1
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Domínguez-Arca V, Sabín J, García-Río L, Bastos M, Taboada P, Barbosa S, Prieto G. On the structure and stability of novel cationic DPPC liposomes doped with gemini surfactants. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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2
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Ahmadi D, Ledder R, Mahmoudi N, Li P, Tellam J, Robinson D, Heenan RK, Smith P, Lorenz CD, Barlow DJ, Lawrence MJ. Supramolecular architecture of a multi-component biomimetic lipid barrier formulation. J Colloid Interface Sci 2021; 587:597-612. [DOI: 10.1016/j.jcis.2020.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/05/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
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3
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Wang KW, Wang Y, Hall CK. Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations. FLUID PHASE EQUILIBRIA 2020; 521:112704. [PMID: 37982069 PMCID: PMC10655612 DOI: 10.1016/j.fluid.2020.112704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
We suggest an improved version of the intermediate resolution implicit solvent model for lipids, LIME, that was previously developed for use with discontinuous molecular dynamics (DMD) simulations. LIME gets its geometrical and the energy parameters between bonded and nonbonded pairs of coarse-grained (CG) sites from atomistic simulations. The improved model, LIME 2.0, uses multiple square wells rather than the single square well used in original LIME to obtain intermolecular interactions that more faithfully mimic those from atomistic simulations. The multi-state iterative Boltzmann inversion (MS-IBI) scheme is used to determine the interaction parameters. This means that a single set of interaction parameters between coarse-grained sites can be used to represent the lipid bilayers at different temperatures. The physical properties of CG DSPE lipid bilayer are calculated using CG simulations and compared to atomistic simulations results to verify the improved model. The phase transition temperature of the lipid bilayer is measured accurately and the lipid translocation phenomenon, " flip-flop" is observed through CG simulation. These results suggest that CG parameterization using multiple square-well and the MS-IBI scheme is well suited to the study of lipid bilayers cross a range of temperatures with DMD simulations.
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Affiliation(s)
- Kye Won Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695
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4
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Wholey WY, Mueller JL, Tan C, Brooks JF, Zikherman J, Cheng W. Synthetic Liposomal Mimics of Biological Viruses for the Study of Immune Responses to Infection and Vaccination. Bioconjug Chem 2020; 31:685-697. [PMID: 31940172 DOI: 10.1021/acs.bioconjchem.9b00825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human viruses possess very complex supramolecular structures. Both icosahedral and enveloped viruses typically display an array of viral-encoded protein antigens at varied spatial densities on the viral particle surface. The viral nucleic acid genome, on the other hand, is encapsulated inside the viral particle. Although both the surface antigen and the interior nucleic acids could independently produce immunological responses, how B cells integrate these two types of signals and respond to a typical virus particle to initiate activation is not well understood at a molecular level. The study of these fundamental biological processes would benefit from the development of viral structural mimics that are well constructed to incorporate both quantitative and qualitative viral features for presentation to B cells. These novel tools would enable researchers to systematically dissect the underlying processes. Here we report the development of such particulate antigens based on liposomes engineered to display a model protein antigen, hen egg lysozyme (HEL). We developed methods to overexpress and purify various affinity mutants of HEL from E. coli. We conjugated the purified recombinant HEL proteins onto the surface of a virion-sized liposome in an orientation-specific manner at defined spatial densities and also encapsulated nucleic acid molecules into the interior of the liposome. Both the chemical conjugation of the HEL antigen on liposome surfaces and the encapsulation of nucleic acids were stable under physiologically relevant conditions. These liposomes elicited antigen-specific B-cell responses in vitro, which validate these supramolecular structures as a novel and effective approach to mimic and systematically isolate the role of essential viral features in directing the B-cell response to particulate antigens.
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Affiliation(s)
- Wei-Yun Wholey
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - James L Mueller
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Corey Tan
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Jeremy F Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Wei Cheng
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States.,Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
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5
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Tong X, Moradipour M, Novak B, Kamali P, Asare SO, Knutson BL, Rankin SE, Lynn BC, Moldovan D. Experimental and Molecular Dynamics Simulation Study of the Effects of Lignin Dimers on the Gel-to-Fluid Phase Transition in DPPC Bilayers. J Phys Chem B 2019; 123:8247-8260. [DOI: 10.1021/acs.jpcb.9b05525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xinjie Tong
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Mahsa Moradipour
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Brian Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Poorya Kamali
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Shardrack O. Asare
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Barbara L. Knutson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Stephen E. Rankin
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Bert C. Lynn
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Dorel Moldovan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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6
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Zaki AM, Carbone P. Amphiphilic copolymers change the nature of the ordered-to-disordered phase transition of lipid membranes from discontinuous to continuous. Phys Chem Chem Phys 2019; 21:13746-13757. [PMID: 31209450 DOI: 10.1039/c9cp01293a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The phase behaviour as a function of temperature is explored for pure phospholipid (DPPC) and hybrid lipid-polymer (DPPC/Pluronic L64) bilayers with the aid of atomistic MD simulations. The range of the fixed-temperature simulations includes temperatures below and above the known melting temperature (Tm) for DPPC membranes. For the pure lipid bilayer, the main phase transition is discontinuous, as verified by the abrupt changes observed in the membrane structure, elasticity and the lipid diffusivity near the critical temperature Tm, which lies in the region 298.15-303.15 K. A pre-transition step is detected at 298.15 K which has been identified as the ripple phase (Pβ'), where ordered and disordered lipids coexist, causing thickness fluctuations. In the ordered gel phase, the positional ordering as assessed by the lipid radial distribution functions is long-range and some degree of hexagonal packing is measured. The hybrid bilayers on the other hand, transform from a more ordered to a disordered phase in a continuous manner, without finite jumps in their properties. No signs of the ripple phase are identified and the ordered phase exhibits very limited hexagonal packing and some positional ordering that decays fast. The effect of the inserted polymers in the two phases is reversed; at low temperatures, they render the membrane thinner, less cohesive and less ordered compared to the pure one, with the lipids assuming faster diffusion rates, whereas at high temperatures, the polymer interaction with the lipids acts reducing their diffusivity, but also increasing the lipid tail ordering and the membrane stiffness. The ability of the amphiphilic L64 copolymers to change the nature of the main phase transition of lipid membranes and their properties both in the ordered and the disordered phase is of vital importance for the prediction of both the efficacy of hybrid lipid/polymer nanoparticles as drug delivery vehicles as well as their potential adverse implications during interactions with healthy cell membranes.
