1
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Hardt M, Busse F, Raschke S, Honnigfort C, Carrascosa-Tejedor J, Wenk P, Gutfreund P, Campbell RA, Heuer A, Braunschweig B. Photo-Responsive Control of Adsorption and Structure Formation at the Air-Water Interface with Arylazopyrazoles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5861-5871. [PMID: 37058525 DOI: 10.1021/acs.langmuir.3c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Smart interfaces that are responsive to external triggers such as light are of great interest for the development of responsive or adaptive materials and interfaces. Using alkyl-arylazopyrazole butyl sulfonate surfactants (alkyl-AAP) that can undergo E/Z photoisomerization when irradiated with green (E) and UV (Z) lights, we demonstrate through a combination of experiments and computer simulations that there can be surprisingly large changes in surface tension and in the molecular structure and order at air-water interfaces. Surface tensiometry, vibrational sum-frequency generation (SFG) spectroscopy, and neutron reflectometry (NR) are applied to the study of custom-synthesized AAP surfactants with octyl- and H-terminal groups at air-water interfaces as a function of their bulk concentration and E/Z configuration. Upon photoswitching, a drastic influence of the alkyl chain on both the surface activity and the responsiveness of interfacial surfactants is revealed from changes in the surface tension, γ, where the largest changes in γ are observed for octyl-AAP (Δγ ∼ 23 mN/m) in contrast to H-AAP with Δγ < 10 mN/m. Results from vibrational SFG spectroscopy and NR show that the interfacial composition and the molecular order of the surfactants drastically change with E/Z photoisomerization and surface coverage. Indeed, from analysis of the S-O (head group) and C-H vibrational bands (hydrophobic tail), a qualitative analysis of orientational and structural changes of interfacial AAP surfactants is provided. The experiments are complemented by resolution of thermodynamic parameters such as equilibrium constants from ultra-coarse-grained simulations, which also capture details like island formation and interaction parameters of interfacial molecules. Here, the interparticle interaction ("stickiness") and the interaction with the surface are adjusted, closely reflecting experimental conditions.
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Affiliation(s)
- Michael Hardt
- Center for Soft Nanoscience, Busso-Peus-Straße 10, 48149 Münster, Germany
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Franziska Busse
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Simon Raschke
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Christian Honnigfort
- Center for Soft Nanoscience, Busso-Peus-Straße 10, 48149 Münster, Germany
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Javier Carrascosa-Tejedor
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
- Division of Pharmacy & Optometry, University of Manchester, M13 9PT Manchester, U.K
| | - Paul Wenk
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Philipp Gutfreund
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Richard A Campbell
- Division of Pharmacy & Optometry, University of Manchester, M13 9PT Manchester, U.K
| | - Andreas Heuer
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
| | - Björn Braunschweig
- Center for Soft Nanoscience, Busso-Peus-Straße 10, 48149 Münster, Germany
- Institute of Physical Chemistry, Corrensstraße 28/30, 48149 Münster, Germany
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2
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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3
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Raschke S, Heuer A. Frame-guided assembly from a theoretical perspective. J Chem Phys 2022; 156:164905. [DOI: 10.1063/5.0084210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress towards fabrics of predefined shape and size, following an initially provided frame of guiding elements. Here we study frame-guided assembly into a two-dimensional membrane via computer simulations, based on a single-bead coarse grained surfactant model in continuous space. In agreement with the experiment the assembly process already starts for surfactant concentrations below the critical micelle concentration. Furthermore, upon increasing temperature the formation process gets more delocalized. Additionally, the assembly process of the resulting membrane plane is modelled by a lattice gas model. It displays a similar phenomenology but additionally allows the derivation of analytical mean-field predictions. In this way a fundamental understanding of frame-guided assembly can be gained.
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Affiliation(s)
- Simon Raschke
- Institute for Physical Chemistry, WWU Münster, Germany
| | - Andreas Heuer
- Physical Chemistry, Westfalische Wilhelms-Universitat Munster Fachbereich 12 Chemie und Pharmazie, Germany
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4
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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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5
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Liu Y, de Vries AH, Pezeshkian W, Marrink SJ. Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:5876-5884. [PMID: 34165988 PMCID: PMC8444333 DOI: 10.1021/acs.jctc.1c00151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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Understanding the
lateral organization in plasma membranes remains
an open problem and is of great interest to many researchers. Model
membranes consisting of coexisting domains are commonly used as simplified
models of plasma membranes. The coarse-grained (CG) Martini force
field has successfully captured spontaneous separation of ternary
membranes into a liquid-disordered and a liquid-ordered domain. With
all-atom (AA) models, however, phase separation is much harder to
achieve due to the slow underlying dynamics. To remedy this problem,
here, we apply the virtual site (VS) hybrid method on a ternary membrane
composed of saturated lipids, unsaturated lipids, and cholesterol
to investigate the phase separation. The VS scheme couples the two
membrane leaflets at CG and AA resolution. We found that the rapid
phase separation reached by the CG leaflet can accelerate and guide
this process in the AA leaflet.
