1
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Majumder A, Gu Y, Chen YC, An X, Reinhard BM, Straub JE. Probing the Origins of the Disorder-to-Order Transition of a Modified Cholesterol in Ternary Lipid Bilayers. J Am Chem Soc 2024; 146:27725-27735. [PMID: 39315765 DOI: 10.1021/jacs.4c09495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
In a recent study, spectroscopic observations of modified cholesterol in both lipid-coated nanoparticles and liposomes provided evidence for a disorder-to-order orientational transition with increasing temperature. Below a critical temperature, in a membrane composed of modified cholesterol, saturated (DPPC) lipid, and anionic (DOPS) lipid, a roughly equal population of head-out and head-in conformations was observed. Surprisingly, as temperature was increased the modified cholesterol presented an abrupt transition to a population of all head-in orientations. Additionally, when saturated DPPC lipids were replaced by unsaturated DOPC the disorder-to-order transition was eliminated. To gain insight into this curious transition, we use all-atom molecular dynamics simulations to characterize the structure and fluctuations of lipid bilayers composed of saturated and unsaturated lipids, in the presence of normal and modified cholesterol. Free energy differences between head-out and head-in conformations are computed as a function of varying lipid membrane composition for normal and modified cholesterol. In bilayers primarily composed of DPPC, the orientation of modified cholesterol is observed to depend sensitively on the orientation of the surrounding normal or modified cholesterol molecules, suggesting cooperative Ising-like interactions favoring an ordered state. In bilayers primarily composed of DOPC, spontaneous flip-flop of modified cholesterol is observed, consistent with the measured small free energy barrier separating the head-in and head-out orientations. This combined experimental and computational study effectively characterizes the orientational dimorphism and provides novel insight into the fundamental nature of cholesterol interactions in membrane.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuanqing Gu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - Yi-Chen Chen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Xingda An
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - Björn M Reinhard
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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2
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Shikata K, Kasahara K, Watanabe NM, Umakoshi H, Kim K, Matubayasi N. Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures. J Chem Phys 2024; 161:015102. [PMID: 38958163 DOI: 10.1063/5.0208008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting a considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoylphosphatidylcholine (DPPC) and palmitoyl sphingomyelin; they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with a particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303 K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5-2.5. In the liquid-crystalline phase at 323 K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems.
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Affiliation(s)
- Kokoro Shikata
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nozomi Morishita Watanabe
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Pantelopulos GA, Abraham CB, Straub JE. Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease. Annu Rev Biophys 2024; 53:455-486. [PMID: 38382114 DOI: 10.1146/annurev-biophys-062823-023436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease. We propose that cholesterol impacts the genesis of Aβ not through direct interaction with proteins in the bilayer, but indirectly by inducing the liquid-ordered phase and accompanying liquid-liquid phase separations, which partition proteins in the amyloid cascade to different lipid domains and ultimately to different endocytotic pathways. We explore the full process of Aβ genesis in the context of liquid-ordered phases induced by cholesterol, including protein partitioning into lipid domains, mechanisms of endocytosis experienced by lipid domains and secretases, and pH-controlled activation of amyloid precursor protein secretases in specific endocytotic environments. Outstanding questions on the essential role of cholesterol in the amyloid cascade are identified for future studies.
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Affiliation(s)
| | - Conor B Abraham
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
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4
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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024; 20:4998-5013. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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5
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Di Bartolo AL, Caparotta M, Polo LM, Masone D. Myomerger Induces Membrane Hemifusion and Regulates Fusion Pore Expansion. Biochemistry 2024; 63:815-826. [PMID: 38349279 DOI: 10.1021/acs.biochem.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Membrane fusion is a crucial mechanism in a wide variety of important events in cell biology from viral infection to exocytosis. However, despite many efforts and much progress, cell-cell fusion has remained elusive to our understanding. Along the life of the fusion pore, large conformational changes take place from the initial lipid bilayer bending, passing through the hemifusion intermediates, and ending with the formation of the first nascent fusion pore. In this sense, computer simulations are an ideal technique for describing such complex lipid remodeling at the molecular level. In this work, we studied the role played by the muscle-specific membrane protein Myomerger during the formation of the fusion pore. We have conducted μs length atomistic and coarse-grained molecular dynamics, together with free-energy calculations using ad hoc collective variables. Our results show that Myomerger favors the hemifusion diaphragm-stalk transition, reduces the nucleation-expansion energy difference, and promotes the formation of nonenlarging fusion pores.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Marcelo Caparotta
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Luis Mariano Polo
- Instituto de Histología y Embriología de Mendoza (IHEM)─Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM)─Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
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6
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Simeral ML, Demers SME, Sheth K, Hafner JH. A Raman spectral marker for the iso-octyl chain structure of cholesterol. ANALYTICAL SCIENCE ADVANCES 2024; 5:2300057. [PMID: 38828085 PMCID: PMC11142391 DOI: 10.1002/ansa.202300057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 06/05/2024]
Abstract
Raman spectroscopy provides label-free, specific analysis of biomolecular structure and interactions. It could have a greater impact with improved characterization of complex fingerprint vibrations. Many Raman peaks have been assigned to cholesterol, for example, but the molecular vibrations associated with those peaks are not known. In this report, time-dependent density functional theory calculations of the Raman spectrum of cholesterol are compared to measurements on microcrystalline powder to identify 23 peaks in the Raman spectrum. Among them, a band of six peaks is found to be sensitive to the conformational structure of cholesterol's iso-octyl chain. Calculations on 10 conformers in this spectral band are fit to experimental spectra to probe the cholesterol chain structure in purified powder and in phospholipid vesicles. In vesicles, the chain is found to bend perpendicular to the steroid rings, supporting the case that the chain is a dynamic structure that contributes to lipid condensation and other effects of cholesterol in biomembranes. Statement of Significance: Here we use density functional theory to identify a band of six peaks in cholesterol's Raman spectrum that is sensitive to the conformational structure of cholesterol's chain. Raman spectra were analyzed to show that in fluid-phase lipid membranes, about half of the cholesterol chains point perpendicular to the steroid rings. This new method of label-free structural analysis could make significant contributions to our understanding of cholesterol's critical role in biomembrane structure and function. More broadly, the results show that computational quantum chemistry Raman spectroscopy can make significant new contributions to molecular structure when spectra are interpreted with computational quantum chemistry.
