1
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Jiang W, Lin YC, Luo YL. Mechanical properties of anionic asymmetric bilayers from atomistic simulations. J Chem Phys 2021; 154:224701. [PMID: 34241213 PMCID: PMC8189722 DOI: 10.1063/5.0048232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/12/2021] [Indexed: 11/14/2022] Open
Abstract
Mechanotransduction, the biological response to mechanical stress, is often initiated by activation of mechanosensitive (MS) proteins upon mechanically induced deformations of the cell membrane. A current challenge in fully understanding this process is in predicting how lipid bilayers deform upon the application of mechanical stress. In this context, it is now well established that anionic lipids influence the function of many proteins. Here, we test the hypothesis that anionic lipids could indirectly modulate MS proteins by alteration of the lipid bilayer mechanical properties. Using all-atom molecular dynamics simulations, we computed the bilayer bending rigidity (KC), the area compressibility (KA), and the surface shear viscosity (ηm) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC) lipid bilayers with and without phosphatidylserine (PS) or phosphatidylinositol bisphosphate (PIP2) at physiological concentrations in the lower leaflet. Tensionless leaflets were first checked for each asymmetric bilayer model, and a formula for embedding an asymmetric channel in an asymmetric bilayer is proposed. Results from two different sized bilayers show consistently that the addition of 20% surface charge in the lower leaflet of the PC bilayer with PIP2 has minimal impact on its mechanical properties, while PS reduced the bilayer bending rigidity by 22%. As a comparison, supplementing the PIP2-enriched PC membrane with 30% cholesterol, a known rigidifying steroid lipid, produces a significant increase in all three mechanical constants. Analysis of pairwise splay moduli suggests that the effect of anionic lipids on bilayer bending rigidity largely depends on the number of anionic lipid pairs formed during simulations. The potential implication of bilayer bending rigidity is discussed in the framework of MS piezo channels.
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Affiliation(s)
- Wenjuan Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, USA
| | - Yi-Chun Lin
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, USA
| | - Yun Lyna Luo
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, USA
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2
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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3
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Ou L, Corradi V, Tieleman DP, Liang Q. Atomistic Simulations on Interactions between Amphiphilic Janus Nanoparticles and Lipid Bilayers: Effects of Lipid Ordering and Leaflet Asymmetry. J Phys Chem B 2020; 124:4466-4475. [DOI: 10.1021/acs.jpcb.9b11989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luping Ou
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
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4
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Galván-Hernández A, Kobayashi N, Hernández-Cobos J, Antillón A, Nakabayashi S, Ortega-Blake I. Morphology and dynamics of domains in ergosterol or cholesterol containing membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183101. [DOI: 10.1016/j.bbamem.2019.183101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/02/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022]
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5
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Nepal B, Leveritt J, Lazaridis T. Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling. Biophys J 2019; 114:2128-2141. [PMID: 29742406 DOI: 10.1016/j.bpj.2018.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/24/2018] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Sensing and generation of lipid membrane curvature, mediated by the binding of specific proteins onto the membrane surface, play crucial roles in cell biology. A number of mechanisms have been proposed, but the molecular understanding of these processes is incomplete. All-atom molecular dynamics simulations have offered valuable insights but are extremely demanding computationally. Implicit membrane simulations could provide a viable alternative, but current models apply only to planar membranes. In this work, the implicit membrane model 1 is extended to spherical and tubular membranes. The geometric change from planar to curved shapes is straightforward but insufficient for capturing the full curvature effect, which includes changes in lipid packing. Here, these packing effects are taken into account via the lateral pressure profile. The extended implicit membrane model 1 is tested on the wild-types and mutants of the antimicrobial peptide magainin, the ALPS motif of arfgap1, α-synuclein, and an ENTH domain. In these systems, the model is in qualitative agreement with experiments. We confirm that favorable electrostatic interactions tend to weaken curvature sensitivity in the presence of strong hydrophobic interactions but may actually have a positive effect when those are weak. We also find that binding to vesicles is more favorable than binding to tubes of the same diameter and that the long helix of α-synuclein tends to orient along the axis of tubes, whereas shorter helices tend to orient perpendicular to it. Adoption of a specific orientation could provide a mechanism for coupling protein oligomerization to tubule formation.