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Affiliation(s)
- Yang Liu
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
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6
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Thallmair S, Javanainen M, Fábián B, Martinez-Seara H, Marrink SJ. Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. J Phys Chem B 2021; 125:9537-9546. [PMID: 34398598 PMCID: PMC8404198 DOI: 10.1021/acs.jpcb.1c03665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Molecular dynamics
(MD) simulations have become an indispensable
tool to investigate phase separation in model membrane systems. In
particular, simulations based on coarse-grained (CG) models have found
widespread use due to their increased computational efficiency, allowing
for simulations of multicomponent lipid bilayers undergoing phase
separation into liquid-ordered and liquid-disordered domains. Here,
we show that a significant temperature difference between molecule
types can artificially arise in CG MD membrane simulations with the
standard Martini simulation parameters in GROMACS. In particular,
the linear constraint solver (LINCS) algorithm does not converge with
its default settings, resulting in serious temperature differences
between molecules in a time step-dependent manner. We demonstrate
that the underlying reason for this behavior is the presence of highly
constrained moieties, such as cholesterol. Their presence can critically
impact numerous structural and dynamic membrane properties obtained
from such simulations. Furthermore, any preference of these molecules
toward a certain membrane phase can lead to spatial temperature gradients,
which can amplify the degree of phase separation or even induce it
in compositions that would otherwise mix well. We systematically investigated
the effect of the integration time step and LINCS settings on membrane
properties. Our data show that for cholesterol-containing membranes,
a time step of 20 fs should be combined with at least lincs_iter = 2 and lincs_order = 12, while using a time
step of 30 fs requires at least lincs_iter =
3 and lincs_order = 12 to bring the temperature
differences to a level where they do not perturb central membrane
properties. Moreover, we show that in cases where stricter LINCS settings
are computationally too demanding, coupling the lipids in multiple
groups to the temperature bath offers a practical workaround to the
problem, although the validity of this approach should be further
verified. Finally, we show that similar temperature gradients can
also emerge in atomistic simulations using the CHARMM force field
in combination with settings that allow for a 5 fs integration step.
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Affiliation(s)
- Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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7
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Yang J, Jin J, Li S. Role of polyunsaturated phospholipids in liquid-ordered and liquid-disordered phases. RSC Adv 2021; 11:27115-27120. [PMID: 35480686 PMCID: PMC9037819 DOI: 10.1039/d1ra02692e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/30/2021] [Indexed: 11/21/2022] Open
Abstract
Polyunsaturated phospholipids play a strong repulsive role in the liquid-disordered phase but a weak role in the liquid-ordered phase.
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Affiliation(s)
- Jing Yang
- College of Education, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Jianyu Jin
- College of Education, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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8
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Mohideen N, Weiner MD, Feigenson GW. Bilayer compositional asymmetry influences the nanoscopic to macroscopic phase domain size transition. Chem Phys Lipids 2020; 232:104972. [PMID: 32941827 DOI: 10.1016/j.chemphyslip.2020.104972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022]
Abstract
The eukaryotic plasma membrane (PM) exhibits lipid mixing heterogeneities known as lipid rafts. These lipid rafts, the result of liquid-liquid phase separation, can be modeled by coexisting liquid ordered (Lo) and liquid disordered (Ld) domains. Four-lipid component systems with a high-melting lipid, a nanodomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol) can give rise to domains of different sizes. These four-component systems have been characterized in experiments, yet there are few studies that model the asymmetric distribution of lipids actually found in the PM. We used molecular dynamics (MD) simulations to analyze the transition from nanoscopic to macroscopic domains in symmetric and in asymmetric model membranes. Using coarse-grained MD simulations, we found that asymmetry promotes macroscopic domain growth in a case where symmetric systems exhibit nanoscopic domains. Also, macroscopic domain formation in symmetric systems is highly dependent on registration of like phases in the cytoplasmic and exoplasmic leaflets. Using united-atom MD simulations, we found that symmetric Lo domains are only slightly more ordered than asymmetric Lo domains. We also found that large Lo domains in our asymmetric systems induce a slight chain ordering in the apposed cytoplasmic regions. The chol fractions of phase-separated Lo and Ld domains of the exoplasmic leaflet were unchanged whether the system was symmetric or asymmetric.
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Affiliation(s)
- Naveen Mohideen
- Cornell University Department of Physics, 117 Clark Hall, Ithaca, New York, 14853, United States; Johns Hopkins University Department of Molecular Biophysics, 101 Jenkins Hall, 3400 N. Charles Street, Baltimore, Maryland, 21218, United States.
| | - Michael D Weiner
- Cornell University Department of Physics, 117 Clark Hall, Ithaca, New York, 14853, United States; Georgia Institute of Technology Partnership for an Advanced Computing Environment, 756 W. Peachtree St. NW, Atlanta, Georgia, 30332, United States.
| | - Gerald W Feigenson
- Cornell University Department of Molecular Biology and Genetics, Room 201 215 Tower Rd. Ithaca, New York, 14853, United States.