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Affiliation(s)
| | | | - Kyle Sheth
- Department of Physics and AstronomyRice UniversityHoustonTexasUSA
| | - Jason H. Hafner
- Department of Physics and AstronomyRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
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7
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Ramirez JM, Calderon-Zavala AC, Balaram A, Heldwein EE. In vitro reconstitution of herpes simplex virus 1 fusion identifies low pH as a fusion co-trigger. mBio 2023; 14:e0208723. [PMID: 37874146 PMCID: PMC10746285 DOI: 10.1128/mbio.02087-23] [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: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE HSV-1 causes lifelong, incurable infections and diseases ranging from mucocutaneous lesions to fatal encephalitis. Fusion of viral and host membranes is a critical step in HSV-1 infection of target cells that requires multiple factors on both the viral and host sides. Due to this complexity, many fundamental questions remain unanswered, such as the identity of the viral and host factors that are necessary and sufficient for HSV-1-mediated membrane fusion and the nature of the fusion trigger. Here, we developed a simplified in vitro fusion assay to examine the fusion requirements and identified low pH as a co-trigger for virus-mediated fusion in vitro. We hypothesize that low pH has a critical role in cell entry and, potentially, pathogenesis.
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Affiliation(s)
- J. Martin Ramirez
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Medical Scientist Training Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Ariana C. Calderon-Zavala
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Ariane Balaram
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Medical Scientist Training Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
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8
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Poruthoor AJ, Sharma A, Grossfield A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophys J 2023; 122:4144-4159. [PMID: 37742069 PMCID: PMC10645549 DOI: 10.1016/j.bpj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
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Affiliation(s)
- Ashlin J Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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9
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Gupta S, Soni J, Kumar A, Mandal T. Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures. J Chem Phys 2023; 159:165102. [PMID: 37873964 DOI: 10.1063/5.0167144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023] Open
Abstract
Structural and mechanical properties of membranes such as thickness, tail order, bending modulus and curvature energetics play crucial role in controlling various cellular functions that depend on the local lipid organization and membrane reshaping. While behavior of these biophysical properties are well understood in single component membranes, very little is known about how do they change in the mixed lipid membranes. Often various properties of the mixed lipid bilayers are assumed to change linearly with the mole fractions of the constituent lipids which, however, is true for "ideal" mixing only. In this study, using molecular dynamics simulations, we show that structural and mechanical properties of binary lipid mixture change nonlinearly with the lipid mole fractions, and the strength of the nonlinearity depends on two factors - spontaneous curvature difference and locally inhomogeneous interactions between the lipid components.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jatin Soni
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Awneesh Kumar
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
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10
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Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
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Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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11
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Abraham CB, Xu L, Pantelopulos GA, Straub JE. Characterizing the transmembrane domains of ADAM10 and BACE1 and the impact of membrane composition. Biophys J 2023; 122:3999-4010. [PMID: 37658602 PMCID: PMC10560698 DOI: 10.1016/j.bpj.2023.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
The β-secretase, BACE1, and the α-secretase, ADAM10, are known to competitively cleave amyloid precursor protein (APP) in the amyloid cascades of Alzheimer's disease. Cleavage of APP by BACE1 produces a 99-residue C-terminal peptide (APP-C99) that is subsequently cleaved by γ-secretase to form amyloid-β (Aβ) protein, whereas cleavage of APP by ADAM10 is nonamyloidogenic. It has been speculated that ADAM10/APP and BACE1/APP interactions are regulated by colocalization within and outside of liquid-ordered membrane domains; however, the mechanism of this regulation and the character of the proteins' transmembrane domains are not well understood. In this work, we have developed and characterized minimal congener sequences for the transmembrane domains of ADAM10 and BACE1 using a multiscale modeling approach combining both temperature replica exchange and conventional molecular dynamics simulations based on the coarse-grained Martini2.2 and all-atom CHARMM36 force fields. Our results show that membrane composition impacts the character of the transmembrane domains of BACE1 and ADAM10, adding credence to the speculation that membrane domains are involved in the etiology of Alzheimer's disease.