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Affiliation(s)
- Binod Nepal
- Department of Chemistry, City College of New York, New York, New York
| | - John Leveritt
- Department of Chemistry, Newman University, Wichita, Kansas
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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6
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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7
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Aguayo-Ortiz R, Straub JE, Dominguez L. Influence of membrane lipid composition on the structure and activity of γ-secretase. Phys Chem Chem Phys 2018; 20:27294-27304. [PMID: 30357233 PMCID: PMC11260083 DOI: 10.1039/c8cp04138e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
γ-Secretase (GS) is a multi-subunit membrane-embedded aspartyl protease that cleaves more than 80 integral membrane proteins, including the amyloid precursor protein (APP) to produce the amyloid-β (Aβ) peptide. Oligomerization and aggregation of the 42-amino acid length Aβ isoform in the brain has been associated with the development and progression of Alzheimer's disease (AD). Based on recent experimental structural studies and using multiscale computational modeling approaches, the conformational states and protein-membrane interactions of the GS complex embedded in six homogeneous and six heterogeneous lipid bilayers were characterized. In order to identify potential lipid and cholesterol binding sites, GS regions with high lipid/cholesterol occupancy values were analyzed using atomistic and coarse-grained simulations. Long lipid residence times were observed to be correlated with a large number of hydrogen bonds between the charged headgroups and key GS amino acids. This observation provides a plausible explanation for the inhibition of GS by charged lipids observed in previous experimental studies. Computed lateral pressure profiles suggest that higher transmembrane pressures favor active state conformations of the catalytic subunit. A probable mechanism for the regulation of the local stress response in cholesterol-rich multicomponent lipid bilayers is identified. Finally, it is demonstrated that interactions between the nicastrin extracellular domain and lipid headgroups leads to a compact structural conformation of the GS complex. Overall, this study provides valuable insight into the effect of bilayer lipid composition on the GS structural ensemble and its function.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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8
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Palaiokostas M, Ding W, Shahane G, Orsi M. Effects of lipid composition on membrane permeation. SOFT MATTER 2018; 14:8496-8508. [PMID: 30346462 DOI: 10.1039/c8sm01262h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Passive permeation through lipid membranes is an essential process in biology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar sheet-like structures, which are predominant in nature. Nonlamellar lipids, when isolated, instead form more geometrically complex nonlamellar phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous lamellar bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties, which in turn may alter related biological processes. This work focuses on one such process, i.e., permeation, by utilising atomistic molecular dynamics simulations in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients for a series of thirteen small molecules and drugs. Each permeant is tested on two bilayer membranes of different lipid composition, i.e., purely lamellar and mixed lamellar/nonlamellar. Our results indicate that the presence of nonlamellar lipids reduces permeation for smaller molecules (molecular weight < 100) but facilitates it for the largest ones (molecular weight > 100). This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
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Affiliation(s)
- Michail Palaiokostas
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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9
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Baul U, Vemparala S. Influence of lipid composition of model membranes on methacrylate antimicrobial polymer-membrane interactions. SOFT MATTER 2017; 13:7665-7676. [PMID: 28991313 DOI: 10.1039/c7sm01211j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using atomistic molecular dynamics simulations, the role of lipid composition in the interactions of multiple methacrylate antimicrobial polymer agents with model membranes, and the consequent response of the membranes is studied. In our earlier study, methacrylate polymers were observed to induce phase demixing and associated thickness mismatch in a POPE-POPG model microbial membrane. In this work, we probe (1) the role of varying the degree of saturation in lipid acyl chains in the membrane interactions of methacrylate polymers, and (2) whether electrostatics (addition of anionic lipids) can influence the interactions of the polymers with model mammalian membranes. Lipid composition is observed to significantly modify membrane-polymer interactions, leading to differences in both the mode of partitioning and the conformations adopted by the polymers, in addition to impacting membrane properties differently. The results strongly suggest that the oft-cited electrostatic interactions between the antimicrobial agents and the microbial membranes do not fully account for the recognition and subsequent partitioning of the antimicrobial agents. The ability of the methacrylate polymers to sense interfacial lipid packing defects, determined by the PE/PC head groups of lipids, is also found to be influential in their membrane partitioning. Deliberate inclusion of charged anionic lipids into a model mammalian membrane, leading to additional favorable electrostatics, does not reproduce a similar polymer partitioning mechanism to that in its microbial counterpart. The differences observed in the interactions of methacrylate polymers with the various model membranes can be instrumental in extending our understanding of underlying modes of membrane disruption by general antimicrobial agents as well.
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Affiliation(s)
- Upayan Baul
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St., A5300, Austin, TX 78712-1224, USA.
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10
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Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW. Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. Biophys J 2017; 112:1198-1213. [PMID: 28355547 DOI: 10.1016/j.bpj.2017.01.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/11/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed. Moreover, it directly controls the sensitivity to curvature stress. The curvature stress and hydrophobic surfaces of the all-atom and continuum models are found to be in excellent agreement. The continuum model is applied to estimate the enrichment of hydrophobically matched lipids near the channel in a mixture, and the results agree with single-channel experiments and extended molecular dynamics simulations from the companion article by Beaven et al. in this issue of Biophysical Journal.