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9
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Gupta A, Phang IY, Wohland T. To Hop or not to Hop: Exceptions in the FCS Diffusion Law. Biophys J 2020; 118:2434-2447. [PMID: 32333863 PMCID: PMC7231916 DOI: 10.1016/j.bpj.2020.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Diffusion obstacles in membranes have not been directly visualized because of fast membrane dynamics and the occurrence of subresolution molecular complexes. To understand the obstacle characteristics, mobility-based methods are often used as an indirect way of assessing the membrane structure. Molecular movement in biological plasma membranes is often characterized by anomalous diffusion, but the exact underlying mechanisms are still elusive. Imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS) is a well-established mobility-based method that provides spatially resolved diffusion coefficient maps and is combined with FCS diffusion law analysis to examine subresolution membrane organization. In recent years, although FCS diffusion law analysis has been instrumental in providing new insights into the membrane structure below the optical diffraction limit, there are certain exceptions and anomalies that require further clarification. To this end, we correlate the membrane structural features imaged by atomic force microscopy (AFM) with the dynamics measured using ITIR-FCS. We perform ITIR-FCS measurements on supported lipid bilayers (SLBs) of various lipid compositions to characterize the anomalous diffusion of lipid molecules in distinct obstacle configurations, along with the high-resolution imaging of the membrane structures with AFM. Furthermore, we validate our experimental results by performing simulations on image grids with experimentally determined obstacle configurations. This study demonstrates that FCS diffusion law analysis is a powerful tool to determine membrane heterogeneities implied from dynamics measurements. Our results corroborate the commonly accepted interpretations of imaging FCS diffusion law analysis, and we show that exceptions happen when domains reach the percolation threshold in a biphasic membrane and a network of domains behaves rather like a meshwork, resulting in hop diffusion.
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Affiliation(s)
- Anjali Gupta
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Inn Yee Phang
- Institute of Materials Research and Engineering, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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10
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Liu Y, De Vries AH, Barnoud J, Pezeshkian W, Melcr J, Marrink SJ. Dual Resolution Membrane Simulations Using Virtual Sites. J Phys Chem B 2020; 124:3944-3953. [PMID: 32314586 PMCID: PMC7232679 DOI: 10.1021/acs.jpcb.0c01842] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
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All-atomistic
(AA) and coarse-grain (CG) simulations have been
successfully applied to investigate a broad range of biomolecular
processes. However, the accessible time and length scales of AA simulation
are limited and the specific molecular details of CG simulation are
simplified. Here, we propose a virtual site (VS) based hybrid scheme
that can concurrently couple AA and CG resolutions in a single membrane
simulation, mitigating the shortcomings of either representation.
With some adjustments to make the AA and CG force fields compatible,
we demonstrate that lipid bilayer properties are well kept in our
hybrid approach. Our VS hybrid method was also applied to simulate
a small lipid vesicle, with the inner leaflet and interior solvent
represented in AA, and the outer leaflet together with exterior solvent
at the CG level. Our multiscale method opens the way to investigate
biomembrane properties at increased computational efficiency, in particular
applications involving large solvent filled regions.
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Affiliation(s)
- Yang Liu
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Alex H De Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands
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11
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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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12
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Raschke S, Heuer A. Non-equilibrium effects of micelle formation as studied by a minimum particle-based model. J Chem Phys 2019; 150:204903. [DOI: 10.1063/1.5086618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Simon Raschke
- Westfälische Wilhelms-Universität Münster, Institut für Physikalische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Andreas Heuer
- Westfälische Wilhelms-Universität Münster, Institut für Physikalische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), Corrensstr. 40, D-48149 Münster, Germany
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13
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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: 410] [Impact Index Per Article: 82.0] [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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14
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Aescin-Cholesterol Complexes in DMPC Model Membranes: A DSC and Temperature-Dependent Scattering Study. Sci Rep 2019; 9:5542. [PMID: 30944386 PMCID: PMC6447539 DOI: 10.1038/s41598-019-41865-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/19/2019] [Indexed: 11/09/2022] Open
Abstract
The saponin aescin, a mixture of triterpenoid saponins, is obtained from the seeds of the horse chestnut tree Aesculus hippocastanum. The β-form employed in this study is haemolytically active. The haemolytic activity results from the ability of aescin to form strong complexes with cholesterol in the red blood cell membrane. In this study, we provide a structural analysis on the complex formation of aescin and cholesterol when embedded in a phospholipid model membrane formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). In this work, the temperatures investigated extend from DMPC’s Lβ′ to its Lα phase in dependence of different amounts of the saponin (0–6 mol% for calorimetric and 0–1 mol% for structural analyses) and the steroid (1–10 mol%). At these aescin contents model membranes are conserved in the form of small unilamellar vesicles (SUVs) and major overall structural modifications are avoided. Additionally, interactions between aescin and cholesterol can be studied for both phase states of the lipid, the gel and the fluid state. From calorimetric experiments by differential scanning calorimetry (DSC), it could be shown that both, the steroid and the saponin content, have a significant impact on the cooperative phase transition behaviour of the DMPC molecules. In addition, it becomes clearly visible that the entire phase behaviour is dominated by phase separation which indeed also depends on the complexes formed between aescin and cholesterol. We show by various methods that the addition of cholesterol alters the impact of aescin on structural parameters ranging from the acyl chain correlation to vesicle-vesicle interactions. While the specific saponin-phospholipid interaction is reduced, addition of cholesterol leads to deformation of SUVs. The analyses of the structures formed were performed by wide-angle X-ray scattering (WAXS), small-angle X-ray scattering (SAXS), and small-angle neutron scattering (SANS).