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Affiliation(s)
- Conor B Abraham
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - Lin Xu
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston, Massachusetts; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
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12
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Poruthoor AJ, Sharma A, Grossfield A. Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526537. [PMID: 36778479 PMCID: PMC9915641 DOI: 10.1101/2023.01.31.526537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid-liquid phase separation (LLPS) inside the cell often results in biological condensates that can critically impact cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the so-called "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For this reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation - essentially measuring the sign (but not the amplitude) of the free energy change upon separation - rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from molecular dynamics simulations. SIGNIFICANCE Standard molecular dynamics simulations can determine the sign the free energy change upon phase separation, but not the amplitude. We present a new method to determine the phase separation free energy for lipid membranes, based on a enhanced sampling using the weighted ensemble method combined with a novel collective variable, validated using coarse-grained simulations applied to several simple systems. The new method will be valuable as a way to develop models that connect molecular-level structural features to the thermodynamics of phase separation.
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Affiliation(s)
- Ashlin J. Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
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13
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Kim N, Lee JH, Song Y, Lee JH, Schatz GC, Hwang H. Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube. J Phys Chem B 2023. [PMID: 37369069 DOI: 10.1021/acs.jpcb.3c02285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The effect of the protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was assessed by using molecular dynamics (MD) simulations. Anionic (GLU-), neutral zwitterionic (GLU0), and cationic (GLU+) forms of glutamic acid were selected as three different protonation states for an analysis of energetics and diffusivity for acid transport across a cyclic decapeptide nanotube. Based on the solubility-diffusion model, permeability coefficients for the three protonation states of the acid were calculated and compared with experimental results for CPN-mediated glutamate transport through CPNs. Potential of mean force (PMF) calculations reveal that, due to the cation-selective nature of the lumen of CPNs, GLU-, so-called glutamate, shows significantly high free energy barriers, while GLU+ displays deep energy wells and GLU0 has mild free energy barriers and wells inside the CPN. The considerable energy barriers for GLU- inside CPNs are mainly attributed to unfavorable interactions with DMPC bilayers and CPNs and are reduced by favorable interactions with channel water molecules through attractive electrostatic interactions and hydrogen bonding. Unlike the distinct PMF curves, position-dependent diffusion coefficient profiles exhibit comparable frictional behaviors regardless of the charge status of three protonation states due to similar confined environments imposed by the lumen of the CPN. The calculated permeability coefficients for the three protonation states clearly demonstrate that glutamic acid has a strong protonation state dependence for its transport through CPNs, as determined by the energetics rather than the diffusivity of the protonation state. In addition, the permeability coefficients also imply that GLU- is unlikely to pass through a CPN due to the high energy barriers inside the CPN, which is in disagreement with experimental measurements, where a considerable amount of glutamate permeating through the CPN was detected. To resolve the discrepancy between this work and the experimental observations, several possibilities are proposed, including a large concentration gradient of glutamate between the inside and outside of lipid vesicles and bilayers in the experiments, the glutamate activity difference between our MD simulations and experiments, an overestimation of energy barriers due to the artifacts imposed in MD simulations, and/or finally a transformation of the protonation state from GLU- to GLU0 to reduce the energy barriers. Overall, our study demonstrates that the protonation state of glutamic acid has a strong effect on the transport of the acid and suggests a possible protonation state change for glutamate permeating through CPNs.
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Affiliation(s)
- Namho Kim
- Department of Biochemistry, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Ji Hye Lee
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Yeonho Song
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Jeong-Hyung Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - George C Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
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14
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Kwon S, Pantelopulos GA, Straub JE. Efficient calculation of the free energy for protein partitioning using restraining potentials. Biophys J 2023; 122:1914-1925. [PMID: 35962549 PMCID: PMC10257010 DOI: 10.1016/j.bpj.2022.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
An approach for the efficient simulation of phase-separated lipid bilayers, for use in the calculation of equilibrium free energies of partitioning between lipid domains, is proposed. The methodology exploits restraint potentials and rectangular aspect ratios that enforce lipid phase separation, allowing for the simulation of smaller systems that approximately reproduce bulk behavior. The utility of this approach is demonstrated through the calculation of potentials of mean force for the translation of a transmembrane protein between lipid domains. The impact of the imposed restraints on lipid tail ordering and lipid packing are explored, providing insight into how restraints can best be employed to compute accurate free-energy surfaces. This approach should be useful in the accurate calculation of equilibrium partition coefficients for transmembrane protein partitioning in heterogeneous membranes, providing insight into the thermodynamic driving forces that control this fundamental biophysical phenomenon.