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Affiliation(s)
- Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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11
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Patrick JW, Gamez RC, Russell DH. The Influence of Lipid Bilayer Physicochemical Properties on Gramicidin A Conformer Preferences. Biophys J 2017; 110:1826-1835. [PMID: 27119642 DOI: 10.1016/j.bpj.2016.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 11/19/2022] Open
Abstract
The conformational preferences adopted by gramicidin A (GA) dimers inserted into phospholipid bilayers are reported as a function of the bilayer cholesterol content, temperature, and incubation time. Through use of vesicle capture-freeze drying methodology, GA dimers were captured in lipid bilayers and the conformational preferences of the complex were analyzed using ion mobility-mass spectrometry. Perturbations that affect the physicochemical interactions in the lipid bilayer such as cholesterol incorporation, temperature, and incubation time directly alter the conformer preferences of the complex. Regardless of bilayer cholesterol concentration, the antiparallel double helix (ADH) conformation was observed to be most abundant for GA dimers in bilayers composed of lipids with 12 to 22 carbon acyl chains. Incorporation of cholesterol into lipid bilayers yields increased bilayer thickness and rigidity, and an increased abundance of parallel double helix (PDH) and single-stranded head-to-head (SSHH) dimers were observed. Bilayers prepared using 1,2-dilauroyl-sn-glycero-3-phosphocholine, a lipid with 12 carbon acyl chains, yielded a nascent conformer that decreased in abundance as a function of bilayer cholesterol content. High resolution ion mobility-mass spectrometry data revealed two peaks in the ADH region suggesting that ADH populations are composed of two distinct conformers. The conformer preferences of GA dimers from 1,2-distearoyl-sn-glycero-3-phosphocholine bilayers were significantly different for samples incubated at 4°C vs. 60°C; increased cholesterol content yielded more PDH and SSHH at 60°C. The addition of cholesterol as well as incubating samples of 1,2-distearoyl-sn-glycero-3-phosphocholine at 60°C for 24-72 h yielded an increase in PDH and SSHH abundance.
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Affiliation(s)
- John W Patrick
- Department of Chemistry, Texas A&M University, College Station, Texas
| | - Roberto C Gamez
- Department of Chemistry, Texas A&M University, College Station, Texas
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas.
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12
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Sciacca MFM, Lolicato F, Di Mauro G, Milardi D, D'Urso L, Satriano C, Ramamoorthy A, La Rosa C. The Role of Cholesterol in Driving IAPP-Membrane Interactions. Biophys J 2017; 111:140-51. [PMID: 27410742 DOI: 10.1016/j.bpj.2016.05.050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/15/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Our knowledge of the molecular events underlying type 2 diabetes mellitus-a protein conformational disease characterized by the aggregation of islet amyloid polypeptide (IAPP) in pancreatic β cells-is limited. However, amyloid-mediated membrane damage is known to play a key role in IAPP cytotoxicity, and therefore the effects of lipid composition on modulating IAPP-membrane interactions have been the focus of intense research. In particular, membrane cholesterol content varies with aging and consequently with adverse environmental factors such as diet and lifestyle, but its role in the development of the disease is controversial. In this study, we employ a combination of experimental techniques and in silico molecular simulations to shed light on the role of cholesterol in IAPP aggregation and the related membrane disruption. We show that if anionic POPC/POPS vesicles are used as model membranes, cholesterol has a negligible effect on the kinetics of IAPP fibril growth on the surface of the bilayer. In addition, cholesterol inhibits membrane damage by amyloid-induced poration on membranes, but enhances leakage through fiber growth on the membrane surface. Conversely, if 1:2 DOPC/DPPC raft-like model membranes are used, cholesterol accelerates fiber growth. Next, it enhances pore formation and suppresses fiber growth on the membrane surface, leading to leakage. Our results highlight a twofold effect of cholesterol on the amyloidogenicity of IAPP and help explain its debated role in type 2 diabetes mellitus.
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Affiliation(s)
- Michele F M Sciacca
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Fabio Lolicato
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy; Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Giacomo Di Mauro
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Danilo Milardi
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Luisa D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Chemistry, University of Michigan, Ann Arbor, Michigan; Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse, Garching, Germany.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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13
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Fábián B, Sega M, Voloshin VP, Medvedev NN, Jedlovszky P. Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics. J Phys Chem B 2017; 121:2814-2824. [DOI: 10.1021/acs.jpcb.7b00990] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Balázs Fábián
- Department of Inorganic
and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
- Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon, France
| | - Marcello Sega
- Faculty of
Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Vladimir P. Voloshin
- Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolai N. Medvedev
- Novosibirsk State University, Novosibirsk 630090, Russia
- Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University, Leányka utca 6, H-3300 Eger, Hungary
- MTA-BME Research Group of Technical Analytical Chemistry, Szent Gellért tér
4, H-1111 Budapest, Hungary
- Laboratory of Interfaces and Nanosize Systems,
Institute of Chemistry, Eötvös Loránd University, Pázmány Peter Stny 1/A, H-1117 Budapest, Hungary
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14
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Ting CL, Müller M. Membrane stress profiles from self-consistent field theory. J Chem Phys 2017; 146:104901. [PMID: 28298095 DOI: 10.1063/1.4977585] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Using self-consistent field theory (SCFT), we develop an accurate, local expression for the stress profiles in membranes and soft matter interfaces, in general. The bond stresses are expressed in terms of pre-computed chain propagators, which are used to describe the statistical weight of the molecules and therefore require minimal additional calculations. In addition, we overcome the resolution limit of the molecular bond length by including the Irving and Kirkwood bond assignment and recover a constant normal stress profile across an interface. Using this theory, we find that the membrane lateral stress profile contains repulsive (positive) stresses in the regions of the head and tail groups, and attractive (negative) stresses near the hydrophobic/hydrophilic interface. We also verify that the zeroth and first moments of the stress profile correspond to the thermodynamic tension and product of the bending modulus and the spontaneous curvature, respectively.