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15
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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16
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Meinhardt S, Schmid F. Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes. SOFT MATTER 2019; 15:1942-1952. [PMID: 30662989 DOI: 10.1039/c8sm02261e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study the lateral domain structure in a coarse-grained molecular model for multicomponent lipid bilayers by semi-grandcanonical Monte Carlo simulations. The membranes are filled with liquid ordered (lo) domains surrounded by a liquid disordered (ld) matrix. Depending on the membrane composition and temperature, we identify different morphological regimes: one regime (I) where the lo domains are small and relatively compact, and two regimes (II, II') where they are larger and often interconnected. In the latter two regimes, the ld matrix forms a network of disordered trenches separating the lo domains, with a relatively high content of interdigitated line defects. Since such defects are also a structural element of the modulated ripple phase in one component membranes, we argue that the regimes II, II' may be amorphous equivalents of the ripple phase in multicomponent membranes. We also analyze the local structure and provide evidence that the domains in regime I are stabilized by a monolayer curvature mechanism postulated in earlier work [S. Meinhardt et al., PNAS, 2013, 110, 4476].
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Affiliation(s)
- Sebastian Meinhardt
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, USA
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17
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Lesch V, Diddens D, Bernardes CES, Golub B, Dequidt A, Zeindlhofer V, Sega M, Schröder C. ForConX: A forcefield conversion tool based on XML. J Comput Chem 2018; 38:629-638. [PMID: 28211110 DOI: 10.1002/jcc.24708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 01/04/2023]
Abstract
The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Volker Lesch
- Westfälische Wilhelms-Universität Münster, Institut für physikalische Chemie, Corrensstraße 28/30, Münster, 48149, Germany
| | - Diddo Diddens
- Westfälische Wilhelms-Universität Münster, Institut für physikalische Chemie, Corrensstraße 28/30, Münster, 48149, Germany
| | - Carlos E S Bernardes
- Centro de Quimica Estrutural, Instituto Superior Técnico, University Lisboa, Av. Rovisco Pais, Lisboa, 1049-001, Portugal
| | - Benjamin Golub
- Institut für Chemie, Physikalische und Theoretische Chemie, Universität Rostock, Dr.-Lorenz-Weg 1, Rostock, 18059, Germany
| | - Alain Dequidt
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6296, Université Blaise Pascal, Université Clermont Auvergne, Aubiere, F-63178, France
| | - Veronika Zeindlhofer
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 19, Vienna 1090, Austria
| | - Marcello Sega
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 19, Vienna 1090, Austria.,Faculty of Physics, University of Vienna, Boltzmanngasse, 5, A-1090, Vienna, Austria
| | - Christian Schröder
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 19, Vienna 1090, Austria
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18
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Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membr Biol 2018; 251:609-631. [PMID: 30350011 PMCID: PMC6244758 DOI: 10.1007/s00232-018-0050-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, UK
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mikkel Christensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark.,Sino-Danish Center for Education and Research, Beijing, China
| | - João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Simona Concilio
- Department of Industrial Engineering, University of Salerno, Fisciano, SA, Italy
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Konstantina Karathanou
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | | | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Antara Mazumdar
- GBB Institute, University of Groningen, Groningen, The Netherlands
| | - Richard Naftalin
- Physiology and Vascular Biology Departments, King's College London School of Medicine, London, UK
| | - Mónica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires, Argentina
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Peter Quinn
- Biochemistry Department, King's College London, London, UK
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
| | - Lucia Sessa
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down Bath, BA2 7AY, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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19
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Pantelopulos GA, Straub JE. Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation. Biophys J 2018; 115:2167-2178. [PMID: 30414630 DOI: 10.1016/j.bpj.2018.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using molecular dynamics simulations, employing a physiologically relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior: 1) miscible liquid-disordered bulk, 2) phase-separated, domain-registered coexistence of liquid-disordered and liquid-ordered domains, and 3) phase-separated, domain-antiregistered coexistence of liquid-disordered and newly identified nanoscopic gel domains composed of cholesterol threads we name "cholesterolic gel" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid-mixture phase separation.
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Affiliation(s)
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
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20
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Carpenter TS, López CA, Neale C, Montour C, Ingólfsson HI, Di Natale F, Lightstone FC, Gnanakaran S. Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. J Chem Theory Comput 2018; 14:6050-6062. [DOI: 10.1021/acs.jctc.8b00496] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timothy S. Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | | | | | - Cameron Montour
- Biochemistry and Molecular Biology Department, Georgetown University, Washington, DC 20057, United States
| | - Helgi I. Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Applications, Simulations, and Quality Division, Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Felice C. Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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21
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Bennett WFD, Shea JE, Tieleman DP. Phospholipid Chain Interactions with Cholesterol Drive Domain Formation in Lipid Membranes. Biophys J 2018; 114:2595-2605. [PMID: 29874610 PMCID: PMC6129184 DOI: 10.1016/j.bpj.2018.04.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 01/13/2023] Open
Abstract
Cholesterol is a key component of eukaryotic membranes, but its role in cellular biology in general and in lipid rafts in particular remains controversial. Model membranes are used extensively to determine the phase behavior of ternary mixtures of cholesterol, a saturated lipid, and an unsaturated lipid with liquid-ordered and liquid-disordered phase coexistence. Despite many different experiments that determine lipid-phase diagrams, we lack an understanding of the molecular-level driving forces for liquid phase coexistence in bilayers with cholesterol. Here, we use atomistic molecular dynamics computer simulations to address the driving forces for phase coexistence in ternary lipid mixtures. Domain formation is directly observed in a long-timescale simulation of a mixture of 1,2-distearoyl-sn-glycero-3-phosphocholine, unsaturated 1,2-dilinoleoyl-sn-glycero-3-phosphocholine, and cholesterol. Free-energy calculations for the exchange of the saturated and unsaturated lipids between the ordered and disordered phases give insight into the mixing behavior. We show that a large energetic contribution to domain formation is favorable enthalpic interactions of the saturated lipid in the ordered phase. This favorable energy for forming an ordered, cholesterol-rich phase is opposed by a large unfavorable entropy. Martini coarse-grained simulations capture the unfavorable free energy of mixing but do not reproduce the entropic contribution because of the reduced representation of the phospholipid tails. Phospholipid tails and their degree of unsaturation are key energetic contributors to lipid phase separation.
