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Shih KC, Leriche G, Liu CH, He J, John VT, Fang J, Barker JG, Nagao M, Yang L, Yang J, Nieh MP. Antivesiculation and Complete Unbinding of Tail-Tethered Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1688-1697. [PMID: 38186288 DOI: 10.1021/acs.langmuir.3c02663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka "bind") due to dominant van der Waals attraction, while the outcome of the nonstacking ("unbinding") membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.
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Affiliation(s)
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Jibao He
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Vijay T John
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - John G Barker
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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2
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Schütz GJ, Pabst G. The asymmetric plasma membrane-A composite material combining different functionalities?: Balancing Barrier Function and Fluidity for Effective Signaling. Bioessays 2023; 45:e2300116. [PMID: 37712937 DOI: 10.1002/bies.202300116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
One persistent puzzle in the life sciences is the asymmetric lipid composition of the cellular plasma membrane: while the exoplasmic leaflet is enriched in lipids carrying predominantly saturated fatty acids, the cytoplasmic leaflet hosts preferentially lipids with (poly-)unsaturated fatty acids. Given the high energy requirements necessary for cells to maintain this asymmetry, the question naturally arises regarding its inherent benefits. In this paper, we propose asymmetry to represent a potential solution for harmonizing two conflicting requirements for the plasma membrane: first, the need to build a barrier for the uncontrolled influx or efflux of substances; and second, the need to form a fluid and dynamic two-dimensional substrate for signaling processes. We hence view here the plasma membrane as a composite material, where the exoplasmic leaflet is mainly responsible for the functional integrity of the barrier and the cytoplasmic leaflet for fluidity. We reinforce the validity of the proposed mechanism by presenting quantitative data from the literature, along with multiple examples that bolster our model.
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Affiliation(s)
| | - Georg Pabst
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth-University of Graz, Graz, Austria
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3
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Frewein MPK, Piller P, Semeraro EF, Czakkel O, Gerelli Y, Porcar L, Pabst G. Distributing aminophospholipids asymmetrically across leaflets causes anomalous membrane stiffening. Biophys J 2023; 122:2445-2455. [PMID: 37120716 PMCID: PMC10322881 DOI: 10.1016/j.bpj.2023.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/10/2023] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
We studied the mechanical leaflet coupling of prototypic mammalian plasma membranes using neutron spin-echo spectroscopy. In particular, we examined a series of asymmetric phospholipid vesicles with phosphatidylcholine and sphingomyelin enriched in the outer leaflet and inner leaflets composed of phosphatidylethanolamine/phosphatidylserine mixtures. The bending rigidities of most asymmetric membranes were anomalously high, exceeding even those of symmetric membranes formed from their cognate leaflets. Only asymmetric vesicles with outer leaflets enriched in sphingolipid displayed bending rigidities in conformity with these symmetric controls. We performed complementary small-angle neutron and x-ray experiments on the same vesicles to examine possible links to structural coupling mechanisms, which would show up in corresponding changes in membrane thickness. In addition, we estimated differential stress between leaflets originating either from a mismatch of their lateral areas or spontaneous curvatures. However, no correlation with asymmetry-induced membrane stiffening was observed. To reconcile our findings, we speculate that an asymmetric distribution of charged or H-bond forming lipids may induce an intraleaflet coupling, which increases the weight of hard undulatory modes of membrane fluctuations and hence the overall membrane stiffness.
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Affiliation(s)
- Moritz P K Frewein
- Biophysics, Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria; Institut Laue-Langevin, Grenoble, France; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth, Graz, Austria
| | - Paulina Piller
- Biophysics, Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth, Graz, Austria
| | - Enrico F Semeraro
- Biophysics, Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth, Graz, Austria
| | | | - Yuri Gerelli
- CNR Institute for Complex Systems, Uos Sapienza, Roma, Italy; Department of Physics, Sapienza University of Rome, Roma, Italy
| | | | - Georg Pabst
- Biophysics, Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth, Graz, Austria.
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4
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Yu Y, Venable RM, Thirman J, Chatterjee P, Kumar A, Pastor RW, Roux B, MacKerell AD, Klauda JB. Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids. J Chem Theory Comput 2023; 19:2590-2605. [PMID: 37071552 PMCID: PMC10404126 DOI: 10.1021/acs.jctc.3c00203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Accurate empirical force fields of lipid molecules are a critical component of molecular dynamics simulation studies aimed at investigating properties of monolayers, bilayers, micelles, vesicles, and liposomes, as well as heterogeneous systems, such as protein-membrane complexes, bacterial cell walls, and more. While the majority of lipid force field-based simulations have been performed using pairwise-additive nonpolarizable models, advances have been made in the development of the polarizable force field based on the classical Drude oscillator model. In the present study, we undertake further optimization of the Drude lipid force field, termed Drude2023, including improved treatment of the phosphate and glycerol linker region of PC and PE headgroups, additional optimization of the alkene group in monounsaturated lipids, and inclusion of long-range Lennard-Jones interactions using the particle-mesh Ewald method. Initial optimization targeted quantum mechanical (QM) data on small model compounds representative of the linker region. Subsequent optimization targeted QM data on larger model compounds, experimental data, and dihedral potentials of mean force from the CHARMM36 additive lipid force field using a parameter reweighting protocol. The use of both experimental and QM target data during the reweighting protocol is shown to produce physically reasonable parameters that reproduce a collection of experimental observables. Target data for optimization included surface area/lipid for DPPC, DSPC, DMPC, and DLPC bilayers and nuclear magnetic resonance (NMR) order parameters for DPPC bilayers. Validation data include prediction of membrane thickness, scattering form factors, electrostatic potential profiles, compressibility moduli, surface area per lipid, water permeability, NMR T1 relaxation times, diffusion constants, and monolayer surface tensions for a variety of saturated and unsaturated lipid mono- and bilayers. Overall, the agreement with experimental data is quite good, though the results are less satisfactory for the NMR T1 relaxation times for carbons near the ester groups. Notable improvements compared to the additive C36 force field were obtained for membrane dipole potentials, lipid diffusion coefficients, and water permeability with the exception of monounsaturated lipid bilayers. It is anticipated that the optimized polarizable Drude2023 force field will help generate more accurate molecular simulations of pure bilayers and heterogeneous systems containing membranes, advancing our understanding of the role of electronic polarization in these systems.
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Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jonathan Thirman
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Payal Chatterjee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Anmol Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jeffery B Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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5
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Heller WT. Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes. Biomolecules 2022; 12:1591. [PMID: 36358941 PMCID: PMC9687511 DOI: 10.3390/biom12111591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 09/23/2023] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.
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Affiliation(s)
- William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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6
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Guéguen N, Maréchal E. Origin of cyanobacterial thylakoids via a non-vesicular glycolipid phase transition and their impact on the Great Oxygenation Event. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2721-2734. [PMID: 35560194 DOI: 10.1093/jxb/erab429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 06/15/2023]
Abstract
The appearance of oxygenic photosynthesis in cyanobacteria is a major event in evolution. It had an irreversible impact on the Earth, promoting the Great Oxygenation Event (GOE) ~2.4 billion years ago. Ancient cyanobacteria predating the GOE were Gloeobacter-type cells lacking thylakoids, which hosted photosystems in their cytoplasmic membrane. The driver of the GOE was proposed to be the transition from unicellular to filamentous cyanobacteria. However, the appearance of thylakoids expanded the photosynthetic surface to such an extent that it introduced a multiplier effect, which would be more coherent with an impact on the atmosphere. Primitive thylakoids self-organize as concentric parietal uninterrupted multilayers. There is no robust evidence for an origin of thylakoids via a vesicular-based scenario. This review reports studies supporting that hexagonal II-forming glucolipids and galactolipids at the periphery of the cytosolic membrane could be turned, within nanoseconds and without any external source of energy, into membrane multilayers. Comparison of lipid biosynthetic pathways shows that ancient cyanobacteria contained only one anionic lamellar-forming lipid, phosphatidylglycerol. The acquisition of sulfoquinovosyldiacylglycerol biosynthesis correlates with thylakoid emergence, possibly enabling sufficient provision of anionic lipids to trigger a hexagonal II-to-lamellar phase transition. With this non-vesicular lipid-phase transition, a framework is also available to re-examine the role of companion proteins in thylakoid biogenesis.