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Affiliation(s)
- Seulki Kwon
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston, Massachusetts; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
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15
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Higuchi Y, Bohinc K, Reščič J, Shimokawa N, Ito H. Coarse-grained molecular dynamics simulation of cation distribution profiles on negatively charged lipid membranes during phase separation. SOFT MATTER 2023; 19:3640-3651. [PMID: 37162535 DOI: 10.1039/d3sm00222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Revealing the ion distributions on a charged lipid membrane in aqueous solution under the influence of long-range interactions is essential for understanding the origin of the stability of the bilayer structure and the interaction between biomembranes and various electrolytes. However, the ion distributions and their dynamics associated with the phase separation process of the lipid bilayer membrane are still unclear. We perform coarse-grained molecular dynamics simulations to reveal the Na+ and Cl- distributions on charged phospholipid bilayer membranes during phase separation. During the phase separation, cations closely follow the position of negatively charged lipids on a microsecond timescale and are rapidly redistributed parallel to the lipid bilayer. In the homogenous mixture of zwitterionic and negatively charged lipids, cations weakly follow negatively charged lipids, indicating the strong interaction between cations and negatively charged lipids. We also compare cation concentrations as a function of surface charge density obtained by our simulation with those obtained by a modified Poisson-Boltzmann theory. Including the ion finite size makes the statistical results consistent, suggesting the importance of the ion-ion interactions in aqueous solution. Our simulation results advance our understanding of ion distribution during phase separation.
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Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena 5, SI 1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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16
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Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proc Natl Acad Sci U S A 2022; 119:e2212207119. [PMID: 36538482 PMCID: PMC9907117 DOI: 10.1073/pnas.2212207119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 99-residue C-terminal domain of amyloid precursor protein (APP-C99), precursor to amyloid beta (Aβ), is a transmembrane (TM) protein containing intrinsically disordered N- and C-terminal extramembrane domains. Using molecular dynamics (MD) simulations, we show that the structural ensemble of the C99 monomer is best described in terms of thousands of states. The C99 monomer has a propensity to form β-strand in the C-terminal extramembrane domain, which explains the slow spin relaxation times observed in paramagnetic probe NMR experiments. Surprisingly, homodimerization of C99 not only narrows the conformational ensemble from thousands to a few states through the formation of metastable β-strands in extramembrane domains but also stabilizes extramembrane α-helices. The extramembrane domain structure is observed to dramatically impact the homodimerization motif, resulting in the modification of TM domain conformations. Our study provides an atomic-level structural basis for communication between the extramembrane domains of the C99 protein and TM homodimer formation. This finding could serve as a general model for understanding the influence of disordered extramembrane domains on TM protein structure.
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17
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Gupta S, Mandal T. Simulation study of domain formation in a model bacterial membrane. Phys Chem Chem Phys 2022; 24:18133-18143. [PMID: 35856570 DOI: 10.1039/d2cp01873j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental studies revealed that functional membrane microdomains (FMMs) are formed in prokaryotic cells which are structurally and functionally similar to the lipid rafts formed in eukaryotic cells. In this study, we employ coarse-grained molecular dynamics simulations to investigate the mechanism of domain formation and its physiochemical properties in a model methicillin-resistant staphylococcus aureus (MRSA) cell membrane. We find that domains are formed through lateral segregation of staphyloxanthin (STX), a carotenoid which shields the bacteria from the host's immune because of its antioxidant nature. Simulation results suggest that membrane integrity increases with the size of the domain, which is assessed by computing bond order parameter of the lipid tails, membrane expansion modulus and water permeability across the membrane. Various membrane domain proteins such as flotillin-like protein floA and penicillin binding protein (PBP2a) preferentially bind with the STX and accumulate in the membrane domain which is consistent with the recent experimental results.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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18
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Majumder A, Kwon S, Straub JE. On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes. J Chem Theory Comput 2022; 18:3961-3971. [PMID: 35580264 PMCID: PMC11260346 DOI: 10.1021/acs.jctc.2c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein association in lipid membranes is fundamental to membrane protein function and of great biomedical relevance. All-atom and coarse-grained models have been extensively used to understand the protein-protein interactions in the membrane and to compute equilibrium association constants. However, slow translational and rotational diffusion of protein in membrane presents challenges to the effective sampling of conformations defining the ensembles of free and bound states contributing to the association equilibrium and the free energy of dimerization. We revisit the homodimerization equilibrium of the TM region of glycophorin A. Conformational sampling is performed using umbrella sampling along previously proposed one-dimensional collective variables and compared with sampling over a two-dimensional collective variable space using the MARTINI v2.2 force field. We demonstrate that the one-dimensional collective variables suffer from restricted sampling of the native homodimer conformations leading to a biased free energy landscape. Conversely, simulations along the two-dimensional collective variable effectively characterize the thermodynamically relevant native and non-native interactions contributing to the association equilibrium. These results demonstrate the challenges associated with accurately characterizing binding equilibria when multiple poses contribute to the bound state ensemble.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Seulki Kwon
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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19
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Qin X, Tieleman DP, Liang Q. Effects of Cholesterol and PIP2 on Interactions between Glycophorin A and Band 3 in Lipid Bilayers. Biophys J 2022; 121:2069-2077. [PMID: 35524411 DOI: 10.1016/j.bpj.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/02/2022] Open
Abstract
In the erythrocyte membrane, the interactions between Glycophorin A (GPA) and Band 3 are associated strongly with the biological function of the membrane and several blood disorders. In this work, using coarse-grained molecular dynamics simulation, we systematically investigate the effects of cholesterol and phosphatidylinositol-4,5-bisphosphate (PIP2) on the interactions of GPA with Band 3 in the model erythrocyte membranes. We examine the dynamics of the interactions of GPA with Band 3 in different lipid bilayers on the microsecond time scale and calculate the binding free energy between GPA and Band 3. The results indicate that cholesterols thermodynamically favor the binding of GPA to Band 3 by increasing the thickness of the lipid bilayer and by producing an effective attraction between the proteins due to the depletion effect. Cholesterols also slow the kinetics of the binding of GPA to Band 3 by reducing the lateral mobility of the lipids and proteins and may influence the binding sites between the proteins. The anionic PIP2 lipids prefer binding to the surface of the proteins through electrostatic attraction between the PIP2 headgroup and the positively charged residues on the protein surface. Ions in the solvent facilitate the PIP2 aggregation which promotes the binding of GPA to Band 3.