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Affiliation(s)
- W F Drew Bennett
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California.
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada.
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22
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He S, Maibaum L. Identifying the Onset of Phase Separation in Quaternary Lipid Bilayer Systems from Coarse-Grained Simulations. J Phys Chem B 2018; 122:3961-3973. [DOI: 10.1021/acs.jpcb.8b00364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shushan He
- Department of Chemistry, University of Washington, Seattle, Washington, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington, United States
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23
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Pantelopulos GA, Nagai T, Bandara A, Panahi A, Straub JE. Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures. J Chem Phys 2017; 147:095101. [PMID: 28886648 PMCID: PMC5648569 DOI: 10.1063/1.4999709] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/19/2017] [Indexed: 12/13/2022] Open
Abstract
Model cellular membranes are known to form micro- and macroscale lipid domains dependent on molecular composition. The formation of macroscopic lipid domains by lipid mixtures has been the subject of many simulation investigations. We present a critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures. In the popular di-C16:0 PC:di-C18:2 PC:cholesterol at 35:35:30 ratio mixture, we find systems with a minimum of 1480 lipids to be necessary for the formation of macroscopic phase separated domains and systems of 10 000 lipids to achieve structurally converged conformations similar to the thermodynamic limit. To understand these results and predict the behavior of any mixture forming two phases, we develop and investigate an analytical Flory-Huggins model which is recursively validated using simulation and experimental data. We find that micro- and macroscale domains can coexist in ternary mixtures. Additionally, we analyze the distributions of specific lipid-lipid interactions in each phase, characterizing domain structures proposed based on past experimental studies. These findings offer guidance in selecting appropriate system sizes for the study of phase separations and provide new insights into the nature of domain structure for a popular ternary lipid mixture.
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Affiliation(s)
- 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
| | - 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
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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24
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Biedermann M, Heuer A. Exploring the free energy gain of phase separation via Markov state modeling. J Chem Phys 2017; 147:034107. [PMID: 28734305 DOI: 10.1063/1.4994065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The gain of free energy upon unmixing is determined via application of Markov state modeling (MSM), using an Ising model with a fixed number of up- and down-spins. MSM yields reasonable estimates of the free energies. However, a closer look reveals significant differences that point to residual non-Markovian effects. These non-Markovian effects are rather unexpected since the typical criteria to study the quality of Markovianity indicate complete Markovian behavior. We identify the sparse connectivity between different Markov states as a likely reason for the observed bias. By studying a simple five state model system, we can analytically elucidate different sources of the bias and thus explain the different deviations that were observed for the Ising model. Based on this insight, we can modify the determination of the count matrix in the MSM approach. In this way, the estimation of the free energy is significantly improved.
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Affiliation(s)
- Myra Biedermann
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
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25
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Hakobyan D, Heuer A. 2D lattice model of a lipid bilayer: Microscopic derivation and thermodynamic exploration. J Chem Phys 2017; 146:064305. [DOI: 10.1063/1.4975163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Davit Hakobyan
- Institute of Physical Chemistry, WWU Münster, Corrensstr. 28/30, 48149 Münster, Germany and Center for Multiscale Theory and Computation (CMTC), WWU Münster, 48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, WWU Münster, Corrensstr. 28/30, 48149 Münster, Germany and Center for Multiscale Theory and Computation (CMTC), WWU Münster, 48149 Münster, Germany
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26
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Ganesan SJ, Xu H, Matysiak S. Influence of Monovalent Cation Size on Nanodomain Formation in Anionic–Zwitterionic Mixed Bilayers. J Phys Chem B 2017; 121:787-799. [DOI: 10.1021/acs.jpcb.6b10099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sai J. Ganesan
- Fischell
Department of Bioengineering and ‡Biophysics Program, Institute of
Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Hongcheng Xu
- Fischell
Department of Bioengineering and ‡Biophysics Program, Institute of
Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell
Department of Bioengineering and ‡Biophysics Program, Institute of
Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
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27
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Schmid F. Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:509-528. [PMID: 27823927 DOI: 10.1016/j.bbamem.2016.10.021] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/19/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium mechanisms induced by the interaction of a biomembrane with the cellular environment, such as membrane recycling and the pinning effects of the cytoplasm. Theoretical predictions are discussed together with simulations and experiments. The presentation is guided by the theory of phase transitions and critical phenomena, and the appendix summarizes the mathematical background in a concise way within the framework of the Ginzburg-Landau theory. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Friederike Schmid
- Institute of Physics, Johannes Gutenberg University, 55099 Mainz, Germany
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28
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Vögele M, Holm C, Smiatek J. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium). J Chem Phys 2016; 143:243151. [PMID: 26723636 DOI: 10.1063/1.4937805] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
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Affiliation(s)
- Martin Vögele
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
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29
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Santos G, Díaz M, Torres NV. Lipid Raft Size and Lipid Mobility in Non-raft Domains Increase during Aging and Are Exacerbated in APP/PS1 Mice Model of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model. Front Physiol 2016; 7:90. [PMID: 27014089 PMCID: PMC4791387 DOI: 10.3389/fphys.2016.00090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/25/2016] [Indexed: 12/13/2022] Open
Abstract
A connection between lipid rafts and Alzheimer's disease has been studied during the last decades. Mathematical modeling approaches have recently been used to correlate the effects of lipid composition changes in the physicochemical properties of raft-like membranes. Here we propose an agent based model to assess the effect of lipid changes in lipid rafts on the evolution and progression of Alzheimer's disease using lipid profile data obtained in an established model of familial Alzheimer's disease. We have observed that lipid raft size and lipid mobility in non-raft domains are two main factors that increase during age and are accelerated in the transgenic Alzheimer's disease mouse model. The consequences of these changes are discussed in the context of neurotoxic amyloid β production. Our agent based model predicts that increasing sterols (mainly cholesterol) and long-chain polyunsaturated fatty acids (LCPUFA) (mainly DHA, docosahexaenoic acid) proportions in the membrane composition might delay the onset and progression of the disease.
