G734E), have been found to be associated with a shift from brown to blond hair color. In two recent follow-up studies a role for TPC2 in pigmentation has been further confirmed. However, these human polymorphic variants have not been functionally characterized until now. The development of endolysosomal patch-clamp techniques has made it possible to investigate directly ion channel activities and characteristics in isolated endolysosomal organelles. We applied this technique here to scrutinize channel characteristics of the polymorphic TPC2 variants in direct comparison with WT. We found that both polymorphisms lead to a gain of channel function by independent mechanisms. We next conducted a clinical study with more than 100 blond- and brown/black-haired individuals. We performed a genotype/phenotype analysis and subsequently isolated fibroblasts from WT and polymorphic variant carriers for endolysosomal patch-clamp experimentation to confirm key in vitro findings.
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6
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Gronnier J, Crowet JM, Habenstein B, Nasir MN, Bayle V, Hosy E, Platre MP, Gouguet P, Raffaele S, Martinez D, Grelard A, Loquet A, Simon-Plas F, Gerbeau-Pissot P, Der C, Bayer EM, Jaillais Y, Deleu M, Germain V, Lins L, Mongrand S. Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains. eLife 2017; 6:e26404. [PMID: 28758890 PMCID: PMC5536944 DOI: 10.7554/elife.26404] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function.
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Affiliation(s)
- Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Jean-Marc Crowet
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Mehmet Nail Nasir
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, CNRS, University of BordeauxBordeauxFrance
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | | | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Axelle Grelard
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Christophe Der
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
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7
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Leung YM, Holdbrook DA, Piggot TJ, Khalid S. The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations. Biophys J 2015; 107:460-468. [PMID: 25028887 DOI: 10.1016/j.bpj.2014.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/19/2023] Open
Abstract
The multidrug and toxic compound extrusion transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. The substrates transported by these proteins include toxic metabolites and antimicrobial drugs. These proteins contribute to multidrug resistance in both mammalian and bacterial cells and are therefore extremely important from a biomedical perspective. Although specific residues of the protein are known to be responsible for the extrusion of solutes, mechanistic details and indeed structures of all the conformational states remain elusive. Here, we report the first, to our knowledge, simulation study of the recently resolved x-ray structure of the multidrug and toxic compound extrusion transporter, NorM from Neisseria gonorrhoeae (NorM_NG). Multiple, atomistic simulations of the unbound and bound forms of NorM in a phospholipid lipid bilayer allow us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein. In particular, we identify the molecular rearrangements that occur to enable the Na(+) ion to enter the cation-binding cavity even in the presence of a bound drug molecule. These include side chain flipping of a key residue, GLU-261 from pointing toward the central cavity to pointing toward the cation binding side when bound to a Na(+) ion. Our simulations also provide support for cation binding in the drug-bound and apo states of NorM_NG.
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Affiliation(s)
- Yuk Ming Leung
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Daniel A Holdbrook
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
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8
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Stanishneva-Konovalova T, Sokolova O. Molecular dynamics simulations of negatively charged DPPC/DPPI lipid bilayers at two levels of resolution. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Abstract
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
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10
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Deleu M, Crowet JM, Nasir MN, Lins L. Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3171-3190. [DOI: 10.1016/j.bbamem.2014.08.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
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11
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Morriss-Andrews A, Brown FLH, Shea JE. A coarse-grained model for peptide aggregation on a membrane surface. J Phys Chem B 2014; 118:8420-32. [PMID: 24791936 DOI: 10.1021/jp502871m] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aggregation of peptides on a lipid bilayer is studied using coarse-grained molecular dynamics in implicit solvent. Peptides bind to and self-assemble on the membrane surface into β-rich fibrillar aggregates, even under conditions where only disordered oligomers form in bulk solution. Relative to a solid surface, the membrane surface facilitates peptide mobility and a more complex network of morphology transitions as aggregation proceeds. Additionally, final aggregate structures realized on the membrane surface are distinct from those observed on a comparable solid surface. The aggregated fibrils alter the local structure and material properties of the lipid bilayer in their immediate vicinity but have only a modest effect on the overall bending rigidity of the bilayer.
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Affiliation(s)
- Alex Morriss-Andrews
- Department of Physics, University of California Santa Barbara , Santa Barbara, California 93106, United States
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12
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Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
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Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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13
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Influence of lipids on protein-mediated transmembrane transport. Chem Phys Lipids 2013; 169:57-71. [PMID: 23473882 DOI: 10.1016/j.chemphyslip.2013.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins are responsible for transporting ions and small molecules across the hydrophobic region of the cell membrane. We are reviewing the evidence for regulation of these transport processes by interactions with the lipids of the membrane. We focus on ion channels, including potassium channels, mechanosensitive and pentameric ligand gated ion channels, and active transporters, including pumps, sodium or proton driven secondary transporters and ABC transporters. For ion channels it has been convincingly shown that specific lipid-protein interactions can directly affect their function. In some cases, a combined approach of molecular and structural biology together with computer simulations has revealed the molecular mechanisms. There are also many transporters whose activity depends on lipids but understanding of the molecular mechanisms is only beginning.
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14
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15
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Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ. The simulation approach to lipid-protein interactions. Methods Mol Biol 2013; 974:435-455. [PMID: 23404287 DOI: 10.1007/978-1-62703-275-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.
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Affiliation(s)
- Teresa Paramo
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK
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16
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Abstract
The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.
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Affiliation(s)
- Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
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17
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Piggot TJ, Piñeiro Á, Khalid S. Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. J Chem Theory Comput 2012; 8:4593-609. [DOI: 10.1021/ct3003157] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas J. Piggot
- School of Chemistry, University
of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Department of Applied Physics,
University of Santiago de Compostela, Campus Vida, 15782, Santiago
de Compostela, Spain
| | - Syma Khalid
- School of Chemistry, University
of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
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18
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Orsi M, Essex JW. The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One 2011; 6:e28637. [PMID: 22194874 PMCID: PMC3241685 DOI: 10.1371/journal.pone.0028637] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/11/2011] [Indexed: 02/05/2023] Open
Abstract
A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r) = 1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Southampton, United Kingdom.
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19
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Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:199-207. [PMID: 22075563 PMCID: PMC3269570 DOI: 10.1007/s00249-011-0773-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/10/2011] [Accepted: 10/24/2011] [Indexed: 01/07/2023]
Abstract
Fukutin-I is localised to the endoplasmic reticulum or Golgi apparatus within the cell, where it is believed to function as a glycosyltransferase. Its localisation within the cell is thought to to be mediated by the interaction of its N-terminal transmembrane domain with the lipid bilayers surrounding these compartments, each of which possesses a distinctive lipid composition. However, it remains unclear at the molecular level how the interaction between the transmembrane domains of this protein and the surrounding lipid bilayer drives its retention within these compartments. In this work, we employed chemical cross-linking and fluorescence resonance energy transfer measurements in conjunction with multiscale molecular dynamics simulations to determine the oligomeric state of the protein within dilauroylphosphatidylcholine bilayers to identify interactions between the transmembrane domains and to ascertain any role these interactions may play in protein localisation. Our studies reveal that the N-terminal transmembrane domain of Fukutin-I exists as dimer within dilauroylphosphatidylcholine bilayers and that this interaction is driven by interactions between a characteristic TXXSS motif. Furthermore residues close to the N-terminus that have previously been shown to play a key role in the clustering of lipids are shown to also play a major role in anchoring the protein in the membrane.
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