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Affiliation(s)
- Xiaoxue Qin
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D Peter Tieleman
- Centre for Molecular Simulations and Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China.
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20
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Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM. Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study. Arch Biochem Biophys 2022; 717:109136. [DOI: 10.1016/j.abb.2022.109136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/02/2022]
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21
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Song ES, Oh Y, Sung BJ. Interdomain exchange and the flip-flop of cholesterol in ternary component lipid membranes and their effects on heterogeneous cholesterol diffusion. Phys Rev E 2021; 104:044402. [PMID: 34781553 DOI: 10.1103/physreve.104.044402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/17/2021] [Indexed: 11/07/2022]
Abstract
Cell membranes are heterogeneous with a variety of lipids, cholesterol, and proteins and are composed of domains of different compositions. Such heterogeneous environments make the transport of cholesterol complicated: cholesterol not only diffuses within a particular domain but also travels between domains. Cholesterol also flip-flops between upper and lower leaflets such that cholesterol may reside both within leaflets and in the central region between two leaflets. How the presence of multiple domains and the interdomain exchange of cholesterol would affect the cholesterol transport, however, remains elusive. In this study, therefore, we perform molecular dynamics simulations up to 100μs for ternary component lipid membranes, which consist of saturated lipids (dipalmitoylphosphatidylcholine, DPPC), unsaturated lipids (dilinoleylphosphatidylcholine, DIPC), and cholesterol. The ternary component membranes in our simulations form two domains readily: DPPC and DIPC domains. We find that the diffusion of cholesterol molecules is much more heterogeneous and non-Gaussian than expected for binary component lipid membranes of lipids and cholesterol. The non-Gaussian parameter of the cholesterol molecules is about four times larger in the ternary component lipid membranes than in the binary component lipid membranes. Such non-Gaussian and heterogeneous transport of cholesterol arises from the interplay among the interdomain kinetics, the different diffusivity of cholesterol in different domains, and the flip-flop of cholesterol. This suggests that in cell membranes that consist of various domains and proteins, the cholesterol transport can be very heterogeneous. We also find that the mechanism of the interdomain exchange differs for different domains: cholesterol tends to exit the DIPC domain along the central region of the membrane for the DIPC-to-DPPC transition, while the cholesterol is likely to exit the DPPC domain within the membrane leaflet for the DPPC-to-DIPC transition. Also, the interdomain exchange kinetics of cholesterol for the DPPC-to-DIPC transition is up to 7.9 times slower than the DIPC-to-DPPC transition.
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Affiliation(s)
- Eun Sub Song
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Younghoon Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
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22
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Suga K, Matsui D, Watanabe N, Okamoto Y, Umakoshi H. Insight into the Exosomal Membrane: From Viewpoints of Membrane Fluidity and Polarity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11195-11202. [PMID: 34528800 DOI: 10.1021/acs.langmuir.1c00687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous research studies have been done for exosomes, particularly focusing on membrane proteins and included nucleic acids, and the volume of the knowledge about the lipids in the exosomal membrane has been increasing. However, the dynamic property of the exosomal membrane is hardly studied. By employing milk exosome as an example, herein the exosomal membrane was characterized focusing on the membrane fluidity and polarity. The lipid composition and phase state of milk exosome (exosome from bovine milk) were estimated. The milk exosome contained enriched Chol (43.6 mol % in total lipid extracts), which made the membrane in the liquid-ordered (lo) phase by interacting with phospholipids. To suggest a model of exosomal vesicle cargo, the liposome compositions that mimic milk exosome were studied: liposomes were made of cholesterol (Chol), milk sphingomyelin (milk SM), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). By using fluorescent probes 1,6-diphenyl-1,3,5-hexatriene and 6-dodecanoyl-2-dimethylaminonaphthalene, the microenvironments of submicron-sized membranes of exosome and model liposomes were investigated. The membrane fluidity of milk exosome was slightly higher than those of Chol/milk SM/POPC liposomes with a similar content of Chol, suggesting the presence of enriched unsaturated lipids. The most purposeful membrane property was obtained by the liposome composition of Chol/milk SM/POPC = 40/15/45. From the above, it is concluded that Chol is a fundamental component of the milk exosomal membrane to construct the enriched lo phase, which could increase the membrane rigidity and contribute to the function of exosome.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
- Department of Chemical Engineering, Tohoku University, 6-6-07 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 9808579, Japan
| | - Daiki Matsui
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Nozomi Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Yukihiro Okamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
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23
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Unguryan VV, Golysheva EA, Dzuba SA. Double Electron-Electron Resonance of Spin-Labeled Cholestane in Model Membranes: Evidence for Substructures inside the Lipid Rafts. J Phys Chem B 2021; 125:9557-9563. [PMID: 34387998 DOI: 10.1021/acs.jpcb.1c05215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasma membranes are assumed to be highly compartmentalized, which is believed to be important for the membrane protein functionality. The liquid ordered-disordered phase segregation in the membranes results in nanoscale liquid-ordered assemblies-lipid rafts. Double electron-electron resonance spectroscopy (DEER, also known as PELDOR) is sensitive to spin-spin dipolar interactions between spin labels at the nanoscale range of distances. Here, DEER is applied to spin-labeled cholestane, 3β-doxyl-5α-cholestane (DChl), diluted in bilayers composed of an equimolar mixture of dioleoyl-glycero-phosphocholine (DOPC) and dipalmitoyl-glycero-phosphocholine (DPPC) phospholipids, with cholesterol (Chol) added. The DEER data allowed us to detect clustering of the DChl molecules. Their lateral distribution in the clusters in the absence of Chol was found to be random, while in the presence of Chol it became quasi-regular. DEER time traces are fairly well simulated within a simple square superlattice model. For the 20 mol % Chol content, for which at physiological temperatures, the lipid rafts are formed, the found superlattice parameter was 3.7 nm. Assuming that lipid rafts are captioned upon shock freezing at the temperature of investigation (80 K), the found regularity of DChl lateral distribution was interpreted by raft substructuring, with the DChl molecules embedded between the substructures.