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Affiliation(s)
- Nolwenn Guéguen
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
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7
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Adhyapak P, Dong W, Dasgupta S, Dutta A, Duan M, Kapoor S. Lipid Clustering in Mycobacterial Cell Envelope Layers Governs Spatially Resolved Solvation Dynamics. Chem Asian J 2022; 17:e202200146. [PMID: 35419975 DOI: 10.1002/asia.202200146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/30/2022] [Indexed: 11/06/2022]
Abstract
The mycobacterial cell envelope acts as a multilayered barrier to drugs. However, the role of lipid composition in the properties of different mycobacterial membranes, otherwise dictating their interactions with drugs, is poorly understood. In this study, we found that hydration states, solvation relaxation kinetics, rotational lipid mobility, and lateral lipid diffusion differed between inner and outer mycobacterial membranes. Molecular modeling showed that lipid clustering patterns governed membrane dynamics in the different layers of the cell envelope. By regulating membrane properties, lipid composition and structure modulated water abundance and interactions with lipid head groups. These findings can help deepen our understanding of the physical chemistry underlying membrane structure and function, as well as the interaction of mycobacterial membranes with drugs and host membranes.
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Affiliation(s)
- Pranav Adhyapak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wanqian Dong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Souradip Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Anindya Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mojie Duan
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India.,Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8528, Japan
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8
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Frallicciardi J, Melcr J, Siginou P, Marrink SJ, Poolman B. Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nat Commun 2022; 13:1605. [PMID: 35338137 PMCID: PMC8956743 DOI: 10.1038/s41467-022-29272-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/02/2022] [Indexed: 12/16/2022] Open
Abstract
Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While the cytoplasmic membrane of bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences can arise from the physical state of the plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, we performed a systematic analysis of the permeability of a variety of small molecules through synthetic membranes of different lipid composition to obtain detailed molecular insight into the permeation mechanisms. While membrane thickness is an important parameter for the permeability through fluid membranes, the largest differences occur when the membranes transit from the liquid-disordered to liquid-ordered and/or to gel state, which is in agreement with previous work on passive diffusion of water. By comparing our results with in vivo measurements from yeast, we conclude that the yeast membrane exists in a highly ordered and rigid state, which is comparable to synthetic saturated DPPC-sterol membranes. Membrane permeability of small molecules depends on the composition of the lipid bilayer. Here, authors compare permeability measured on membranes in different physical states and conclude that the yeast membrane exists in a highly ordered phase.
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Affiliation(s)
- Jacopo Frallicciardi
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Josef Melcr
- Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Pareskevi Siginou
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Siewert J Marrink
- Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands.
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands.
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9
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Maer AM, Rusinova R, Providence LL, Ingólfsson HI, Collingwood SA, Lundbæk JA, Andersen OS. Regulation of Gramicidin Channel Function Solely by Changes in Lipid Intrinsic Curvature. Front Physiol 2022; 13:836789. [PMID: 35350699 PMCID: PMC8957996 DOI: 10.3389/fphys.2022.836789] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Membrane protein function is regulated by the lipid bilayer composition. In many cases the changes in function correlate with changes in the lipid intrinsic curvature (c 0), and c 0 is considered a determinant of protein function. Yet, water-soluble amphiphiles that cause either negative or positive changes in curvature have similar effects on membrane protein function, showing that changes in lipid bilayer properties other than c 0 are important-and may be dominant. To further investigate the mechanisms underlying the bilayer regulation of protein function, we examined how maneuvers that alter phospholipid head groups effective "size"-and thereby c 0-alter gramicidin (gA) channel function. Using dioleoylphospholipids and planar bilayers, we varied the head groups' physical volume and the electrostatic repulsion among head groups (and thus their effective size). When 1,2-dioleyol-sn-glycero-3-phosphocholine (DOPC), was replaced by 1,2-dioleyol-sn-glycero-3-phosphoethanolamine (DOPE) with a smaller head group (causing a more negative c 0), the channel lifetime (τ) is decreased. When the pH of the solution bathing a 1,2-dioleyol-sn-glycero-3-phosphoserine (DOPS) bilayer is decreased from 7 to 3 (causing decreased head group repulsion and a more negative c 0), τ is decreased. When some DOPS head groups are replaced by zwitterionic head groups, τ is similarly decreased. These effects do not depend on the sign of the change in surface charge. In DOPE:DOPC (3:1) bilayers, pH changes from 5→9 to 5→0 (both increasing head group electrostatic repulsion, thereby causing a less negative c 0) both increase τ. Nor do the effects depend on the use of planar, hydrocarbon-containing bilayers, as similar changes were observed in hydrocarbon-free lipid vesicles. Altering the interactions among phospholipid head groups may alter also other bilayer properties such as thickness or elastic moduli. Such changes could be excluded using capacitance measurements and single channel measurements on gA channels of different lengths. We conclude that changes gA channel function caused by changes in head group effective size can be predicted from the expected changes in c 0.
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Affiliation(s)
| | | | | | | | | | | | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States
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10
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The Elucidation of the Molecular Mechanism of the Extrusion Process. MATERIALS 2021; 14:ma14154278. [PMID: 34361472 PMCID: PMC8348501 DOI: 10.3390/ma14154278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 02/02/2023]
Abstract
Extrusion is a popular method for producing homogenous population of unilamellar liposomes. The technique relies on forcing a lipid suspension through cylindrical pores in a polycarbonate membrane. The quantification of the extrusion and/or recalibration processes make possible the acquisition of experimental data, which can be correlated with the mechanical properties of the lipid bilayer. In this work, the force needed for the extrusion process was correlated with the mechanical properties of a lipid bilayer derived from other experiments. Measurements were performed using a home-made dedicated device capable of maintaining a stable volumetric flux of a liposome suspension through well-defined pores and to continuously measure the extrusion force. Based on the obtained results, the correlation between the lipid bilayer bending rigidity and extrusion force was derived. Specifically, it was found that the bending rigidity of liposomes formed from well-defined lipid mixtures agrees with data obtained by others using flicker-noise spectroscopy or micromanipulation. The other issue addressed in the presented studies was the identification of molecular mechanisms leading to the formation of unilamellar vesicles in the extrusion process. Finally, it was demonstrated that during the extrusion, lipids are not exchanged between vesicles, i.e., vesicles can divide but no membrane fusion or lipid exchange between bilayers was detected.
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11
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Non-Polar Lipids as Regulators of Membrane Properties in Archaeal Lipid Bilayer Mimics. Int J Mol Sci 2021; 22:ijms22116087. [PMID: 34200063 PMCID: PMC8200183 DOI: 10.3390/ijms22116087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
The modification of archaeal lipid bilayer properties by the insertion of apolar molecules in the lipid bilayer midplane has been proposed to support cell membrane adaptation to extreme environmental conditions of temperature and hydrostatic pressure. In this work, we characterize the insertion effects of the apolar polyisoprenoid squalane on the permeability and fluidity of archaeal model membrane bilayers, composed of lipid analogues. We have monitored large molecule and proton permeability and Laurdan generalized polarization from lipid vesicles as a function of temperature and hydrostatic pressure. Even at low concentration, squalane (1 mol%) is able to enhance solute permeation by increasing membrane fluidity, but at the same time, to decrease proton permeability of the lipid bilayer. The squalane physicochemical impact on membrane properties are congruent with a possible role of apolar intercalants on the adaptation of Archaea to extreme conditions. In addition, such intercalant might be used to cheaply create or modify chemically resistant liposomes (archeaosomes) for drug delivery.