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Affiliation(s)
- Guido Santos
- Systems Biology and Mathematical Modelling Group, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto de Tecnologías Biomédicas, CIBICAN, Universidad de La Laguna San Cristóbal de La Laguna, Spain
| | - Mario Díaz
- Laboratorio de Fisiología y Biofísica de Membranas, Departamento de Biología Animal y Edafología y Geología, Facultad de Ciencias, Unidad Asociada de Investigación ULL-CSIC, Universidad de La Laguna San Cristóbal de La Laguna, Spain
| | - Néstor V Torres
- Systems Biology and Mathematical Modelling Group, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Instituto de Tecnologías Biomédicas, CIBICAN, Universidad de La Laguna San Cristóbal de La Laguna, Spain
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30
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Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1635-51. [PMID: 26766517 DOI: 10.1016/j.bbamem.2015.12.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Takaharu Mori
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Miyashita
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Faculty of Biology-Oriented Science and Technology, KINDAI University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Wonpil Im
- Department of Molecular Sciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
| | - Yuji Sugita
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States; Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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López CA, Sethi A, Goldstein B, Wilson BS, Gnanakaran S. Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR. Biophys J 2015; 108:2481-2491. [PMID: 25992726 PMCID: PMC4457001 DOI: 10.1016/j.bpj.2015.03.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/27/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022] Open
Abstract
The regulation of T-cell-mediated immune responses depends on the phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) on T-cell receptors. Although many details of the signaling cascades are well understood, the initial mechanism and regulation of ITAM phosphorylation remains unknown. We used molecular dynamics simulations to study the influence of different compositions of lipid bilayers on the membrane association of the CD3ϵ cytoplasmic tails of the T-cell receptors. Our results show that binding of CD3ϵ to membranes is modulated by both the presence of negatively charged lipids and the lipid order of the membrane. Free-energy calculations reveal that the protein-membrane interaction is favored by the presence of nearby basic residues and the ITAM tyrosines. Phosphorylation minimizes membrane association, rendering the ITAM motif more accessible to binding partners. In systems mimicking biological membranes, the CD3ϵ chain localization is modulated by different facilitator lipids (e.g., gangliosides or phosphoinositols), revealing a plausible regulatory effect on activation through the regulation of lipid composition in cell membranes.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anurag Sethi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Byron Goldstein
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Bridget S Wilson
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico; New Mexico Consortium, Los Alamos, New Mexico.
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Eckstein J, Berndt N, Holzhütter HG. Computer simulations suggest a key role of membranous nanodomains in biliary lipid secretion. PLoS Comput Biol 2015; 11:e1004033. [PMID: 25692493 PMCID: PMC4333117 DOI: 10.1371/journal.pcbi.1004033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/12/2014] [Indexed: 01/06/2023] Open
Abstract
The bile fluid contains various lipids that are secreted at the canalicular membrane of hepatocytes. As the secretion mechanism is still a matter of debate and a direct experimental observation of the secretion process is not possible so far, we used a mathematical model to simulate the extraction of the major bile lipids cholesterol, phosphatidylcholine and sphingomyelin from the outer leaflet of the canalicular membrane. Lipid diffusion was modeled as random movement on a triangular lattice governed by next-neighbor interaction energies. Phase separation in liquid-ordered and liquid-disordered domains was modeled by assigning two alternative ordering states to each lipid species and minimization of next-neighbor ordering energies. Parameterization of the model was performed such that experimentally determined diffusion rates and phases in ternary lipid mixtures of model membranes were correctly recapitulated. The model describes the spontaneous formation of nanodomains in the external leaflet of the canalicular membrane in a time window between 0.1 ms to 10 ms at varying lipid proportions. The extraction of lipid patches from the bile salt soluble nanodomain into the bile reproduced observed biliary phospholipid compositions for a physiologi-cal membrane composition. Comparing the outcome of model simulations with available experi-mental observations clearly favors the extraction of tiny membrane patches composed of about 100–400 lipids as the likely mechanism of biliary lipid secretion. Formation of the bile is one of the central functions of the liver. The bile fluid aids in the digestion of edible fats and removal of drugs and toxins from the body. The bile fluid is mainly composed of bile salts (BS), phosphatidylcholine (PC) and cholesterol (CH) in a fairly fixed proportion that prevents liver impairment by gallstone formation or cholestasis. During bile formation, BS are actively pumped out of the hepatocyte into the extracellular space where they extract PC and CH from the canalicular membrane. This extraction process bears the risk for the canalicular membrane to be destructed. Hence, only a certain fraction of the membrane should be accessible to the solubilizing activity of BS. We have developed a mathematical model that describes the temporal formation of CH-enriched ordered and PC-enriched disordered nanodomains in the canalicular membrane. Model simulations reveal that the disordered nanodomains exhibit a composition of PC and CH similar to that also found in the bile. From this finding and the good concordance of model simulations with experimental data we conclude that PC and CH are mainly secreted into the bile from the disordered nanodomain. Our work adds a new layer of physiological importance to the spontaneous formation of lipid domains in biological membranes.