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Affiliation(s)
- Vasily V Unguryan
- Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
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24
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Dutta A, Vreeken J, Ghiringhelli LM, Bereau T. Data-driven equation for drug-membrane permeability across drugs and membranes. J Chem Phys 2021; 154:244114. [PMID: 34241352 DOI: 10.1063/5.0053931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally consider the functional relationship between passive permeation and acidity. To discover easily interpretable equations that explain the data well, we use the recently proposed sure-independence screening and sparsifying operator (SISSO), an artificial-intelligence technique that combines symbolic regression with compressed sensing. Our study is based on a large in silico dataset of 0.4 × 106 small molecules extracted from coarse-grained simulations. We rationalize the equation suggested by SISSO via an analysis of the inhomogeneous solubility-diffusion model in several asymptotic acidity regimes. We further extend our analysis to the dependence on lipid-membrane composition. Lipid-tail unsaturation plays a key role but surprisingly contributes stepwise rather than proportionally. Our results are in line with previously observed changes in permeability, suggesting the distinction between liquid-disordered and liquid-ordered permeation. Together, compressed sensing with analytically derived asymptotes establish and validate an accurate, broadly applicable, and interpretable equation for passive permeability across both drug and lipid-tail chemistry.
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Affiliation(s)
- Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Luca M Ghiringhelli
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
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25
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Novinger Q, Suma A, Sigg D, Gonnella G, Carnevale V. Particle-based Ising model. Phys Rev E 2021; 103:012125. [PMID: 33601607 DOI: 10.1103/physreve.103.012125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/01/2021] [Indexed: 01/13/2023]
Abstract
We characterize equilibrium properties and relaxation dynamics of a two-dimensional lattice containing, at each site, two particles connected by a double-well potential (dumbbell). Dumbbells are oriented in the orthogonal direction with respect to the lattice plane and interact with each other through a Lennard-Jones potential truncated at the nearest neighbor distance. We show that the system's equilibrium properties are accurately described by a two-dimensional Ising model with an appropriate coupling constant. Moreover, we characterize the coarsening kinetics by calculating the cluster size as a function of time and compare the results with Monte Carlo simulations based on Glauber or reactive dynamics rate constants.
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Affiliation(s)
- Quentin Novinger
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA.,Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, 70126 Bari, Italy
| | | | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, 70126 Bari, Italy
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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26
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Elkins MR, Bandara A, Pantelopulos GA, Straub JE, Hong M. Direct Observation of Cholesterol Dimers and Tetramers in Lipid Bilayers. J Phys Chem B 2021; 125:1825-1837. [DOI: 10.1021/acs.jpcb.0c10631] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Matthew R. Elkins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - George A. Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E. Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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27
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Kamble S, Patil S, Kulkarni M, Appala VRM. Interleaflet Decoupling in a Lipid Bilayer at Excess Cholesterol Probed by Spectroscopic Ellipsometry and Simulations. J Membr Biol 2020; 253:647-659. [PMID: 33221946 DOI: 10.1007/s00232-020-00156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/11/2020] [Indexed: 11/26/2022]
Abstract
Artificial lipid membranes are often investigated as a replica of the cell membrane in the form of supported lipid bilayers (SLBs). In SLBs, the phase state of a lipid bilayer strongly depends on the presence of molecules such as cholesterol, ceramide, and physical parameters such as temperature. Cholesterol is a key molecule of biological membranes and it exerts condensing effect on lipid bilayers. In this paper, we demonstrate the influence of excess cholesterol content on a supported lipid bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (fluid-phase) using spectroscopic ellipsometry (SE) and coarse-grained (CG) molecular dynamics (MD) simulations. The results show the condensation effect due to cholesterol addition up to 30% and interleaflet decoupling at excess cholesterol beyond 30%. SE results show the separation of individual leaflets of the bilayer and influence of cholesterol on the biophysical properties such as thickness and optical index. CG simulations were performed at different ratios of DOPC:cholesterol mixtures to explore cholesterol-driven bilayer properties and stability. The simulations displayed the accumulation of cholesterol molecules at the interface of the lower and upper leaflets of the bilayer, thus leading to undulations in the bilayer. This work reports the successful application of SE technique to study lipid-cholesterol interactions for the first time.