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12
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Loney RW, Brandner B, Dagan MP, Smith PN, Roche M, Fritz JR, Hall SB, Tristram-Nagle SA. Changes in membrane elasticity caused by the hydrophobic surfactant proteins correlate poorly with adsorption of lipid vesicles. SOFT MATTER 2021; 17:3358-3366. [PMID: 33630985 PMCID: PMC8016726 DOI: 10.1039/d0sm02223c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To establish how the hydrophobic surfactant proteins, SP-B and SP-C, promote adsorption of lipids to an air/water interface, we used X-ray diffuse scattering (XDS) to determine an order parameter of the lipid chains (Sxray) and the bending modulus of the lipid bilayers (KC). Samples contained different amounts of the proteins with two sets of lipids. Dioleoylphosphatidylcholine (DOPC) provided a simple, well characterized model system. The nonpolar and phospholipids (N&PL) from extracted calf surfactant provided the biological mix of lipids. For both systems, the proteins produced changes in Sxray that correlated well with KC. The dose-response to the proteins, however, differed. Small amounts of protein generated large decreases in Sxray and KC for DOPC that progressed monotonically. The changes for the surfactant lipids were erratic. Our studies then tested whether the proteins produced correlated effects on adsorption. Experiments measured the initial fall in surface tension during adsorption to a constant surface area, and then expansion of the interface during adsorption at a constant surface tension of 40 mN m-1. The proteins produced a sigmoidal increase in the rate of adsorption at 40 mN m-1 for both lipids. The results correlated poorly with the changes in Sxray and KC in both cases. Disordering of the lipid chains produced by the proteins, and the softening of the bilayers, fail to explain how the proteins promote adsorption of lipid vesicles.
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Affiliation(s)
- Ryan W Loney
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA.
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13
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Yu Y, Krämer A, Venable RM, Brooks BR, Klauda JB, Pastor RW. CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. J Chem Theory Comput 2021; 17:1581-1595. [PMID: 33620194 PMCID: PMC8130185 DOI: 10.1021/acs.jctc.0c01327] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Long-range Lennard-Jones (LJ) interactions have been incorporated into the CHARMM36 (C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to remove the inconsistency of bilayer and monolayer properties arising from the exclusion of long-range dispersion [Yu, Y.; Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J. Chem. Theory Comput. 2021, 10.1021/acs.jctc.0c01326. (preceding article in this issue)]. The new FF is denoted C36/LJ-PME. While the first optimization was based on three phosphatidylcholines (PCs), this work extends the validation and parametrization to more lipids including PC, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and ether lipids. The agreement with experimental structure data is excellent for PC, PE, and ether lipids. C36/LJ-PME also compares favorably with scattering data of PG bilayers but less so with NMR deuterium order parameters of 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) at 303.15 K, indicating a need for future optimization regarding PG-specific parameters. Frequency dependence of NMR T1 spin-lattice relaxation times is well-described by C36/LJ-PME, and the overall agreement with experiment is comparable to C36. Lipid diffusion is slower than C36 due to the added long-range dispersion causing a higher viscosity, although it is still too fast compared to experiment after correction for periodic boundary conditions. When using a 10 Å real-space cutoff, the simulation speed of C36/LJ-PME is roughly equal to C36. While more lipids will be incorporated into the FF in the future, C36/LJ-PME can be readily used for common lipids and extends the capability of the CHARMM FF by supporting monolayers and eliminating the cutoff dependence.
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Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jeffery B Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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14
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Pérez HA, Cejas JP, Rosa AS, Giménez RE, Disalvo EA, Frías MA. Modulation of Interfacial Hydration by Carbonyl Groups in Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2644-2653. [PMID: 32073276 DOI: 10.1021/acs.langmuir.9b03551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lack of carbonyl groups and the presence of ether bonds give the lipid interphase a different water organization around the phosphate groups that affects the compressibility and electrical properties of lipid membranes. Generalized polarization of 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14:0 diether PC) in correlation with Fourier transform infrared (FTIR) analysis indicates a higher level of polarizability of water molecules in the membrane phase around the phosphate groups both below and above Tm. This reorganization of water promotes a different response in compressibility and dipole moment of the interphase, which is related to different H bonding of water molecules with phosphates (PO) and carbonyl (CO) groups.
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Affiliation(s)
- H A Pérez
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
| | - J P Cejas
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
| | - A S Rosa
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
| | - R E Giménez
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
| | - E A Disalvo
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
| | - M A Frías
- Applied Biophysics and Food Research Center (Centro de Investigaciones en Biofisica Aplicada y Alimentos, CIBAAL), National University of Santiago del Estero and CONICET, RN 9, Km 1125, 4206 Santiago del Estero, Argentina
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15
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Salvador-Castell M, Demé B, Oger P, Peters J. Structural Characterization of an Archaeal Lipid Bilayer as a Function of Hydration and Temperature. Int J Mol Sci 2020; 21:ijms21051816. [PMID: 32155764 PMCID: PMC7084678 DOI: 10.3390/ijms21051816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 11/16/2022] Open
Abstract
Archaea, the most extremophilic domain of life, contain ether and branched lipids which provide extraordinary bilayer properties. We determined the structural characteristics of diether archaeal-like phospholipids as functions of hydration and temperature by neutron diffraction. Hydration and temperature are both crucial parameters for the self-assembly and physicochemical properties of lipid bilayers. In this study, we detected non-lamellar phases of archaeal-like lipids at low hydration levels, and lamellar phases at levels of 90% relative humidity or more exclusively. Moreover, at 90% relative humidity, a phase transition between two lamellar phases was discernible. At full hydration, lamellar phases were present up to 70ᵒC and no phase transition was observed within the temperature range studied (from 25 °C to 70 °C). In addition, we determined the neutron scattering length density and the bilayer's structural parameters from different hydration and temperature conditions. At the highest levels of hydration, the system exhibited rearrangements on its corresponding hydrophobic region. Furthermore, the water uptake of the lipids examined was remarkably high. We discuss the effect of ether linkages and branched lipids on the exceptional characteristics of archaeal phospholipids.
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Affiliation(s)
| | - Bruno Demé
- Institut Laue Langevin, 38000 Grenoble, France;
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS, UMR 5240, 69211 Villeurbanne, France;
- Correspondence: (P.O.); (J.P.)
| | - Judith Peters
- Institut Laue Langevin, 38000 Grenoble, France;
- Université Grenoble Alpes, LiPhy, CNRS, 38000 Grenoble, France
- Correspondence: (P.O.); (J.P.)
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16
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Rao BD, Chakraborty H, Chaudhuri A, Chattopadhyay A. Differential sensitivity of pHLIP to ester and ether lipids. Chem Phys Lipids 2019; 226:104849. [PMID: 31836521 DOI: 10.1016/j.chemphyslip.2019.104849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
pH (low) insertion peptide (pHLIP) is a polypeptide from the third transmembrane helix of bacteriorhodopsin. The pH-dependent membrane insertion of pHLIP has been conveniently exploited for translocation of cargo molecules and as a novel imaging agent in cancer biology due to low extracellular pH in cancer tissues. Although the application of pHLIP for imaging tumor and targeted drug delivery is well studied, literature on pHLIP-membrane interaction is relatively less studied. Keeping this in mind, we explored the differential interaction of pHLIP with ester and ether lipid membranes utilizing fluorescence and CD spectroscopy. We report, for the first time, higher binding affinity of pHLIP toward ether lipid relative to ester lipid membranes. There results gain relevance since Halobacterium halobium (source of bacteriorhodopsin) is enriched with ether lipids. In addition, we monitored the difference in microenvironment around pHLIP tryptophans utilizing red edge excitation shift and observed increased motional restriction of water molecules in the interfacial region in ether lipid membranes. These changes were accompanied with increase in helicity of pHLIP in ether lipid relative to ester lipid membranes. Our results assume further relevance since ether lipids are upregulated in cancer cells and have emerged as potential biomarkers of various diseases including cancer.