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Affiliation(s)
- Johannes Eckstein
- Charité—University Medicine Berlin, Institute of Biochemistry, Berlin, Germany
| | - Nikolaus Berndt
- Charité—University Medicine Berlin, Institute of Biochemistry, Berlin, Germany
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Ackerman DG, Feigenson GW. Multiscale modeling of four-component lipid mixtures: domain composition, size, alignment, and properties of the phase interface. J Phys Chem B 2015; 119:4240-50. [PMID: 25564922 DOI: 10.1021/jp511083z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Simplified lipid mixtures are often used to model the complex behavior of the cell plasma membrane. Indeed, as few as four components-a high-melting lipid, a nandomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol)-can give rise to a wide range of domain sizes and patterns that are highly sensitive to lipid compositions. Although these systems are studied extensively with experiments, the molecular-level details governing their phase behavior are not yet known. We address this issue by using molecular dynamics simulations to analyze how phase separation evolves in a four-component system as it transitions from small domains to large domains. To do so, we fix concentrations of the high-melting lipid 16:0,16:0-phosphatidylcholine (DPPC) and chol, and incrementally replace the nanodomain-inducing low-melting lipid 16:0,18:2-PC (PUPC) by the macrodomain-inducing low-melting lipid 18:2,18:2-PC (DUPC). Coarse-grained simulations of this four-component system reveal that lipid demixing increases as the amount of DUPC increases. Additionally, we find that domain size and interleaflet alignment change sharply over a narrow range of replacement of PUPC by DUPC, indicating that intraleaflet and interleaflet behaviors are coupled. Corresponding united atom simulations show that only lipids within ∼2 nm of the phase interface are significantly perturbed regardless of domain composition or size. Thus, whereas the fraction of interface-perturbed lipids is negligible for large domains, it is significant for smaller ones. Together, these results reveal characteristic traits of bilayer thermodynamic behavior in four-component mixtures, and provide a baseline for investigation of the effects of proteins and other lipids on membrane phase properties.
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Affiliation(s)
- David G Ackerman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Gerald W Feigenson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
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Baoukina S, Tieleman DP. Computer simulations of phase separation in lipid bilayers and monolayers. Methods Mol Biol 2015; 1232:307-322. [PMID: 25331143 DOI: 10.1007/978-1-4939-1752-5_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Studying phase coexistence in lipid bilayers and monolayers is important for understanding lipid-lipid interactions underlying lateral organization in biological membranes. Computer simulations follow experimental approaches and use model lipid mixtures of simplified composition. Atomistic simulations give detailed information on the specificity of intermolecular interactions, while coarse-grained simulations achieve large time and length scales and provide a bridge towards state-of-the-art experimental techniques. Computer simulations allow characterizing the structure and composition of domains during phase transformations at Angstrom and picosecond resolution, and bring new insights into phase behavior of lipid membranes.
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Affiliation(s)
- Svetlana Baoukina
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4,
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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Koldsø H, Shorthouse D, Hélie J, Sansom MSP. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers. PLoS Comput Biol 2014; 10:e1003911. [PMID: 25340788 PMCID: PMC4207469 DOI: 10.1371/journal.pcbi.1003911] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 09/16/2014] [Indexed: 12/21/2022] Open
Abstract
Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. Cell membranes play important roles in vivo both in shielding the cell interior from the surrounding environment and in cell function through lipid components of the membrane having roles in controlling protein function, cell signaling etc. We employ molecular dynamics simulations to explore the behavior of biologically realistic membrane models. Our simulations reveal nano-domain clustering of the glycolipid GM3 and to a lesser extent of the anionic lipid phosphatidylinositol 4,5-bisphophate (PIP2). When including transmembrane proteins we are able to observe preferential interactions of known regulatory lipids (e.g. GM3, PIP2 and cholesterol) with the proteins. Membrane curvature is shown to be coupled to the local lipid composition, suggestive of a link between lipid nano-domains and membrane geometry.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David Shorthouse
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Chavent M, Reddy T, Goose J, Dahl ACE, Stone JE, Jobard B, Sansom MSP. Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discuss 2014; 169:455-75. [PMID: 25341001 PMCID: PMC4208077 DOI: 10.1039/c3fd00145h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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38
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Sun D, Lin X, Gu N. Cholesterol affects C₆₀ translocation across lipid bilayers. SOFT MATTER 2014; 10:2160-2168. [PMID: 24652350 DOI: 10.1039/c3sm52211c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cholesterol plays an important role in regulating the structural properties of phospholipid membranes and further influences the permeability of molecules and nanoparticles. However, nanoparticles' translocation across phospholipid membranes in the presence of cholesterol on the molecular scale is rarely studied. Here, we performed coarse-grained molecular dynamics simulations to probe the translocation of C60, one of the most popular nanoparticles, across dipalmitoylphosphatidylcholine bilayers with different concentrations of cholesterol molecules (0-50 mol%). The results reveal that the presence of cholesterol molecules induces lower area per lipid, larger bilayer thickness, and more ordered orientation of lipid tails. The higher the concentration of cholesterol molecules, the more significant is the condensing effect of lipid bilayer as just mentioned. Besides, dynamic processes, free energy profiles and permeability coefficients further indicate that the permeability of C60 decreases with increasing cholesterol concentration, which can be explained by the condensation effect and reduced free volume. Our researches provide an explicit description of the impact of cholesterol on C60 translocation across lipid bilayers.