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Affiliation(s)
- Sagar Kamble
- Department of Applied Physics, Defence Institute of Advanced Technology (DIAT) DU, Girinagar, Pune, India
| | - Snehal Patil
- Department of Applied Physics, Defence Institute of Advanced Technology (DIAT) DU, Girinagar, Pune, India
| | - Mandar Kulkarni
- Division of Biophysical Chemistry, Chemical Center, Lund University, 22100, Lund, Sweden.
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28
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Pantelopulos GA, Panahi A, Straub JE. Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein. J Phys Chem B 2020; 124:10173-10185. [PMID: 33135883 PMCID: PMC7958706 DOI: 10.1021/acs.jpcb.0c07615] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Elevated levels of cellular cholesterol have been identified as one factor contributing to the onset of Alzheimer's disease (AD). Specific interaction between cholesterol and the amyloid precursor protein (APP), investigated via NMR experiments and computational studies, has been proposed to play a critical role in the processing of APP by secretases and the biogenesis of amyloid-β (Aβ) protein. We present all-atom molecular dynamics simulations of the 40-residue congener of the C-terminal domain of APP, C9916-55 (C99), in cholesterol-enriched DMPC lipid bilayers. We investigated the effect of cholesterol concentration on the conformational ensemble of wild-type C99 and C99-cholesterol associations at the low pH of endosomal environments, at which residues E22 and D23 are neutral. C99 was also characterized in liquid ordered domains for Dutch (E22Q) and Iowa (D23N) Familial AD mutants at low pH and for the wild-type sequence using protonation states characteristic of neutral pH. Our results reproduce the equilibrium constant of past NMR characterizations of the C99-cholesterol interaction but are not consistent with the C99-cholesterol binding hypothesis. We find that the lifetimes of both DMPC and cholesterol complexed with C99 display a power-law distribution of residence lifetimes. Longer-lived C99-DMPC and C99-cholesterol complexes are primarily stabilized by salt bridges and hydrogen bonds of lysine amines to phosphate and hydroxyl groups. Nevertheless, specific interfaces for C99-cholesterol association which are not present for DMPC can be identified. Changes to C99-cholesterol interfaces are found to depend on C99 tilt angle and orientation of the juxtamembrane domain of C99 containing residues E22 and D23. These observations support a more nuanced view of the C99-cholesterol interaction than has previously been suggested. We propose that cholesterol modulates the conformation and activity of C99 and other small transmembrane proteins indirectly through induction of the liquid ordered phase and directly through hydrogen bonding. This suggests a critical role for membrane heterogeneity introduced by cholesterol in modulating the structural ensemble of C99 and the production of Aβ.
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Affiliation(s)
- George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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29
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Sahoo A, Matysiak S. Microscopic Picture of Calcium-Assisted Lipid Demixing and Membrane Remodeling Using Multiscale Simulations. J Phys Chem B 2020; 124:7327-7335. [PMID: 32786720 DOI: 10.1021/acs.jpcb.0c03067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The specificity of anionic phospholipids-calcium ion interaction and lipid demixing has been established as a key regulatory mechanism in several cellular signaling processes. The mechanism and implications of this calcium-assisted demixing have not been elucidated from a microscopic point of view. Here, we present an overview of atomic interactions between calcium and phospholipids that can drive nonideal mixing of lipid molecules in a model lipid bilayer composed of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) lipids with computer simulations at multiple resolutions. Lipid nanodomain formation and growth were driven by calcium-enabled lipid bridging of the charged phosphatidylserine (PS) headgroups, which were favored against inter-POPS dipole interactions. Consistent with several experimental studies of calcium-associated membrane sculpting, our analyses also suggest modifications in local membrane curvature and cross-leaflet couplings as a response to such induced lateral heterogeneity. In addition, reverse mapping to a complementary atomistic description revealed structural insights in the presence of anionic nanodomains, at timescales not accessed by previous computational studies. This work bridges information across multiple scales to reveal a mechanistic picture of calcium ion's impact on membrane biophysics.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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30
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Girard M, Bereau T. Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms. Biophys J 2020; 119:892-899. [PMID: 32814063 DOI: 10.1016/j.bpj.2020.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with phospholipid saturation for reasons that remain unclear. To better understand the link between cell membrane regulation and chemical composition, we establish a computational framework based on chemical reaction networks, resulting in multiple semigrand canonical ensembles. By running computer simulations, we show that regulating the chemical potential of lipid species is sufficient to reproduce the experimentally observed increase in acyl tail saturation with added cholesterol. Our model proposes a different picture of lipid regulation in which components can be regulated passively instead of actively. In this picture, phospholipid acyl tail composition naturally adapts to added molecules such as cholesterol or proteins. A comparison between regulated membranes with commonly studied ternary model membranes shows stark differences: for instance, correlation lengths and viscosities observed are independent of lipid chemical affinity.