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Affiliation(s)
- Bhagyashree D Rao
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201 002, India
| | - Hirak Chakraborty
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India
| | - Arunima Chaudhuri
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201 002, India.
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17
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Ghysels A, Krämer A, Venable RM, Teague WE, Lyman E, Gawrisch K, Pastor RW. Permeability of membranes in the liquid ordered and liquid disordered phases. Nat Commun 2019; 10:5616. [PMID: 31819053 PMCID: PMC6901538 DOI: 10.1038/s41467-019-13432-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 11/09/2022] Open
Abstract
The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence of cellular rafts and liquid ordered (Lo) phases of three-component lipid bilayers to examine permeability. Molecular dynamics simulations of Lo phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol show that oxygen and water transit a leaflet through the DOPC and cholesterol rich boundaries of hexagonally packed DPPC microdomains, freely diffuse along the bilayer midplane, and escape the membrane along the boundary regions. Electron paramagnetic resonance experiments provide critical validation: the measured ratio of oxygen concentrations near the midplanes of liquid disordered (Ld) and Lo bilayers of DPPC/DOPC/cholesterol is 1.75 ± 0.35, in very good agreement with 1.3 ± 0.3 obtained from simulation. The results show how cellular rafts can be structurally rigid signaling platforms while remaining nearly as permeable to small molecules as the Ld phase.
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Affiliation(s)
- An Ghysels
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052, Gent, Belgium.
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Walter E Teague
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy and Department of Chemistry and Biochemistry, University of Delaware, Newark, 19716, DE, USA
| | - Klaus Gawrisch
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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18
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Shen H, Zhao K, Wu Z. Effects of Ether Linkage on Membrane Dipole Potential and Cholesterol Flip-Flop Motion in Lipid Bilayer Membranes. J Phys Chem B 2019; 123:7818-7828. [DOI: 10.1021/acs.jpcb.9b06570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University No.115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- Guizhou University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Kun Zhao
- Guizhou University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Zhenhua Wu
- Guizhou University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
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19
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Prislan I, Lokar M, Zirdum M, Valant J, Poklar Ulrih N. Contribution of headgroup and chain length of glycerophospholipids to thermal stability and permeability of liposomes loaded with calcein. Chem Phys Lipids 2019; 225:104807. [PMID: 31390525 DOI: 10.1016/j.chemphyslip.2019.104807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022]
Abstract
Biological membranes are complex systems that are composed of lipids, proteins and carbohydrates. They are difficult to study, so it is established practice to use lipid vesicles that consist of closed 'shells' of phospholipid bilayers as model systems to study various functional and structural aspects of lipid organisation. To define the effects of the structural properties of lipid vesicles on their phase behaviour, we investigated their headgroup and chain length, and the chemical bonds by which their acyl chains are attached to the glycerol moiety of glycerophospholipid species, in terms of phase transition temperature, enthalpy change and calcein permeability. We used differential scanning calorimetry to measure the temperature and enthalpy changes of phase transition, and fluorescence to follow calcein release through the bilayer structure. Our data show that longer acyl chains increase the stability of the lipid bilayers, whereas higher salt concentrations decrease the thermal stability and widen the phase transitions of these lipid bilayers. We discuss the possible reasons for the observed phase transition behaviour.
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Affiliation(s)
- Iztok Prislan
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Maruša Lokar
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Martina Zirdum
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Janez Valant
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
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20
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Krämer A, Pickard FC, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR. Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects. J Chem Theory Comput 2019; 15:3854-3867. [PMID: 31002505 DOI: 10.1021/acs.jctc.9b00016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic nonbonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol overestimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. In contrast, the polarizable SWM4-NDP and SWM6 water models reproduce experimental values to within statistical error. As an alternative to explicitly modeling polarizability, this paper develops an efficient automated workflow to optimize pair-specific Lennard-Jones parameters within an additive FF. Water/hexadecane is used as a prototype and the free energy of water transfer to hexadecane as a target. The optimized model yields quantitative agreement with the experimental transfer free energy and improves the water/hexadecane interfacial tension by 6%. Simulations of five different lipid bilayers show a strong increase of water permeabilities compared to the unmodified CHARMM36 lipid FF which consistently improves match with experiment: the order-of-magnitude underestimate for monounsaturated bilayers is rectified and the factor of 2.8-4 underestimate for saturated bilayers is turned into a factor of 1.5-3 overestimate. While agreement with experiment is decreased for the diffusion constant of water in hexadecane, alkane transfer free energies, and the bilayers' area per lipid, the method provides a permeant-specific route to achieve a wide range of heterogeneous observables via rapidly optimized pairwise parameters.
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Affiliation(s)
- Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,School of Life Sciences , Westlake University , 18 Shilongshan Road , Hangzhou 310024 , Zhejiang China.,Department of Pharmaceutical Science, School of Pharmacy , University of Maryland , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Dirk Reith
- Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Karl N Kirschner
- Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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21
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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22
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Saunders M, Steele M, Lavigne W, Varma S, Pandit SA. Interaction of salt with ether- and ester-linked phospholipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:907-915. [PMID: 30742804 DOI: 10.1016/j.bbamem.2019.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
Abstract
A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. Experiments show that this chemical difference in headgroup-tail linkage does produce distinct differences in model bilayer properties. Here we examine the effects of salt on bilayer structure in the case of an ether-linked lipid bilayer. We use molecular dynamics simulations and compare equilibrium properties of two model lipid bilayers in NaCl salt solution - POPC and its ether-linked analog that we refer to as HOPC. We make the following key observations. The headgroup region of HOPC "adsorbs" fewer ions compared to the headgroup region of POPC. Consistent with this, we note that the Debye screening length in the HOPC system is ∼ 10% shorter than that in the POPC system. Herein, we introduce a protocol to identify the lipid-water interfacial boundary that reproduces the bulk salt distribution consistent with Gouy-Chapman theory. We also note that the HOPC bilayer has excess solvent in the headgroup region when compared to POPC, coinciding with a trough in the electrostatic potential. Waters in this region have longer autocorrelation times and smaller lateral diffusion rates compared to the corresponding region in the POPC bilayer, suggesting that the waters in HOPC are more strongly coordinated to the lipid headgroups. Furthermore, we note that it is this region of tightly coordinated waters in the HOPC system that has a lower density of Na+ ions. Based on these observations we conclude that an ether-linked lipid bilayer has a lower binding affinity for Na+ compared to an ester-linked lipid bilayer.
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Affiliation(s)
- Matthew Saunders
- Department of Cell biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, United States of America.
| | - Mark Steele
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Wyatt Lavigne
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Sameer Varma
- Department of Cell biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, United States of America; Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Sagar A Pandit
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America.
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23
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Hoejholt KL, Mužić T, Jensen SD, Dalgaard LT, Bilgin M, Nylandsted J, Heimburg T, Frandsen SK, Gehl J. Calcium electroporation and electrochemotherapy for cancer treatment: Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy. Sci Rep 2019; 9:4758. [PMID: 30894594 PMCID: PMC6427041 DOI: 10.1038/s41598-019-41188-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2019] [Indexed: 12/21/2022] Open
Abstract
Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy.
