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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: 422] [Impact Index Per Article: 84.4] [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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Almiñana N, Alsina MA, Reig F. New GHK hydrophobic derivatives: Interaction with phospholipid bilayers. Colloids Surf B Biointerfaces 2007; 57:243-9. [PMID: 17383163 DOI: 10.1016/j.colsurfb.2007.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 02/05/2007] [Accepted: 02/05/2007] [Indexed: 11/28/2022]
Abstract
Three hydrophobic derivatives of GHK peptide containing either N-terminal hexanoyl, decanoyl or myristoyl acyl moieties were synthesized. The binding of these peptidolipids to phospholipid bilayers as well as their hemolytic activity were determined. Moreover, the influence of these peptidolipids on several physicochemical properties of liposomes was studied. Binding experiments indicate a high affinity of these peptidolipids for lipids ordered in liposomes. Nevertheless, this interaction does not promote the release of entrapped carboxyfluorescein. Experiments carried out by the asymmetric membrane method (NBD-PE/dithionite) and quenching studies (PC-pyrene/KI) indicate that this association has a protective effect suggesting that the hydrophobic moiety inserts in the external part of the bilayer and the peptide chain remains protruding from the surface hindering the entrance or the approach of reactants to it. The microviscosity of DPPC bilayers determined using TMA-DPH as fluorescent marker was not affected by the presence of peptidolipids. Besides, results indicate that myristoyl-GHK produces total hemolysis at 2.5x10(-4)M but decanoyl and hexanoyl derivatives at 5x10(-4)M induce only 10% of hemolysis.
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Crosas E, Egea MA, Reig F. Spectroscopic techniques applied to the study of laminin fragments inserted into model membranes. J Colloid Interface Sci 2006; 295:264-9. [PMID: 16162352 DOI: 10.1016/j.jcis.2005.07.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/27/2005] [Accepted: 07/29/2005] [Indexed: 11/27/2022]
Abstract
The influence of four laminin-derived peptides on bilayer organization is studied. Spectroscopic methods applied were based on pyrene fluorescence properties (quenching, I1/I3, and monomer/excimer equilibrium), asymmetric membrane fluorescence (NBD-PE/dithionite), and polarization fluorescence (TMA-DPH). Also, the ability of these peptides to release carboxyfluorescein entrapped in vesicles was determined. Results suggest that these peptides do not noticeably modify the packing and motion of lipids (in the gel state), but coat its surface, preventing penetration of quenchers and chemical reactants. Nevertheless, their presence promotes a soft release of entrapped CF after incubation at 37 degrees C.
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Affiliation(s)
- E Crosas
- Peptides Department, Institute for Chemical and Environmental Research, Jordi Girona 18, 08034 Barcelona, Spain
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Nakano M, Kamo T, Sugita A, Handa T. Detection of Bilayer Packing Stress and Its Release in Lamellar-Cubic Phase Transition by Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2005; 109:4754-60. [PMID: 16851558 DOI: 10.1021/jp046181z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An introduction of nonlamellar-forming lipids into planar bilayers generates packing stress, which is important for the biological functions of plasma membranes and is a driving force for the lamellar-nonlamellar phase transition. We have investigated the phase behavior of a binary system consisting of egg yolk phosphatidylcholine and monoolein (MO) and the changes in the local orientation order of lipids in a lamellar-bicontinuous cubic phase transition. Small-angle X-ray scattering has revealed that the lamellar-bicontinuous cubic phase transition occurs at an MO molar fraction (X(MO)) between 0.6 and 0.7. These phases were dispersed to form liposomes and cubosomes to monitor the anisotropy of the incorporated fluorescence probe, in which Pluronic F127, used as a dispersion stabilizer of the cubic phase, has been proven not to alter the cubic structure and the location of the probes. Time-resolved fluorescence anisotropy measurements on these dispersions have revealed that the order parameter of the probe in the lamellar phase increases with increasing X(MO), and that it decreases during the transition to the cubic phase. This observation suggests that packing stress generated by the addition of the nonlamellar-forming lipid is released by the phase transition.