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Affiliation(s)
- Christina L Ting
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Göttingen 37077, Germany
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15
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Poger D, Caron B, Mark AE. Validating lipid force fields against experimental data: Progress, challenges and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1556-65. [DOI: 10.1016/j.bbamem.2016.01.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/07/2016] [Accepted: 01/27/2016] [Indexed: 01/16/2023]
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16
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Meikle TG, Conn CE, Separovic F, Drummond CJ. Exploring the structural relationship between encapsulated antimicrobial peptides and the bilayer membrane mimetic lipidic cubic phase: studies with gramicidin A′. RSC Adv 2016. [DOI: 10.1039/c6ra13658c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Lipid based bicontinuous cubic mesophases provide a low-cost, robust membrane mimetic nanomaterial which allows for the incorporation of membrane peptides and proteins.
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Affiliation(s)
- Thomas G. Meikle
- School of Chemistry
- Bio21 Institute
- University of Melbourne
- Australia
- CSIRO Manufacturing Flagship
| | - Charlotte E. Conn
- School of Science
- College of Science, Engineering and Health
- RMIT University
- Melbourne
- Australia
| | | | - Calum J. Drummond
- CSIRO Manufacturing Flagship
- Clayton
- Australia
- School of Science
- College of Science, Engineering and Health
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17
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Ding W, Palaiokostas M, Wang W, Orsi M. Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics. J Phys Chem B 2015; 119:15263-74. [PMID: 26560961 DOI: 10.1021/acs.jpcb.5b06604] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase, ubiquitous in biology. Nonlamellar lipids, such as dioleoylphosphatidylethanolamine (DOPE), prefer instead to form nonlamellar phases, which are mostly nonbiological. However, nonlamellar lipids mix with lamellar lipids in biomembrane structures that remain overall lamellar. Importantly, changes in the lamellar vs nonlamellar lipid composition are believed to affect membrane function and modulate membrane proteins. In this work, we employ atomistic molecular dynamics simulations to quantify how a range of bilayer properties are altered by variations in the lamellar vs nonlamellar lipid composition. Specifically, we simulate five DOPC/DOPE bilayers at mixing ratios of 1/0, 3/1, 1/1, 1/3, and 0/1. We examine properties including lipid area and bilayer thickness, as well as the transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. While the bilayer structure is only marginally altered by lipid composition changes, dramatic effects are observed for the lateral pressure, electric field, and dipole potential profiles. Possible implications for membrane function are discussed.
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Affiliation(s)
- Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Wen Wang
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Mario Orsi
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
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18
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Baul U, Kuroda K, Vemparala S. Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes. J Chem Phys 2015; 141:084902. [PMID: 25173040 DOI: 10.1063/1.4893440] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.
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Affiliation(s)
- Upayan Baul
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109, USA
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
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19
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Molecular dynamics simulations of lipid membranes with lateral force: Rupture and dynamic properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:994-1002. [DOI: 10.1016/j.bbamem.2013.12.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 12/15/2013] [Accepted: 12/18/2013] [Indexed: 01/06/2023]
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20
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Vanegas JM, Torres-Sánchez A, Arroyo M. Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations. J Chem Theory Comput 2014; 10:691-702. [DOI: 10.1021/ct4008926] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Juan M. Vanegas
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | | | - Marino Arroyo
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
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21
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Zhan H, Lazaridis T. Inclusion of lateral pressure/curvature stress effects in implicit membrane models. Biophys J 2013; 104:643-54. [PMID: 23442915 DOI: 10.1016/j.bpj.2012.12.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 02/06/2023] Open
Abstract
Implicit membrane models usually treat the membrane as a hydrophobic slab and neglect lateral pressure/curvature stress effects. As a result, they cannot distinguish, for example, PE from PC lipids. Here, the implicit membrane model IMM1 is extended to include these effects using a combination of classical thermodynamics and membrane elasticity theory. The proposed model is tested by molecular dynamics simulation of the peptides alamethicin, melittin, cyclotide kalata B1, 18A, and KKpL15. The lateral pressure term stabilizes interfacial binding due to the negative pressure at the hydrocarbon-water interface. In agreement with experiment, increase in the peptide/lipid molar ratio shifts the equilibrium from the interfacial to the transmembrane orientation. Simulations of mixed DOPC/DOPE bilayers show that increase of the DOPE mole fraction in general stabilizes interfacial orientations and destabilizes transmembrane orientations. The extent of the stabilization or destabilization varies depending on the exact position of the peptides. The computational results are in good agreement with experiments.
