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Patterning-mediated supramolecular assembly of lipids into nanopalms. iScience 2022; 25:105344. [DOI: 10.1016/j.isci.2022.105344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/04/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
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2
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Reyes-Figueroa AD, Karttunen M, Ruiz-Suárez JC. Cholesterol sequestration by xenon nano bubbles leads to lipid raft destabilization. SOFT MATTER 2020; 16:9655-9661. [PMID: 33078812 DOI: 10.1039/d0sm01256d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Combined coarse-grained (CG) and atomistic molecular dynamics (MD) simulations were performed to study the interactions of xenon with model lipid rafts consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and cholesterol (Chol). At a concentration of 2 Xe/lipid we observed an unexpected result: spontaneous nucleation of Xe nano bubbles which rapidly plunged into the bilayer. In this process Chol, essential for raft stabilization, was pulled out from the raft into the hydrophobic zone. When concentration was further increased (3 Xe/lipid), the bubbles increase in size and disrupted both the membrane and raft. We computed the radial distribution functions, pair-wise potentials, second virial coefficients and Schlitter entropy to scrutinize the nature of the interactions. Our findings, concurring with a recent report on the origin of general anaesthesia (M. A. Pavel, E. N. Petersen, H. Wang, R. A. Lerner and S. B. Hansen, Proc. Natl. Acad. Sci. U. S. A., 2020, 117(24), 13757-13766), suggest that the well-known anaesthetic effect of Xe could be mediated by sequestration of Chol, which, in turn, compromises the stability of rafts where specialized proteins needed to produce the nervous signal are anchored.
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Puigpelat E, Ignés-Mullol J, Sagués F, Reigada R. Interaction of Graphene Nanoparticles and Lipid Membranes Displaying Different Liquid Orderings: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16661-16668. [PMID: 31750663 DOI: 10.1021/acs.langmuir.9b03008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Understanding the effects of graphene-based nanomaterials on lipid membranes is fundamental to determine their environmental impact and the efficiency of their biomedical use. By means of molecular dynamics simulations of simple model lipid bilayers, we analyze in detail the different interaction modes. We have studied bilayers consisting of lipid species (including cholesterol) which display different internal liquid orderings. Nanometric graphene layers can be transiently adsorbed onto the lipid membrane and/or inserted in its hydrophobic region. Once inserted, graphene nanometric flakes display a diffusive dynamics in the membrane plane, they adopt diverse orientations depending on their size and oxidation degree, and they show a particular aversion to be placed close to cholesterol molecules in the membrane. Addition of graphene to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the lipid organization of biological membranes. Our simulation results show that graphene layers can be inserted indistinctly in the ordered and disordered regions. Once inserted, nanometric flakes migrate to disordered and cholesterol-poor lipid phases.
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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: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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Effects of Passive Phospholipid Flip-Flop and Asymmetric External Fields on Bilayer Phase Equilibria. Biophys J 2018; 115:1956-1965. [PMID: 30393103 DOI: 10.1016/j.bpj.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Compositional asymmetry between the leaflets of bilayer membranes modifies their phase behavior and is thought to influence other important features such as mechanical properties and protein activity. We address here how phase behavior is affected by passive phospholipid flip-flop, such that the compositional asymmetry is not fixed. We predict transitions from "pre-flip-flop" behavior to a restricted set of phase equilibria that can persist in the presence of passive flip-flop. Surprisingly, such states are not necessarily symmetric. We further account for external symmetry breaking, such as a preferential substrate interaction, and show how this can stabilize strongly asymmetric equilibrium states. Our theory explains several experimental observations of flip-flop-mediated changes in phase behavior and shows how domain formation and compositional asymmetry can be controlled in concert, by manipulating passive flip-flop rates and applying external fields.
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Sastre J, Mannelli I, Reigada R. Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study. Biochim Biophys Acta Gen Subj 2017; 1861:2872-2882. [PMID: 28780125 DOI: 10.1016/j.bbagen.2017.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND The toxic effects and environmental impact of nanomaterials, and in particular of Fullerene particles, are matters of serious concern. It has been reported that fullerene molecules enter the cell membrane and occupy its hydrophobic region. Understanding the effects of carbon-based nanoparticles on biological membranes is therefore of critical importance to determine their exposure risks. METHODS We report on a systematic coarse-grained molecular dynamics study of the interaction of fullerene molecules with simple model cell membranes. We have analyzed bilayers consisting of lipid species with different degrees of unsaturation and a variety of cholesterol fractions. Addition of fullerene particles to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the organization of the cell membrane. RESULTS Fullerene addition to lipid membranes modifies their structural properties like thickness, area and internal ordering of the lipid species, as well as dynamical aspects such as molecular diffusion and cholesterol flip-flop. Interestingly, we show that phase-segregating ternary lipid membranes accumulate fullerene molecules preferentially in the liquid-disordered domains promoting phase-segregation and domain alignment across the membrane. CONCLUSIONS Lipid membrane internal ordering determines the behavior and distribution of fullerene particle, and this, in turn, determines the influence of fullerene on the membrane. Lipid membranes are good solvents of fullerene molecules, and in particular those with low internal ordering. GENERAL SIGNIFICANCE Preference of fullerene molecules to be dissolved in the more disordered hydrophobic regions of a lipid bilayer and the consequent alteration of its phase behavior may have important consequences on the activity of biological cell membranes and on the bioconcentration of fullerene in living organisms.