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Affiliation(s)
- Martin Girard
- Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany; Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, the Netherlands
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31
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Jin Y, Liang Q, Tieleman DP. Interactions between Band 3 Anion Exchanger and Lipid Nanodomains in Ternary Lipid Bilayers: Atomistic Simulations. J Phys Chem B 2020; 124:3054-3064. [DOI: 10.1021/acs.jpcb.0c01055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yapan Jin
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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32
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Centi A, Dutta A, Parekh SH, Bereau T. Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force. Biophys J 2020; 118:1321-1332. [PMID: 32075746 DOI: 10.1016/j.bpj.2020.01.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/27/2020] [Indexed: 11/29/2022] Open
Abstract
Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.
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Affiliation(s)
- Alessia Centi
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Mainz, Germany; Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany.
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33
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Gupta R, Badhe Y, Mitragotri S, Rai B. Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations. NANOSCALE 2020; 12:6318-6333. [PMID: 32133467 DOI: 10.1039/c9nr09947f] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanoparticles are being explored for topical and oral drug delivery applications as they can cross various biological barriers, for example, the intestinal epithelium. The ability of nanoparticles to cross barriers depends on their morphological and surface properties such as size, surface chemistry and shape, among others. The effect of nanoparticle size on their membrane permeability has been well studied both experimentally and theoretically. However, less attention has been given to understand the role of nanoparticle shape in their translocation across biological barrier membranes. Here, we report on the influence of the nanoparticle's shape, surface chemistry and concentration on their permeation across a human intestinal apical cell membrane model. A representative multicomponent lipid bilayer model of the human intestinal apical membrane was built. The free energy of permeation of nanoparticles across the model lipid bilayer was calculated using multiple umbrella sampling simulations. The interaction of these nanoparticles with the model lipid bilayer was captured using extensive microsecond unrestrained molecular dynamics simulations. We observed that: (a) irrespective of the surface chemistry, the efficacy of nanoparticle penetration across the lipid layer was in the order of rod > disc > sphere; (b) irrespective of the shape, apolar and nonpolar nanoparticles were found to locate in the interior of the lipid bilayer, whereas charged and polar nanoparticles were either adsorbed on the lipid headgroups or remained in the water layer; (c) apolar and nonpolar disc shaped nanoparticles had higher efficacy in permeation across the lipid bilayer as compared to disc and sphere shaped nanoparticles; and (d) at a higher concentration of nanoparticles, sphere and disc shaped nanoparticles exhibited more agglomeration as compared to rod shaped nanoparticles. Based on these outcomes, a few nanoparticles were designed which penetrated readily into the lipid layer and these nanoparticles were also able to co-deliver a therapeutic protein inside the lipid layer. The apical model lipid membrane and protocols used in this study can thus be utilized for the in silico design of nanoparticles for the oral delivery of therapeutics.
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Affiliation(s)
- Rakesh Gupta
- Physical Science Research Area, Tata Research Development and Design Centre, TCS Research, Tata Consultancy Services, 54B, Hadapsar Industrial Estate, Pune 411013, India.
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34
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Hakobyan D, Heuer A. Comparing an All-Atom and a Coarse-Grained Description of Lipid Bilayers in Terms of Enthalpies and Entropies: From MD Simulations to 2D Lattice Models. J Chem Theory Comput 2019; 15:6393-6402. [DOI: 10.1021/acs.jctc.9b00390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Davit Hakobyan
- Institute of Physical Chemistry, WWU Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
- Center for Multiscale Theory and Computation (CMTC), WWU Muenster, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, WWU Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
- Center for Multiscale Theory and Computation (CMTC), WWU Muenster, 48149 Muenster, Germany
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35
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Bandara A, Panahi A, Pantelopulos GA, Nagai T, Straub JE. Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture. J Chem Phys 2019; 150:204702. [PMID: 31153187 DOI: 10.1063/1.5091450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The separation of lipid mixtures into thermodynamically stable phase-separated domains is dependent on lipid composition, temperature, and system size. Using molecular dynamics simulations, the line tension between thermodynamically stable lipid domains formed from ternary mixtures of di-C16:0 PC:di-C18:2 PC:cholesterol at 40:40:20 mol. % ratio was investigated via two theoretical approaches. The line tension was found to be 3.1 ± 0.2 pN by capillary wave theory and 4.7 ± 3.7 pN by pressure tensor anisotropy approaches for coarse-grained models based on the Martini force field. Using an all-atom model of the lipid membrane based on the CHARMM36 force field, the line tension was found to be 3.6 ± 0.9 pN using capillary wave theory and 1.8 ± 2.2 pN using pressure anisotropy approaches. The discrepancy between estimates of the line tension based on capillary wave theory and pressure tensor anisotropy methods is discussed. Inclusion of protein in Martini membrane lipid mixtures was found to reduce the line tension by 25%-35% as calculated by the capillary wave theory approach. To further understand and predict the behavior of proteins in phase-separated membranes, we have formulated an analytical Flory-Huggins model and parameterized it against the simulation results. Taken together these results suggest a general role for proteins in reducing the thermodynamic cost associated with domain formation in lipid mixtures and quantifies the thermodynamic driving force promoting the association of proteins to domain interfaces.
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Affiliation(s)
- Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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36
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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