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Affiliation(s)
- Huan Zhan
- Department of Chemistry, City College of New York/City University of New York, New York, New York, USA
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22
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West A, Ma K, Chung JL, Kindt JT. Simulation Studies of Structure and Edge Tension of Lipid Bilayer Edges: Effects of Tail Structure and Force-Field. J Phys Chem A 2013; 117:7114-23. [DOI: 10.1021/jp400371k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ana West
- Department
of Chemistry, Emory University, Atlanta,
Georgia 30322, United States
| | - Kevin Ma
- Department
of Chemistry, Emory University, Atlanta,
Georgia 30322, United States
| | - Jonathan L. Chung
- Department
of Chemistry, Emory University, Atlanta,
Georgia 30322, United States
| | - James T. Kindt
- Department
of Chemistry, Emory University, Atlanta,
Georgia 30322, United States
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23
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López Cascales J, Oliveira Costa S. Effect of the interfacial tension and ionic strength on the thermodynamic barrier associated to the benzocaine insertion into a cell membrane. Biophys Chem 2013; 172:1-7. [DOI: 10.1016/j.bpc.2012.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/04/2012] [Accepted: 12/05/2012] [Indexed: 11/29/2022]
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24
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Reigada R. Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia. PLoS One 2013; 8:e52631. [PMID: 23300982 PMCID: PMC3534722 DOI: 10.1371/journal.pone.0052631] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/20/2012] [Indexed: 01/29/2023] Open
Abstract
The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic) and carbon tetrachloride (non-anesthetic). Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.
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Affiliation(s)
- Ramon Reigada
- Departament de Química Física and Institut de Química Teòrica i Computacional, Universitat de Barcelona, Barcelona, Spain.
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25
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Orsi M, Essex JW. Physical properties of mixed bilayers containing lamellar and nonlamellar lipids: insights from coarse-grain molecular dynamics simulations. Faraday Discuss 2013; 161:249-72; discussion 273-303. [DOI: 10.1039/c2fd20110k] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Polley A, Vemparala S. Partitioning of ethanol in multi-component membranes: Effects on membrane structure. Chem Phys Lipids 2013; 166:1-11. [DOI: 10.1016/j.chemphyslip.2012.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/23/2012] [Accepted: 11/24/2012] [Indexed: 12/12/2022]
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27
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Polley A, Vemparala S, Rao M. Atomistic Simulations of a Multicomponent Asymmetric Lipid Bilayer. J Phys Chem B 2012; 116:13403-10. [DOI: 10.1021/jp3032868] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anirban Polley
- Raman Research Institute, C. V. Raman Avenue, Bangalore 560 080, India
| | | | - Madan Rao
- Raman Research Institute, C. V. Raman Avenue, Bangalore 560 080, India
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore
560 065, India
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28
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Maftouni N, Amininasab M, Vali M, Ejtehadi M, Kowsari F. A Molecular Dynamics Simulation Study of Nanomechanical Properties of Asymmetric Lipid Bilayer. J Membr Biol 2012; 246:67-73. [DOI: 10.1007/s00232-012-9505-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 09/19/2012] [Indexed: 11/30/2022]
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29
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Frink LJD, Frischknecht AL, Heroux MA, Parks ML, Salinger AG. Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory. J Chem Theory Comput 2012; 8:1393-408. [DOI: 10.1021/ct200707b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Michael A. Heroux
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United
States
| | - Michael L. Parks
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United
States
| | - Andrew G. Salinger
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United
States
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30
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Nelson SC, Neeley SK, Melonakos ED, Bell JD, Busath DD. Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane. BMC BIOPHYSICS 2012; 5:5. [PMID: 22444827 PMCID: PMC3359235 DOI: 10.1186/2046-1682-5-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 03/24/2012] [Indexed: 12/02/2022]
Abstract
Background The mechanism of action of volatile general anesthetics has not yet been resolved. In order to identify the effects of isoflurane on the membrane, we measured the steady-state anisotropy of two fluorescent probes that reside at different depths. Incorporation of anesthetic was confirmed by shifting of the main phase transition temperature. Results In liquid crystalline dipalmitoylphosphatidylcholine liposomes, isoflurane (7-25 mM in the bath) increases trimethylammonium-diphenylhexatriene fluorescence anisotropy by ~0.02 units and decreases diphenylhexatriene anisotropy by the same amount. Conclusions The anisotropy data suggest that isoflurane decreases non-axial dye mobility in the headgroup region, while increasing it in the tail region. We propose that these results reflect changes in the lateral pressure profile of the membrane.