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Affiliation(s)
- K L Hoejholt
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - T Mužić
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S D Jensen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - L T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - M Bilgin
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - J Nylandsted
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - T Heimburg
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S K Frandsen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
| | - J Gehl
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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24
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Kumagai A, Dupuy FG, Arsov Z, Elhady Y, Moody D, Ernst RK, Deslouches B, Montelaro RC, Peter Di Y, Tristram-Nagle S. Elastic behavior of model membranes with antimicrobial peptides depends on lipid specificity and d-enantiomers. SOFT MATTER 2019; 15:1860-1868. [PMID: 30702120 PMCID: PMC7485610 DOI: 10.1039/c8sm02180e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In an effort to provide new treatments for the global crisis of bacterial resistance to current antibiotics, we have used a rational approach to design several new antimicrobial peptides (AMPs). The present study focuses on 24-mer WLBU2 and its derivative, D8, with the amino acid sequence, RRWVRRVRRWVRRVVRVVRRWVRR. In D8, all of the valines are the d-enantiomer. We use X-ray low- and wide-angle diffuse scattering data to measure elasticity and lipid chain order. We show a good correlation between in vitro bacterial killing efficiency and both bending and chain order behavior in bacterial lipid membrane mimics; our results suggest that AMP-triggered domain formation could be the mechanism of bacterial killing in both Gram-positive and Gram-negative bacteria. In red blood cell lipid mimics, D8 stiffens and orders the membrane, while WLBU2 softens and disorders it, which correlate with D8's harmless vs. WLBU2's toxic behavior in hemolysis tests. These results suggest that elasticity and chain order behavior can be used to predict mechanisms of bactericidal action and toxicity of new AMPs.
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Affiliation(s)
- Akari Kumagai
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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25
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Chakraborty S, Abbasi A, Bothun GD, Nagao M, Kitchens CL. Phospholipid Bilayer Softening Due to Hydrophobic Gold Nanoparticle Inclusions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13416-13425. [PMID: 30350687 DOI: 10.1021/acs.langmuir.8b02553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Liposome-nanoparticle assemblies (LNAs) are vital in the context of novel targeted drug-delivery systems, in addition to investigating nanoparticle-lipid bilayer interactions. Quantifying membrane structural properties and dynamics in presence of nanoparticle inclusions provides a simple model to elucidate nanoparticle effects on membrane biophysical properties. We present experimental evidences of bilayer softening due to small hydrophobic gold nanoparticle inclusions. LNA structure has been investigated by a combination of cryo-transmission electron microscopy, dynamic light scattering, and small-angle neutron scattering. Neutron spin echo spectroscopy demonstrated a remarkable ∼15% bending modulus decrease for LNAs relative to pure liposomes. Clear dependence of bending modulus on gold nanoparticle diameter and concentration was observed from our observations. Our findings point toward local bilayer fluidization by nanoparticle inclusions leading to an overall bilayer softening. These findings add valuable information to liposomal drug-delivery vehicle design and membrane biophysics research.
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Affiliation(s)
- Saptarshi Chakraborty
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634 , United States
| | - Akram Abbasi
- Department of Chemical Engineering , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| | - Geoffrey D Bothun
- Department of Chemical Engineering , University of Rhode Island , Kingston , Rhode Island 02881 , United States
| | - Michihiro Nagao
- NIST Center for Neutron Research , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
- Center for Exploration of Energy and Matter, Department of Physics , Indiana University , Bloomington , Indiana 47408 , United States
| | - Christopher L Kitchens
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634 , United States
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26
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Shen H, Wu Z, Deng M, Wen S, Gao C, Li S, Wu X. Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipid Bilayers: A Comparative Study of Water Models. J Phys Chem B 2018; 122:9399-9408. [DOI: 10.1021/acs.jpcb.8b06726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Zhenhua Wu
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Mingsen Deng
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Shuiguo Wen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Chenggui Gao
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Shixiong Li
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Xupu Wu
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
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27
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Leonard AN, Pastor RW, Klauda JB. Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers. J Phys Chem B 2018; 122:6744-6754. [PMID: 29870257 DOI: 10.1021/acs.jpcb.8b02743] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Linear ethers such as polyethylene glycol have extensive industrial and medical applications. Additionally, phospholipids containing an ether linkage between the glycerol backbone and hydrophobic tails are prevalent in human red blood cells and nerve tissue. This study uses ab initio results to revise the CHARMM additive (C36) partial-charge and dihedral parameters for linear ethers and develop parameters for the ether-linked phospholipid 1,2-di- O-hexadecyl- sn-glycero-3-phosphocholine (DHPC). The new force field, called C36e, more accurately represents the dihedral potential energy landscape and improves the densities and free energies of hydration of linear ethers. C36e allows more water to penetrate into a DHPC bilayer, increasing the surface area per lipid compared to simulations carried out with the original C36 ether parameters and improving the overall structural properties obtained from X-ray and neutron scattering. Comparison with an ester-linked DPPC bilayer (1,2-dipalmitoyl- sn-phosphatidylcholine) reveals that the ether linkage increases water organization in the headgroup region. This effect is a likely explanation for the experimentally lower water permeability of bilayers composed of ether-linked lipids.
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Affiliation(s)
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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28
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Ether-linked lipids: Spin-label EPR and spin echoes. Chem Phys Lipids 2018; 212:130-137. [DOI: 10.1016/j.chemphyslip.2018.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/22/2022]
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29
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Arsov Z, González-Ramírez EJ, Goñi FM, Tristram-Nagle S, Nagle JF. Phase behavior of palmitoyl and egg sphingomyelin. Chem Phys Lipids 2018; 213:102-110. [PMID: 29689259 DOI: 10.1016/j.chemphyslip.2018.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/02/2018] [Accepted: 03/06/2018] [Indexed: 01/28/2023]
Abstract
Despite the biological significance of sphingomyelins (SMs), there is far less structural information available for SMs compared to glycerophospholipids. Considerable confusion exists in the literature regarding even the phase behavior of SM bilayers. This work studies both palmitoyl (PSM) and egg sphingomyelin (ESM) in the temperature regime from 3 °C to 55 °C using X-ray diffraction and X-ray diffuse scattering on hydrated, oriented thick bilayer stacks. We observe clear evidence for a ripple phase for ESM in a large temperature range from 3 °C to the main phase transition temperature (TM) of ∼38 °C. This unusual stability of the ripple phase was not observed for PSM, which was in a gel phase at 3 °C, with a gel-to-ripple transition at ∼24 °C and a ripple-to-fluid transition at ∼41 °C. We also report structural results for all phases. In the gel phase at 3 °C, PSM has chains tilted by ∼30° with an area/lipid ∼45 Å2 as determined by wide angle X-ray scattering. The ripple phases for both PSM and ESM have temperature dependent ripple wavelengths that are ∼145 Å near 30 °C. In the fluid phase, our electron density profiles combined with volume measurements allow calculation of area/lipid to be ∼64 Å2 for both PSM and ESM, which is larger than that from most of the previous molecular dynamics simulations and experimental studies. Our study demonstrates that oriented lipid films are particularly well-suited to characterize ripple phases since the scattering pattern is much better resolved than in unoriented samples.
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Affiliation(s)
- Zoran Arsov
- Department of Condensed Matter Physics, Laboratory of Biophysics, Jozef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Emilio J González-Ramírez
- Instituto Biofísika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain
| | - Felix M Goñi
- Instituto Biofísika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain
| | | | - John F Nagle
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
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30
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Doktorova M, Harries D, Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys Chem Chem Phys 2018. [PMID: 28627570 DOI: 10.1039/c7cp01921a] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.