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Affiliation(s)
- Minoru Nakano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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Abstract
Pyrene is one of the most frequently used lipid-linked fluorophores. Its most characteristic features are a long excited state lifetime and (local) concentration-dependent formation of excimers. Pyrene is also hydrophobic and thus does not significantly distort the conformation of the labeled lipid molecule. These characteristics make pyrene lipids well-suited for studies on a variety of biophysical phenomena like lateral diffusion, inter- or transbilayer movement of lipids and lateral organization of membranes. Pyrene lipids have also been widely employed to determine protein binding to membranes, lipid conformation and the activity of lipolytic enzymes. In cell biology, pyrene lipids are promising tools for studies on lipid trafficking and metabolism, as well as for microscopic mapping of membrane properties. The main disadvantage of pyrene lipids is the relatively large size of the fluorophore. Another disadvantage is that they require UV-excitation, which is not feasible with all microscopes.
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Affiliation(s)
- Pentti Somerharju
- Institute of Biomedicine, Biomedicum, Room C205b, Haartmaninkatu 8, P.O. Box 63, University of Helsinki, 00014 Helsinki, Finland.
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Tanhuanpää K, Cheng KH, Anttonen K, Virtanen JA, Somerharju P. Characteristics of pyrene phospholipid/gamma-cyclodextrin complex. Biophys J 2001; 81:1501-10. [PMID: 11509363 PMCID: PMC1301628 DOI: 10.1016/s0006-3495(01)75804-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Recently, it was demonstrated that gamma-cyclodextrins (gamma-CDs) greatly accelerates transfer of hydrophobic pyrene-labeled and other fluorescent phospholipid derivatives from vesicles to cells in culture (). To understand better the characteristics of this process, we studied the interaction of gamma-CD with pyrene-labeled phosphatidylcholines (PyrPCs) using a variety of physical methods. Either one or both of the acyl chains of PC was labeled with a pyrene moiety (monoPyrPCs and diPyrPCs, respectively), and the length of the labeled chain(s) varied from 4 to 14 carbons. Fluorescent binding assays showed that the association constant decreases strongly with increasing acyl chain length. PyrPC/gamma-CD stoichiometry was 1:2 for the shorter chain species, but changed to 1:3 when the acyl chain length exceeded 8 (diPyrPCs) or 10 (monoPyrPCs) carbons. The activation energy for the formation of diPyr(10)PC/gamma-CD complex was high, i.e., +92 kJ/mol, indicating that the phospholipid molecule has to fully emerge from the bilayer before complex formation can take place. The free energy, enthalpy, and entropy of transfer of monoPyrPC from bilayer to gamma-CD complex were close to zero. The absorption, Fourier transform infrared, and fluorescence spectral measurements and lifetime analysis indicated that the pyrene moiety lies inside the CD cavity and is conformationally restricted, particularly when the labeled chain is short. The acyl chains of a PyrPC molecule seem to share a CD cavity rather than occupy different ones. The present data provide strong evidence that the ability of gamma-CD to enhance intermembrane transfer of pyrene-labeled phospholipids is based on the formation of stoichiometric complexes in the aqueous phase. This information should help in designing CD derivatives that are more efficient lipid carriers then those available at present.