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Affiliation(s)
- Steven C Nelson
- WIDB 574, Dept, of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
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31
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Prakash A, Janosi L, Doxastakis M. GxxxG motifs, phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors. Biophys J 2012; 101:1949-58. [PMID: 22004749 DOI: 10.1016/j.bpj.2011.09.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/30/2011] [Accepted: 09/15/2011] [Indexed: 11/28/2022] Open
Abstract
GxxxG motifs are common in transmembrane domains of membrane proteins and are often introduced to artificial peptides to inhibit or promote association to stable structures. The transmembrane domain of ErbB2 presents two separate such motifs that are proposed to be connected to stability and activity of the dimer. Using molecular simulations, we show that these sequences play a critical role during the recognition stage, forming transient complexes that lead to stable dimers. In pure phospholipid bilayers association occurs by contacts formed at the C-terminus promoted by the presence of phenylalanine residues. Helices subsequently rotate to eventually pack at short separations favored by lipid entropic contributions. In contrast, at intermediate cholesterol concentrations, a different pathway is followed that involves dimers with a weaker interface toward the N-terminus. However, at high cholesterol content, a switch toward the C-terminus is observed with an overall nonmonotonic change of the dimerization affinity. This conformational switch modulated by cholesterol has important implications on the thermodynamic, structural, and kinetic characteristics of helix-helix association in lipid membranes.
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Affiliation(s)
- Anupam Prakash
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
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32
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Cascales JJL, Costa SDO, Garro A, Enriz RD. Mechanical properties of binary DPPC/DPPS bilayers. RSC Adv 2012. [DOI: 10.1039/c2ra21977h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Molecular dynamics simulation of phase transitions in model lung surfactant monolayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2450-65. [DOI: 10.1016/j.bbamem.2011.06.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 01/13/2023]
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34
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Nakamura T, Shinoda W, Ikeshoji T. Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems. J Chem Phys 2011; 135:094106. [DOI: 10.1063/1.3626410] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Abstract
Ever since it was discovered that biological membranes have a core of a bimolecular sheet of lipid molecules, lipid bilayers have been a model laboratory for investigating physicochemical and functional properties of biological membranes. Experimental and theoretical models help the experimental scientist to plan experiments and interpret data. Theoretical models are the theoretical scientist's preferred toys to make contact between membrane theory and experiments. Most importantly, models serve to shape our intuition about which membrane questions are the more fundamental and relevant ones to pursue. Here we review some membrane models for lipid self-assembly, monolayers, bilayers, liposomes, and lipid-protein interactions and illustrate how such models can help answering questions in modern lipid cell biology.
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Affiliation(s)
- Ole G Mouritsen
- MEMPHYS-Center for Biomembrane Physics, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark.
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36
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Vanegas JM, Longo ML, Faller R. Crystalline, Ordered and Disordered Lipid Membranes: Convergence of Stress Profiles due to Ergosterol. J Am Chem Soc 2011; 133:3720-3. [DOI: 10.1021/ja110327r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan M. Vanegas
- Biophysics Graduate Group and ‡Chemical Engineering and Materials Science Department, University of California, Davis, California 95616, United States
| | - Marjorie L. Longo
- Biophysics Graduate Group and ‡Chemical Engineering and Materials Science Department, University of California, Davis, California 95616, United States
| | - Roland Faller
- Biophysics Graduate Group and ‡Chemical Engineering and Materials Science Department, University of California, Davis, California 95616, United States
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37
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Muddana HS, Gullapalli RR, Manias E, Butler PJ. Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension. Phys Chem Chem Phys 2010; 13:1368-78. [PMID: 21152516 DOI: 10.1039/c0cp00430h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing.