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Affiliation(s)
- M Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
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31
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Aloi E, Oranges M, Guzzi R, Bartucci R. Low-Temperature Dynamics of Chain-Labeled Lipids in Ester- and Ether-Linked Phosphatidylcholine Membranes. J Phys Chem B 2017; 121:9239-9246. [PMID: 28892381 DOI: 10.1021/acs.jpcb.7b07386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Continuous wave electron paramagnetic resonance spectroscopy and two-pulse echo detected spectra of chain-labeled lipids are used to study the dynamics of frozen lipid membranes over the temperature range 77-260 K. Bilayers of ester-linked dihexadecanoylphosphatidylcholine (DPPC) with noninterdigitated chains and ether-linked dihexadecyl phosphatidylcholine (DHPC) with interdigitated chains are considered. Rapid stochastic librations of small angular amplitude are found in both lipid matrices. In noninterdigitated DPPC bilayers, the mean-square angular amplitude, [Formula: see text], of the motion increases with temperature and it is larger close to the chain termini than close to the polar/apolar interface. In contrast, in interdigitated DHPC lamellae, [Formula: see text] is small and temperature and label-position independent at low temperature and increases steeply at high temperature. The rotational correlation time, τc, of librations lies in the subnanosecond range for DPPC and in the nanosecond range for DHPC. In all membrane samples, the temperature dependence of [Formula: see text] resembles that of the mean-square atomic displacement revealed by neutron scattering and a dynamical transition is detected in the range 210-240 K. The results highlight the librational oscillations and the glass-like behavior in bilayer and interdigitated lipid membranes.
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Affiliation(s)
- Erika Aloi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Maria Oranges
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rita Guzzi
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
| | - Rosa Bartucci
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria , 87036 Rende (CS), Italy
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32
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Kruczek J, Saunders M, Khosla M, Tu Y, Pandit SA. Molecular dynamics simulations of ether- and ester-linked phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2297-2307. [PMID: 28882547 DOI: 10.1016/j.bbamem.2017.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
Abstract
Dissimilarities in the bulk structure of bilayers composed of ether- vs ester-linked lipids are well-established; however, the atomistic interactions responsible for these differences are not well known. These differences are important in understanding of why archaea have a different bilayer composition than the other domains of life and why humans have larger concentrations of plasmalogens in specialized membranes? In this paper, we simulate two lipid bilayers, the ester linked dipalmitoylphosphatidylcholine (DPPC) and the ether lined dihexadecylphosphatidylcholine (DHPC), to study these variations. The structural analysis of the bilayers reveals that DPPC is more compressible than DHPC. A closer examination of dipole potential shows DHPC, despite having a smaller dipole potential of the bilayer, has a higher potential barrier than DPPC at the surface. Analysis of water order and dynamics suggests DHPC has a more ordered, less mobile layer of water in the headgroup. These results seem to resolve the issue as to whether the decrease in permeability of DHPC is due to of differences in minimum area per lipid (A0) or diffusion coefficient of water in the headgroup region (Dhead) (Guler et al., 2009) since we have shown significant changes in the order and mobility of water in that region.
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Affiliation(s)
- James Kruczek
- Department of Physics, University of South Florida, Tampa, FL 33620, United States.
| | - Matthew Saunders
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Meghna Khosla
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Yicheng Tu
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL 33620, United States
| | - Sagar A Pandit
- Department of Physics, University of South Florida, Tampa, FL 33620, United States.
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33
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Nagle JF. Experimentally determined tilt and bending moduli of single-component lipid bilayers. Chem Phys Lipids 2017; 205:18-24. [PMID: 28412174 DOI: 10.1016/j.chemphyslip.2017.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/24/2017] [Accepted: 04/10/2017] [Indexed: 01/14/2023]
Abstract
Values of the bending modulus KC and the tilt modulus Kθ are reported for single component lipid bilayers. The lipids studied have the common names DOPC, DMPC, diC22:1PC, SOPC, POPC, diPhyPC, DLPC, DPPC, DHPC and DEPC, listed in the order of number of samples examined. The experimental method, thus far the only one that measures the tilt modulus of lipid bilayers, first obtains diffuse X-ray scattering data from oriented stacks of bilayers. The values of the moduli emerge from fitting the data to the accepted tilt-dependent continuum model for the free energy of a single bilayer, further enhanced by interactions between bilayers in the stack. The results indicate the broad trend that the tilt modulus for these PC lipids is smaller the closer the temperature is to the main transition temperature. Another trend is that inclusion of tilt raises the value of the bending modulus more for lipids with smaller values of the tilt modulus. Values of both moduli are compared to recent literature values obtained from simulations and values of the bending modulus are compared to the literature values obtained by other experimental methods.
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Affiliation(s)
- John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
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34
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Jefferies D, Hsu PC, Khalid S. Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes. Biochemistry 2017; 56:1672-1679. [DOI: 10.1021/acs.biochem.6b01063] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
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35
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Carrillo JMY, Katsaras J, Sumpter BG, Ashkar R. A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers. J Chem Theory Comput 2017; 13:916-925. [DOI: 10.1021/acs.jctc.6b00968] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - John Katsaras
- Department
of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
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36
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Tristram-Nagle S. Use of X-Ray and Neutron Scattering Methods with Volume Measurements to Determine Lipid Bilayer Structure and Number of Water Molecules/Lipid. Subcell Biochem 2015; 71:17-43. [PMID: 26438260 DOI: 10.1007/978-3-319-19060-0_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this chapter I begin with a historical perspective of membrane models, starting in the early twentieth century. As these membrane models evolved, so did experiments to characterize the structure and water content of purified lipid bilayers. The wide-spread use of the X-ray gravimetric, or Luzzati method, is critically discussed. The main motivation of the gravimetric technique is to determine the number of water molecules/lipid, n(W), and then derive other important structural quantities, such as area/lipid, A(L). Subsequent experiments from the Nagle/Tristram-Nagle laboratory using X-ray and neutron scattering, first determine A(L) and then calculate n(W), using molecular lipid V(L) and water V(W) volumes. This chapter describes the details of our volume experiments to carefully measure V(L). Our results also determine n(W)', the steric water associated with the lipid headgroup, and how our calculated value compares to many literature values of tightly-associated headgroup water.
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Affiliation(s)
- Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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37
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Milianta PJ, Muzzio M, Denver J, Cawley G, Lee S. Water Permeability across Symmetric and Asymmetric Droplet Interface Bilayers: Interaction of Cholesterol Sulfate with DPhPC. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12187-12196. [PMID: 26492572 DOI: 10.1021/acs.langmuir.5b02748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cellular membranes employ a variety of strategies for controlling the flow of small molecules into the cytoplasmic space, including incorporation of sterols for modulation of permeability and maintenance of lipid asymmetry to provide both sides of the membrane with differing biophysical properties. The specific case of cholesterol asymmetry, especially, is known to have profound effects in neurological cellular systems. Synthetic membrane models that can readily determine valuable physical parameters, such as water transport rates, for sterol-containing membranes of defined lipid composition remain in demand. We report the use of the droplet interface bilayer (DIB), composed of adherent aqueous droplets surrounded by a lipid monolayer and immersed in a hydrophobic medium, for measurement of water permeability across the membrane, with rapid visualization and ease of experimental setup. We studied droplet bilayer membranes composed of the prototypical synthetic membrane lipid (i.e., the archaeal lipid DPhPC) as well as of symmetric and asymmetric DIBs formed by DPhPC and sodium cholesterol sulfate (S-Chol). The presence of S-Chol in DPhPC in symmetric DIB reduced the passive water permeability rate (P(f)) at all concentrations and increased the activation energy (E(a)) to 17-18 kcal/mol. When only one side of the DIB contains S-Chol (asymmetric DIB), an E(a) of 14-15 kcal/mol was obtained, a value intermediate that of pure lipid and symmetrical DIB containing lipid and S-Chol. Our data are consistent with a capability for regulation of water transport by one leaflet independent of the other. The engineering of our various systems is believed to have implications for garnering detailed knowledge regarding the transport of small moieties across bilayers in a wide variety of lipid systems.