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Affiliation(s)
- Judit Sastre
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona, c/Marti i Franqués 1, Pta 4, 08028 Barcelona, Spain
| | - Ilaria Mannelli
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Ramon Reigada
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona, c/Marti i Franqués 1, Pta 4, 08028 Barcelona, Spain; Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Marti i Franqués 1, Pta 4, 08028 Barcelona, Spain.
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Reigada R. Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes. Sci Rep 2016; 6:32934. [PMID: 27596355 PMCID: PMC5011781 DOI: 10.1038/srep32934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/17/2016] [Indexed: 12/02/2022] Open
Abstract
The spatial coincidence of lipid domains at both layers of the cell membrane is expected to play an important role in many cellular functions. Competition between the surface interleaflet tension and a line hydrophobic mismatch penalty are conjectured to determine the transversal behavior of laterally heterogeneous lipid membranes. Here, by a combination of molecular dynamics simulations, a continuum field theory and kinetic equations, I demonstrate that the presence of small, rapidly translocating molecules residing in the lipid bilayer may alter its transversal behavior by favoring the spatial coincidence of similar lipid phases.
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Affiliation(s)
- Ramon Reigada
- Department de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/ Martí i Franqués 1, Pta 4, 08028 Barcelona Spain
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Fowler PW, Williamson JJ, Sansom MSP, Olmsted PD. Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics. J Am Chem Soc 2016; 138:11633-42. [PMID: 27574865 PMCID: PMC5025830 DOI: 10.1021/jacs.6b04880] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Characterizing
the nanoscale dynamic organization within lipid
bilayer
membranes is central
to our understanding of cell membranes at a molecular level. We investigate
phase separation and communication across leaflets in ternary lipid
bilayers, including saturated lipids with between 12 and 20 carbons
per tail. Coarse-grained molecular dynamics simulations reveal a novel
two-step kinetics due to hydrophobic mismatch, in which the initial
response of the apposed leaflets upon quenching is to increase local
asymmetry (antiregistration), followed by dominance of symmetry (registration)
as the bilayer equilibrates. Antiregistration can become thermodynamically
preferred if domain size is restricted below ∼20 nm, with implications
for the symmetry of rafts and nanoclusters in cell membranes, which
have similar reported sizes. We relate our findings to theory derived
from a semimicroscopic model in which the leaflets experience a “direct”
area-dependent coupling, and an “indirect” coupling
that arises from hydrophobic mismatch and is most important at domain
boundaries. Registered phases differ in composition from antiregistered
phases, consistent with a direct coupling between the leaflets. Increased
hydrophobic mismatch purifies the phases, suggesting that it contributes
to the molecule-level lipid immiscibility. Our results demonstrate
an interplay of competing interleaflet couplings that affect phase
compositions and kinetics, and lead to a length scale that
can influence lateral and transverse bilayer organization within cells.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford, OX1 3QU, U.K
| | - John J Williamson
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University , 37th and O Streets, N.W., Washington, D.C. 20057, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford, OX1 3QU, U.K
| | - Peter D Olmsted
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University , 37th and O Streets, N.W., Washington, D.C. 20057, United States
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Williamson JJ, Olmsted PD. Nucleation of symmetric domains in the coupled leaflets of a bilayer. SOFT MATTER 2015; 11:8948-8959. [PMID: 26412192 DOI: 10.1039/c5sm01328c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We study the kinetics governing the attainment of inter-leaflet domain symmetry in a phase-separating amphiphilic bilayer. "Indirect" inter-leaflet coupling via hydrophobic mismatch can induce an instability towards a metastable pattern of locally asymmetric domains upon quenching from high temperature. This necessitates a nucleation step to form the conventional symmetric domains, which are favoured by a "direct" inter-leaflet coupling. We model the energetics for a symmetric domain to nucleate from the metastable state, and find that an interplay between hydrophobic mismatch and thickness stretching/compression causes the effective hydrophobic mismatch, and thus line tension, to depend on domain size. This leads to strong departure from classical nucleation theory. We speculate on implications for cell membrane rafts or clusters, whose size may be of similar magnitude to estimated critical radii for domain symmetry.
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Affiliation(s)
- J J Williamson
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, 37th and O Streets, N.W., Washington, D.C. 20057, USA.
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Williamson JJ, Olmsted PD. Kinetics of symmetry and asymmetry in a phase-separating bilayer membrane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052721. [PMID: 26651737 DOI: 10.1103/physreve.92.052721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 06/05/2023]
Abstract
We simulate a phase-separating bilayer in which the leaflets experience a direct coupling favoring local compositional symmetry ("registered" bilayer phases), and an indirect coupling due to hydrophobic mismatch that favors strong local asymmetry ("antiregistered" bilayer phases). For wide ranges of overall leaflet compositions, multiple competing states are possible. For estimated physical parameters, a quenched bilayer may first evolve toward a metastable state more asymmetric than if the leaflets were uncorrelated; subsequently, it must nucleate to reach its equilibrium, more symmetric, state. These phase-transition kinetics exhibit characteristic signatures through which fundamental and opposing interleaflet interactions may be probed. We emphasize how bilayer phase diagrams with a separate axis for each leaflet can account for overall and local symmetry or asymmetry, and capture a range of observations in the experiment and simulation literature.
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Affiliation(s)
- J J Williamson
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, 37th and O Streets, N.W., Washington, D.C. 20057, USA
| | - P D Olmsted
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, 37th and O Streets, N.W., Washington, D.C. 20057, USA
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