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Affiliation(s)
- Hari S Muddana
- Department of Bioengineering, The Pennsylvania State University, 230 Hallowell Building, University Park, PA, USA
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38
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Yuet PK, Blankschtein D. Molecular Dynamics Simulation Study of Water Surfaces: Comparison of Flexible Water Models. J Phys Chem B 2010; 114:13786-95. [DOI: 10.1021/jp1067022] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pak K. Yuet
- Department of Process Engineering and Applied Science, Dalhousie University, P.O. Box 1000, Halifax, Nova Scotia, Canada B3J 2X4, and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel Blankschtein
- Department of Process Engineering and Applied Science, Dalhousie University, P.O. Box 1000, Halifax, Nova Scotia, Canada B3J 2X4, and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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39
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Parisio G, Ferrarini A. Solute Partitioning into Lipid Bilayers: An Implicit Model for Nonuniform and Ordered Environment. J Chem Theory Comput 2010; 6:2267-80. [DOI: 10.1021/ct100210u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giulia Parisio
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova Via Marzolo, 1 - 35131 Padova, Italy
| | - Alberta Ferrarini
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova Via Marzolo, 1 - 35131 Padova, Italy
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40
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Finol-Urdaneta RK, McArthur JR, Juranka PF, French RJ, Morris CE. Modulation of KvAP unitary conductance and gating by 1-alkanols and other surface active agents. Biophys J 2010; 98:762-72. [PMID: 20197029 DOI: 10.1016/j.bpj.2009.10.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 10/23/2009] [Accepted: 10/26/2009] [Indexed: 11/18/2022] Open
Abstract
The actions of alcohols and anesthetics on ion channels are poorly understood. Controversy continues about whether bilayer restructuring is relevant to the modulatory effects of these surface active agents (SAAs). Some voltage-gated K channels (Kv), but not KvAP, have putative low affinity alcohol-binding sites, and because KvAP structures have been determined in bilayers, KvAP could offer insights into the contribution of bilayer mechanics to SAA actions. We monitored KvAP unitary conductance and macroscopic activation and inactivation kinetics in PE:PG/decane bilayers with and without exposure to classic SAAs (short-chain 1-alkanols, cholesterol, and selected anesthetics: halothane, isoflurane, chloroform). At levels that did not measurably alter membrane specific capacitance, alkanols caused functional changes in KvAP behavior including lowered unitary conductance, modified kinetics, and shifted voltage dependence for activation. A simple explanation is that the site of SAA action on KvAP is its entire lateral interface with the PE:PG/decane bilayer, with SAA-induced changes in surface tension and bilayer packing order combining to modulate the shape and stability of various conformations. The KvAP structural adjustment to diverse bilayer pressure profiles has implications for understanding desirable and undesirable actions of SAA-like drugs and, broadly, predicts that channel gating, conductance and pharmacology may differ when membrane packing order differs, as in raft versus nonraft domains.
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Affiliation(s)
- Rocio K Finol-Urdaneta
- Hotchkiss Brain Institute and Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada
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41
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Baoukina S, Marrink SJ, Tieleman DP. Lateral pressure profiles in lipid monolayers. Faraday Discuss 2010; 144:393-409; discussion 445-81. [DOI: 10.1039/b905647e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Poger D, Mark AE. On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment. J Chem Theory Comput 2009; 6:325-36. [PMID: 26614341 DOI: 10.1021/ct900487a] [Citation(s) in RCA: 234] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy. Specifically, the solvation and the orientation of the dipole of the phosphocholine headgroup and of the ester carbonyls show that the structure of the primary hydration shell in the simulations closely matches experimental findings. This work highlights the need to reproduce a broad range of properties beyond the area per lipid, which is poorly defined experimentally, and to consider the effect of system size and sampling times well beyond those commonly used.
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Affiliation(s)
- David Poger
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane St Lucia, QLD 4072, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane St Lucia, QLD 4072, Australia
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43
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Xing C, Faller R. Density imbalances and free energy of lipid transfer in supported lipid bilayers. J Chem Phys 2009; 131:175104. [DOI: 10.1063/1.3262315] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Miller D, Charalambous K, Rotem D, Schuldiner S, Curnow P, Booth PJ. In vitro Unfolding and Refolding of the Small Multidrug Transporter EmrE. J Mol Biol 2009; 393:815-32. [DOI: 10.1016/j.jmb.2009.08.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 11/28/2022]
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45
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Alakoskela JM, Vitovic P, Kinnunen PKJ. Screening for the drug-phospholipid interaction: correlation to phospholipidosis. ChemMedChem 2009; 4:1224-51. [PMID: 19551800 DOI: 10.1002/cmdc.200900052] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phospholipid bilayers represent a complex, anisotropic environment fundamentally different from bulk oil or octanol, for instance. Even "simple" drug association to phospholipid bilayers can only be fully understood if the slab-of-hydrocarbon approach is abandoned and the complex, anisotropic properties of lipid bilayers reflecting the chemical structures and organization of the constituent phospholipids are considered. The interactions of drugs with phospholipids are important in various processes, such as drug absorption, tissue distribution, and subcellular distribution. In addition, drug-lipid interactions may lead to changes in lipid-dependent protein activities, and further, to functional and morphological changes in cells, a prominent example being the phospholipidosis (PLD) induced by cationic amphiphilic drugs. Herein we briefly review drug-lipid interactions in general and the significance of these interactions in PLD in particular. We also focus on a potential causal connection between drug-induced PLD and steatohepatitis, which is induced by some cationic amphiphilic drugs.
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Affiliation(s)
- Juha-Matti Alakoskela
- Division of Biochemistry, Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland.