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Affiliation(s)
- Peter J Milianta
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michelle Muzzio
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Jacqueline Denver
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Geoffrey Cawley
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
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38
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Venable RM, Brown FLH, Pastor RW. Mechanical properties of lipid bilayers from molecular dynamics simulation. Chem Phys Lipids 2015; 192:60-74. [PMID: 26238099 PMCID: PMC4684433 DOI: 10.1016/j.chemphyslip.2015.07.014] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/11/2015] [Accepted: 07/25/2015] [Indexed: 01/21/2023]
Abstract
Lipid areas (Aℓ), bilayer area compressibilities (KA), bilayer bending constants (KC), and monolayer spontaneous curvatures (c0) from simulations using the CHARMM36 force field are reported for 12 representative homogenous lipid bilayers. Aℓ (or their surrogate, the average deuterium order parameter in the "plateau region" of the chain) agree very well with experiment, as do the KA. Simulated KC are in near quantitative agreement with vesicle flicker experiments, but are somewhat larger than KC from X-ray, pipette aspiration, and neutron spin echo for saturated lipids. Spontaneous curvatures of bilayer leaflets from the simulations are approximately 30% smaller than experimental values of monolayers in the inverse hexagonal phase.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, CA 93106, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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39
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Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophys J 2015; 107:134-45. [PMID: 24988348 DOI: 10.1016/j.bpj.2014.05.034] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/02/2014] [Accepted: 05/23/2014] [Indexed: 12/17/2022] Open
Abstract
The C36 CHARMM lipid force field has been extended to include sphingolipids, via a combination of high-level quantum mechanical calculations on small molecule fragments, and validation by extensive molecular dynamics simulations on N-palmitoyl and N-stearoyl sphingomyelin. NMR data on these two molecules from several studies in bilayers and micelles played a strong role in the development and testing of the force field parameters. Most previous force fields for sphingomyelins were developed before the availability of the detailed NMR data and relied on x-ray diffraction of bilayers alone for the validation; these are shown to be too dense in the bilayer plane based on published chain order parameter data from simulations and experiments. The present simulations reveal O-H:::O-P intralipid hydrogen bonding occurs 99% of the time, and interlipid N-H:::O=C (26-29%, depending on the lipid) and N-H:::O-H (17-19%). The interlipid hydrogen bonds are long lived, showing decay times of 50 ns, and forming strings of lipids, and leading to reorientational correlation time of nearly 100 ns. The spontaneous radius of curvature for pure N-palmitoyl sphingomyelin bilayers is estimated to be 43-100 Å, depending on the assumptions made in assigning a bending constant; this unusual positive curvature for a two-tailed neutral lipid is likely associated with hydrogen bond networks involving the NH of the sphingosine group.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Alexander J Sodt
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Brent Rogaski
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland
| | - Huan Rui
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Elizabeth Hatcher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland.
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Balleza D, Garcia-Arribas AB, Sot J, Ruiz-Mirazo K, Goñi FM. Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains. Biophys J 2015; 107:1364-74. [PMID: 25229144 DOI: 10.1016/j.bpj.2014.07.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/03/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022] Open
Abstract
We studied the properties of bilayers formed by ether-and ester-containing phospholipids, whose hydrocarbon chains can be either linear or branched, using sn-1,2 dipalmitoyl, dihexadecyl, diphytanoyl, and diphytanyl phosphatidylcholines (DPPC, DHPC, DPhoPC, and DPhPC, respectively) either pure or in binary mixtures. Differential scanning calorimetry and confocal fluorescence microscopy of giant unilamellar vesicles concurred in showing that equimolar mixtures of linear and branched lipids gave rise to gel/fluid phase coexistence at room temperature. Mixtures containing DHPC evolved in time (0.5 h) from initial reticulated domains to extended solid ones when an equilibrium was achieved. The nanomechanical properties of supported planar bilayers formed by each of the four lipids studied by atomic force microscopy revealed average breakdown forces Fb decreasing in the order DHPC ≥ DPPC > DPhoPC >> DPhPC. Moreover, except for DPPC, two different Fb values were found for each lipid. Atomic force microscopy imaging of DHPC was peculiar in showing two coexisting phases of different heights, probably corresponding to an interdigitated gel phase that gradually transformed, over a period of 0.5 h, into a regular tilted gel phase. Permeability to nonelectrolytes showed that linear-chain phospholipids allowed a higher rate of solute + water diffusion than branched-chain phospholipids, yet the former supported a smaller extent of swelling of the corresponding vesicles. Ether or ester bonds appeared to have only a minor effect on permeability.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Aritz B Garcia-Arribas
- Unidad de Biofísica CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Jesús Sot
- Unidad de Biofísica CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Kepa Ruiz-Mirazo
- Unidad de Biofísica CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain; Departamento de Lógica y Filosofía de la Ciencia, UPV/EHU, Donostia-San Sebastián, Spain
| | - Félix M Goñi
- Unidad de Biofísica CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain.
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Yasmann A, Sukharev S. Properties of diphytanoyl phospholipids at the air-water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:350-357. [PMID: 25474305 DOI: 10.1021/la503800g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diphytanoylphosphatidyl choline (DPhPC) is a synthetic ester lipid with methylated tails found in archaeal ether lipids. Because of the stability of DPhPC bilayers and the absence of phase transitions over a broad range of temperatures, the lipid is used as an artificial membrane matrix for the reconstitution of channels, pumps, and membrane-active peptides. We characterized monomolecular films made of DPhPC and its natural ether analog DOPhPC at the air-water interface. We measured compression isotherms and dipole potentials of films made of DPhPC, DPhPE, and DOPhPC. We determined that at 40 mN/m the molecular area of DPhPC is 81.2 Å(2), consistent with X-ray and neutron scattering data obtained in liposomes. This indicates that 40 mN/m is the monolayer-bilayer equivalence pressure for this lipid. At this packing density, the compressibility modulus (Cs(-1 )= 122 ± 7 mN/m) and interfacial dipole potential (V = 355 ± 16 mV) were near their maximums. The molecular dipole moment was estimated to be 0.64 ± 0.02 D. The ether DOPhPC compacted to 70.4 Å(2)/lipid at 40 mN/m displaying a peak compressibility similar to that of DPhPC. The maximal dipole potential of the ether lipid was about half of that for DPhPC at this density, and the elemental dipole moment was about a quarter. The spreading of DPhPC and DOPhPC liposomes reduced the surface tension of the aqueous phase by 46 and 49 mN/m, respectively. This corresponds well to the monolayer collapse pressure. The equilibration time shortened as the temperature increased from 20 to 60 °C, but the surface pressure at equilibrium did not change. The data illustrates the properties of branched chains and the contributions of ester bonds in setting the mechanical and electrostatic parameters of diphytanoyl lipids. These properties determine an environment in which reconstituted voltage- or mechano-activated proteins may function. Electrostatic properties are important in the preparation of asymmetric folded bilayers, whereas lateral compressibility defines the tension in mechanically stimulated droplet interface bilayers.