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Affiliation(s)
- Dandan Sun
- State Key Laboratory of Bioelectronics, Jiangsu key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, People's Republic of China.
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Effect of cholesterol on behavior of 5-fluorouracil (5-FU) in a DMPC lipid bilayer, a molecular dynamics study. Biophys Chem 2014; 187-188:43-50. [DOI: 10.1016/j.bpc.2014.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/18/2014] [Accepted: 01/25/2014] [Indexed: 11/19/2022]
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Bag N, Yap DHX, Wohland T. Temperature dependence of diffusion in model and live cell membranes characterized by imaging fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2013.10.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Hakobyan D, Heuer A. Key molecular requirements for raft formation in lipid/cholesterol membranes. PLoS One 2014; 9:e87369. [PMID: 24498317 PMCID: PMC3911970 DOI: 10.1371/journal.pone.0087369] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/20/2013] [Indexed: 11/25/2022] Open
Abstract
The lipid mixture of DPPC (saturated lipid)/DUPC (unsaturated lipid)/CHOL (cholesterol) is studied with respect to its ability to form liquid-ordered and liquid-disordered phases. We employ coarse-grained simulations with MARTINI force field. All three components are systematically modified in order to explore the relevant molecular properties, leading to phase separation. Specifically, we show that the DPPC/DUPC/CHOL system unmixes due to enthalpic DPPC-DPPC and DPPC-CHOL interactions. The phase separation remains unchanged, except for the formation of a gel phase at long times after decreasing the conformational degrees of freedom of the unsaturated DUPC. In contrast, the phase separation can be suppressed by softening the DPPC chains. In an attempt to mimic the ordering and unmixing effect of CHOL the latter is replaced by a stiff and shortened DPPC-like lipid. One still observes phase separation, suggesting that it is mainly the rigid and planar structure of CHOL which is important for raft formation. Addition of an extra bead to the head of CHOL has no notable impact on the phase separation of the system, supporting the irrelevance of the Umbrella model for the phase separation. Reduction of the conformational entropy of CHOL by stiffening its last bead results in a significant increase of the order of the DPPC/CHOL domain. This suggests that the conformational entropy of CHOL is important to prohibit the gelation process. The interleaflet interactions as mediated by the terminal molecular groups seem to have a strong impact on the possibility of a subsequent gelation process after phase separation.
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Affiliation(s)
- Davit Hakobyan
- Theory of Complex Systems, University of Muenster, Muenster, Germany
- * E-mail:
| | - Andreas Heuer
- Theory of Complex Systems, University of Muenster, Muenster, Germany
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Khandelia H, Loubet B, Olzyńska A, Jurkiewicz P, Hof M. Pairing of cholesterol with oxidized phospholipid species in lipid bilayers. SOFT MATTER 2014; 10:639-647. [PMID: 24795978 DOI: 10.1039/c3sm52310a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We claim that (1) cholesterol protects bilayers from disruption caused by lipid oxidation by sequestering conical shaped oxidized lipid species such as 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PZPC) away from phospholipid, because cholesterol and the oxidized lipid have complementary shapes and (2) mixtures of cholesterol and oxidized lipids can self-assemble into bilayers much like lysolipid–cholesterol mixtures. The evidence for bilayer protection comes from molecular dynamics (MD) simulations and dynamic light scattering (DLS) measurements. Unimodal size distributions of extruded vesicles (LUVETs) made up of a mixture of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and PZPC containing high amounts of PZPC are only obtained when cholesterol is present in high concentrations. In simulations, bilayers containing high amounts of PZPC become porous, unless cholesterol is also present. The protective effect of cholesterol on oxidized lipids has been observed previously using electron paramagnetic resonance (EPR) and electron microscopy imaging of vesicles. The evidence for the pairing of cholesterol and PZPC comes mainly from correlated 2-D density and thickness plots from simulations, which show that these two molecules co-localize in bilayers. Further evidence that the two molecules can cohabitate comes from self-assembly simulations, where we show that cholesterol-oxidized lipid mixtures can form lamellar phases at specific concentrations, reminiscent of lysolipid–cholesterol mixtures. The additivity of the packing parameters of cholesterol and PZPC explains their cohabitation in a planar bilayer. Oxidized lipids are ubiquitously present in significant amounts in high- and low-density lipoprotein (HDL and LDL) particles, diseased tissues, and in model phospholipid mixtures containing polyunsaturated lipids. Therefore, our hypothesis has important consequences for cellular cholesterol trafficking; diseases related to oxidized lipids, and to biophysical studies of phase behaviour of cholesterol-containing phospholipid mixtures.
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