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Niemelä PS, Castillo S, Sysi-Aho M, Orešič M. Bioinformatics and computational methods for lipidomics. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2855-62. [DOI: 10.1016/j.jchromb.2009.01.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 10/21/2022]
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Wang JA, Lin W, Morris T, Banderali U, Juranka PF, Morris CE. Membrane trauma and Na+ leak from Nav1.6 channels. Am J Physiol Cell Physiol 2009; 297:C823-34. [PMID: 19657055 DOI: 10.1152/ajpcell.00505.2008] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During brain trauma, white matter experiences shear and stretch forces that, without severing axons, nevertheless trigger their secondary degeneration. In central nervous system (CNS) trauma models, voltage-gated sodium channel (Nav) blockers are neuroprotective. This, plus the rapid tetrodotoxin-sensitive Ca2+ overload of stretch-traumatized axons, points to "leaky" Nav channels as a pivotal early lesion in brain trauma. Direct effects of mechanical trauma on neuronal Nav channels have not, however, been tested. Here, we monitor immediate responses of recombinant neuronal Nav channels to stretch, using patch-clamp and Na+-dye approaches. Trauma constituted either bleb-inducing aspiration of cell-attached oocyte patches or abrupt uniaxial stretch of cells on an extensible substrate. Nav1.6 channel transient current displayed irreversible hyperpolarizing shifts of steady-state inactivation [availability(V)] and of activation [g(V)] and, thus, of window current. Left shift increased progressively with trauma intensity. For moderately intense patch trauma, a approximately 20-mV hyperpolarizing shift was registered. Nav1.6 voltage sensors evidently see lower energy barriers posttrauma, probably because of the different bilayer mechanics of blebbed versus intact membrane. Na+ dye-loaded human embryonic kidney (HEK) cells stably transfected with alphaNav1.6 were subjected to traumatic brain injury-like stretch. Cytoplasmic Na+ levels abruptly increased and the trauma-induced influx had a significant tetrodotoxin-sensitive component. Nav1.6 channel responses to cell and membrane trauma are therefore consistent with the hypothesis that mechanically induced Nav channel leak is a primary lesion in traumatic brain injury. Nav1.6 is the CNS node of Ranvier Nav isoform. When, during head trauma, nodes experienced bleb-inducing membrane damage of varying intensities, nodal Nav1.6 channels should immediately "leak" over a broadly left-smeared window current range.
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Affiliation(s)
- Jun A Wang
- Neuroscience, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, Ontario, Canada
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Asakawa H, Fukuma T. The molecular-scale arrangement and mechanical strength of phospholipid/cholesterol mixed bilayers investigated by frequency modulation atomic force microscopy in liquid. NANOTECHNOLOGY 2009; 20:264008. [PMID: 19509439 DOI: 10.1088/0957-4484/20/26/264008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cholesterols play key roles in controlling molecular fluidity in a biological membrane, yet little is known about their molecular-scale arrangements in real space. In this study, we have directly imaged lipid-cholesterol complexes in a model biological membrane consisting of dipalmitoylphosphatidylcholine (DPPC) and cholesterols by frequency modulation atomic force microscopy (FM-AFM) in phosphate buffer solution. FM-AFM images of a DPPC/cholesterol bilayer in the liquid-ordered phase showed higher energy dissipation values compared to those measured on a nanoscale DPPC domain in the gel phase, reflecting the increased molecular fluidity due to the insertion of cholesterols. Molecular-resolution FM-AFM images of a DPPC/cholesterol bilayer revealed the existence of a rhombic molecular arrangement (lattice constants: a = 0.46 nm, b = 0.71 nm) consisting of alternating rows of DPPC and cholesterols as well as the increased defect density and reduced molecular ordering. The mechanical strength of a DPPC/cholesterol bilayer was quantitatively evaluated by measuring a loading force required to penetrate the membrane with an AFM tip. The result revealed the significant decrease of mechanical strength upon insertion of cholesterols. Based on the molecular-scale arrangement found in this study, we propose a model to explain the reduced mechanical strength in relation to the formation of lipid-ion networks.
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Affiliation(s)
- Hitoshi Asakawa
- Frontier Science Organization, Kanazawa University, Kakuma-machi, 920-1192 Kanazawa, Japan.
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Skaug MJ, Longo ML, Faller R. Computational Studies of Texas Red−1,2-Dihexadecanoyl-sn-glycero-3-phosphoethanolamine—Model Building and Applications. J Phys Chem B 2009; 113:8758-66. [DOI: 10.1021/jp902877y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael J. Skaug
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
| | - Marjorie L. Longo
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
| | - Roland Faller
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
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Abstract
The multiscale coarse-graining (MS-CG) approach developed in our previous work is extended here to model solvent-free lipid bilayers. The water (solvent) molecules are completely integrated out of the coarse-grained (CG) effective force field. The MS-CG potential, a sum of pairwise central terms, accurately approximates the many-body potential of mean force in the coarse-grained coordinates. It thus incorporates both energetic and entropic contributions. To improve the stability and elastic properties of the MS-CG simulated bilayer, an additional constraint was adopted: the partial virial associated with CG bilayer sites was matched to its corresponding atomistic value for each configuration of the system. The resulting solvent-free MS-CG model reproduces a liquid-state lipid bilayer with accurate structural and elastic properties. Finally, the solvent-free MS-CG model is used to simulate a very large, flat bilayer and two liposome geometries, demonstrating its greatly enhanced computational efficiency.
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Affiliation(s)
- Sergei Izvekov
- Department of Chemistry and Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, 84112-0850, USA
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