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Affiliation(s)
- Anthony Yasmann
- Department of Biology, University of Maryland , College Park, Maryland 20742, United States
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Chen D, Santore MM. 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)-rich domain formation in binary phospholipid vesicle membranes: two-dimensional nucleation and growth. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:9484-9493. [PMID: 25084141 DOI: 10.1021/la502089t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Decades of study have probed phase transitions in model phospholipid bilayers and vesicles, especially in the context of the equilibrium phase diagram. Critical to the response of vesicles to environmental triggers, to the ultimate domain morphology, and to the approach to equilibrium (or not), we present here a study of domain formation in vesicles, focusing on a mechanism by which the cooling rate, tension, and composition affect the first appearance (nucleation) and subsequent growth of solid membrane domains. Employing a popular mixed membrane model based on DOPC and DPPC (1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, respectively), we examined phase separation in giant two-component vesicles that were cooled from the one-phase fluid (Lα) region of the phase diagram into a region of fluid (Lα)-solid coexistence. At moderate and low membrane tensions, cooling produced solid DPPC-rich domains appearing as compact patches or irregular hexagons and likely with a Pβ' (ripple) arrangement. (The compact solid domains in this study differed distinctly from striped domains in vesicles of the same composition, in terms of molecular organization and conditions of first appearance during cooling.) The amounts of these solid domains were shown to adhere to the lever arm rule for a tie line on the phase diagram, with a solid composition near 95 mol % DPPC. The nucleation of the compact solid domains occurred in a short period, followed by rapid addition of ordered molecules to the nucleated domains, excluding tracer dye. The two-dimensional nucleation density of these compact solid domains (in the range of 10(-2)-10(-1) μm(-2)) was found to increase with the cooling rate (equivalent to the quench depth) with a greater than linear dependence. The 2-D nucleation density was also seen to decrease with membrane tension, presumably because membrane tension increases the line tension around a domain that opposes nucleation. A sigmoidal dependence of the nucleation density on the DPPC concentration was also found. With cooling rates in excess of ∼1 °C/min, solid domains persisted down to room temperature, likely passing from a preferred equilibrium to a local equilibrium with continued cooling. As a result of the persistence of the originally nucleated domains and the conservation of DPPC in the membrane, we observed an increasingly greater number of smaller domains with increased cooling rates. The domains in these vesicles were compact or hexagonal-shaped in contrast to flower-shaped dendritic domains in the same membrane system in a supported membrane configuration.
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Affiliation(s)
- Dong Chen
- Department of Physics and ‡Department of Polymer Science and Engineering, University of Massachusetts , Amherst, Massachusetts 01003, United States
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43
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Jiménez-Rojo N, García-Arribas AB, Sot J, Alonso A, Goñi FM. Lipid bilayers containing sphingomyelins and ceramides of varying N-acyl lengths: A glimpse into sphingolipid complexity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:456-64. [DOI: 10.1016/j.bbamem.2013.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 12/15/2022]
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The alteration of lipid bilayer dynamics by phloretin and 6-ketocholestanol. Chem Phys Lipids 2013; 178:38-44. [PMID: 24316311 DOI: 10.1016/j.chemphyslip.2013.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/13/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023]
Abstract
Lipid bilayer properties are quantified with a variety of arbitrary selected parameters such as molecular packing and dynamics, electrostatic potentials or permeability. In the paper we determined the effect of phloretin and 6-ketocholestanol (dipole potential modifying agents) on the membrane hydration and efficiency of the trans-membrane water flow. The dynamics of water molecules within the lipid bilayer interface was evaluated using solvent relaxation method, whereas the osmotically induced trans-membrane water flux was estimated with the stopped-flow method using the liposome shrinkage kinetics. The presence of phloretin or 6-ketocholestanol resulted in a change of both, the interfacial hydration level and osmotically driven water fluxes. Specifically, the presence of 6-ketocholestanol reduced the amount and mobility of water in the membrane interface. It also slows the osmotically induced water flow. The interfacial hydration change caused by phloretin was much smaller and the effect on osmotically induced water flow was opposite to that of 6-ketocholestanol.
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45
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Oger PM, Cario A. Adaptation of the membrane in Archaea. Biophys Chem 2013; 183:42-56. [PMID: 23915818 DOI: 10.1016/j.bpc.2013.06.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 06/25/2013] [Accepted: 06/25/2013] [Indexed: 12/11/2022]
Abstract
Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life.
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Affiliation(s)
- Philippe M Oger
- CNRS UMR 5276, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon cedex 07, France.
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Budvytyte R, Valincius G, Niaura G, Voiciuk V, Mickevicius M, Stauffer H, Goh HZ, Shekhar P, Heinrich F, Shenoy S, Lösche M, Vanderah DJ. Structure and properties of tethered bilayer lipid membranes with unsaturated anchor molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8645-56. [PMID: 23745652 PMCID: PMC3753044 DOI: 10.1021/la401132c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The self-assembled monolayers (SAMs) of new lipidic anchor molecule HC18 [Z-20-(Z-octadec-9-enyloxy)-3,6,9,12,15,18,22-heptaoxatetracont-31-ene-1-thiol] and mixed HC18/β-mercaptoethanol (βME) SAMs were studied by spectroscopic ellipsometry, contact angle measurements, reflection-absorption infrared spectroscopy, and electrochemical impedance spectroscopy (EIS) and were evaluated in tethered bilayer lipid membranes (tBLMs). Our data indicate that HC18, containing a double bond in the alkyl segments, forms highly disordered SAMs up to anchor/βME molar fraction ratios of 80/20 and result in tBLMs that exhibit higher lipid diffusion coefficients relative to those of previous anchor compounds with saturated alkyl chains, as determined by fluorescence correlation spectroscopy. EIS data shows the HC18 tBLMs, completed by rapid solvent exchange or vesicle fusion, form more easily than with saturated lipidic anchors, exhibit excellent electrical insulating properties indicating low defect densities, and readily incorporate the pore-forming toxin α-hemolysin. Neutron reflectivity measurements on HC18 tBLMs confirm the formation of complete tBLMs, even at low tether compositions and high ionic lipid compositions. Our data indicate that HC18 results in tBLMs with improved physical properties for the incorporation of integral membrane proteins (IMPs) and that 80% HC18 tBLMs appear to be optimal for practical applications such as biosensors where high electrical insulation and IMP/peptide reconstitution are imperative.
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Affiliation(s)
- Rima Budvytyte
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Gintaras Valincius
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Gediminas Niaura
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | - Vladislava Voiciuk
- Institute of Biochemistry, Vilnius University, Vilnius, LT-08662, Lithuania
| | | | - Hilary Stauffer
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Hood College, Frederick, MD 21701
| | - Haw-Zan Goh
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | | | - Frank Heinrich
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Siddharth Shenoy
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Mathias Lösche
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - David J. Vanderah
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850
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Pogozheva ID, Tristram-Nagle S, Mosberg HI, Lomize AL. Structural adaptations of proteins to different biological membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2592-608. [PMID: 23811361 DOI: 10.1016/j.bbamem.2013.06.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 06/19/2013] [Indexed: 02/06/2023]
Abstract
To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds.
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Affiliation(s)
- Irina D Pogozheva
- College of Pharmacy, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.
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Pan J, Cheng X, Heberle FA, Mostofian B, Kučerka N, Drazba P, Katsaras J. Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations. J Phys Chem B 2012. [PMID: 23199292 DOI: 10.1021/jp310345j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup's phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.
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Affiliation(s)
- Jianjun Pan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.
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Smith EA, Dea PK. Influence of the interdigitated gel phase in mixtures of ether-linked and monofluorinated ester-linked phospholipids. Chem Phys Lipids 2012; 165:818-25. [DOI: 10.1016/j.chemphyslip.2012.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
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50
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Heberle FA, Pan J, Standaert RF, Drazba P, Kučerka N, Katsaras J. Model-based approaches for the determination of lipid bilayer structure from small-angle neutron and X-ray scattering data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:875-90. [PMID: 22588484 DOI: 10.1007/s00249-012-0817-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/29/2012] [Accepted: 04/15/2012] [Indexed: 10/28/2022]
Abstract
Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Kučerka et al. (Biophys J 95:2356-2367, 2008; J Phys Chem B 116:232-239, 2012). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent to these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of naturally disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structure parameters, including the much-sought-after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data, as well as the implementation of local volume conservation within the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.
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Affiliation(s)
- Frederick A Heberle
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6100, USA.
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