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Affiliation(s)
- K Tanhuanpää
- Institute of Biomedicine, Department of Biochemistry, University of Helsinki, Finland
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Cheng KH, Ruonala M, Virtanen J, Somerharju P. Evidence for superlattice arrangements in fluid phosphatidylcholine/phosphatidylethanolamine bilayers. Biophys J 1997; 73:1967-76. [PMID: 9336192 PMCID: PMC1181097 DOI: 10.1016/s0006-3495(97)78227-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recently, evidence for cholesterol and phosphatidylcholine (PC) molecules to adapt superlattice arrangements in fluid lipid bilayers has been presented. Whether superlattice arrangements exist in other biologically relevant lipid membranes, such as phosphatidylethanolamine (PE)/PC, is still speculative. In this study, we have examined the physical properties of fluid 1-palmitoyl-2-oleoyl-PC (POPC) and 1-palmitoyl-2-oleoyl-PE (POPE) binary mixtures as a function of the POPE mole fraction (X(PE)) using fluorescence and Fourier transform infrared spectroscopy. At 30 degrees C, i.e., above the Tm of POPE and POPC, deviations, or dips, as well as local data scattering in the excimer-to-monomer fluorescence intensity ratio of intramolecular excimer forming dipyrenylphosphatidylcholine probe in POPE/POPC mixtures were detected at X(PE) approximately 0.04, 0.11, 0.16, 0.26, 0.33, 0.51, 0.66, 0.75, 0.82, 0.91, and 0.94. The above critical values of X(PE) coincide (within +/-0.03) with the critical mole fractions X(HX,PE) or X(R,PE) predicted by a headgroup superlattice model, which assumes that the lipid headgroups form hexagonal or rectangular superlattice, respectively, in the bilayer. Other spectroscopic data, generalized polarization of Laurdan and infrared carbonyl and phosphate stretching frequency, were also collected. Similar agreements between some of the observed critical values of X(PE) from these data and the X(HX,PE) or X(R,PE) values were also found. However, all techniques yielded critical values of X(PE) (e.g., 0.42 and 0.58) that cannot be explained by the present headgroup superlattice model. The effective cross-sectional area of the PE headgroup is smaller than that of the acyl chains. Hence, the relief of "packing frustration" of PE in the presence of PC (larger headgroup than PE) may be one of the major mechanisms in driving the PE and PC components to superlattice-like lateral distributions in the bilayer. We propose that headgroup superlattices may play a significant role in the regulation of membrane lipid compositions in cells.
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Affiliation(s)
- K H Cheng
- Department of Physics, Texas Tech University, Lubbock 79409, USA.
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Abstract
Packing defects in lipid bilayer play a significant role in the biological activities of cell membranes. Time-resolved fluorescence depolarization has been used to detect and characterize the onset of packing defects in binary mixtures of dilinoleoylphosphatidylethanolamine/1-palmitoyl-2- oleoylphosphatidylcholine (PE/PC). These PE/PC mixtures exhibit mesoscopic packing defect state (D), as well as one-dimensional lambellar liquid crystalline (L alpha) and two-dimensional inverted hexagonal (HII) ordered phases. Based on previous electron microscopic investigations, this D state is characterized by the presence of interlamellar attachments and precursors of HII phase between the lipid layers. Using a rotational diffusion model for rod-shaped fluorophore in a curved matrix, rotational dynamics parameters, second rank order parameter, localized wobbling diffusion, and curvature-dependent rotational diffusion constants of dipyenylhexatriene (DPH)-labeled PC (DPH-PC) in the host PE/PC matrix were recovered from the measured fluorescence depolarization decays of DPH fluorescence. At approximately 60% PE, abrupt increases in these rotational dynamics parameters were observed, reflecting the onset of packing defects in the host PE/PC matrix. We have demonstrated that rotational dynamics parameters are very sensitive in detecting the onset of curvature-associating packing defects in lipid membranes. In addition, the presence of the D state can be characterized by the enhanced wobbling diffusional motion and order packing of lipid molecules, and by the presence of localized curvatures in the lipid layers.
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Affiliation(s)
- S Y Chen
- Department of Physics, Texas Tech University, Lubbock 79409-1051, USA
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Warner IM, Soper SA, McGown LB. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 1996. [DOI: 10.1021/a19600045] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isiah M. Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708-0346
| | - Steven A. Soper
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708-0346
| | - Linda B. McGown
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708-0346
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