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Affiliation(s)
- Afroditi Maria Zaki
- School of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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7
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Zhao X, Zhai L, Dang L, Wei H. Impact of Additives on the Microstructural Properties of DIDMAMS Bilayers: Studied by Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6112-6119. [PMID: 30938534 DOI: 10.1021/acs.langmuir.9b00605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To further understand the mechanism of the impact of perfume raw materials (PRMs) such as allyl heptoate (AHT) and cashmeran (CMR) on distearoyl isopropyl dimethylammonium methyl sulfate (DIDMAMS) bilayers, 90 ns molecular dynamics simulations were conducted to investigate the structure of bilayers consisting of DIDMAMS and PRMs at 350 K on the molecular scale. Structural properties such as density profiles, order parameters, radial distribution functions (RDFs), and bilayer thickness were analyzed. The bilayers appear to be the structure of the ripple phase whether PRMs are added or not. The RDF and density profiles show that CMR molecules tend to locate in the region close to head groups and AHT molecules prefer to uniformly distribute among hydrocarbon chains. The special distribution of CMR molecules results in hydrocarbon chains twining around CMR molecules. The existence of CMR molecules between bilayers and the consequent highest bilayer thickness may be the main cause of higher viscosity. We expect that this work can help to screen stable vesicular formula and understand the relationship between microstructures of the vesicles and macroscopic fluidic properties.
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Affiliation(s)
- Xueying Zhao
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
| | - Lina Zhai
- Tianjin TJU-XEDA Synergetic Innovation Institute Co., Ltd , No.5 Xinghua 8th Branch Rd , Xiqing Economic-Technological Development Area, Tianjin 300385 , China
| | - Leping Dang
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
| | - Hongyuan Wei
- School of Chemical Engineering and Technology , Tianjin University , No.135 Yaguan Road , Jinnan District, Tianjin 300072 , P.R. China
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8
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Kheyfets B, Galimzyanov T, Mukhin S. Lipid lateral self-diffusion drop at liquid-gel phase transition. Phys Rev E 2019; 99:012414. [PMID: 30780230 DOI: 10.1103/physreve.99.012414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/06/2022]
Abstract
A drop of lipid lateral self-diffusion coefficient at the liquid-gel phase transition in lipid membranes is calculated. So far this drop was missing theoretical description. Our microscopic model captures so-called subdiffusion regime, which takes place on 1 ps-100 ns timescale and reveals a jump of self-diffusion coefficient. Calculation of the jump is based on our recent study of liquid-gel phase transition. Subdiffusive regime is described within the free volume theory. Calculated values of self-diffusion coefficient are in agreement with quasielastic neutron scattering measurements. Self-diffusion coefficient is found to be composed of two factors: one is related to an area per lipid change at the phase transition, and the other one is due to an order of magnitude change in the stiffness of entropic repulsive potential.
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Affiliation(s)
- Boris Kheyfets
- National University of Science and Technology MISIS, Moscow, Russia
| | - Timur Galimzyanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Moscow, Russia
| | - Sergei Mukhin
- National University of Science and Technology MISIS, Moscow, Russia
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9
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Bourgeois C, Gomaa AI, Lefèvre T, Cansell M, Subirade M. Interaction of oil bodies proteins with phospholipid bilayers: A molecular level elucidation as revealed by infrared spectroscopy. Int J Biol Macromol 2019; 122:873-881. [DOI: 10.1016/j.ijbiomac.2018.10.211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
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10
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Importance of Hydrophilic Groups on Modulating the Structural, Mechanical, and Interfacial Properties of Bilayers: A Comparative Molecular Dynamics Study of Phosphatidylcholine and Ion Pair Amphiphile Membranes. Int J Mol Sci 2018; 19:ijms19061552. [PMID: 29882873 PMCID: PMC6032153 DOI: 10.3390/ijms19061552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 12/25/2022] Open
Abstract
An ion pair amphiphile (IPA), a molecular complex composed of two oppositely charged amphiphiles, is a phospholipid mimic which differs from a phospholipid only in the hydrophilic compositions. Here, we utilized molecular dynamics (MD) simulations to compare the bilayer systems composed of phosphatidylcholines (PC) and alkyltrimethylammonium-alkylsulfate IPAs with various alkyl chain lengths. The membrane properties for both liquid-disordered (Ld) and gel (S) phase bilayers were examined via running simulations above and below the main transition temperatures. The electrostatic attraction between the IPA hydrophilic groups leads to a more ordered molecular packing within both S and Ld phase IPA membranes, as revealed by the molecular area, deuterium order parameter, and gauche conformation analyses. Furthermore, IPA bilayers possess a higher area compressibility modulus, molecular tilt modulus, and effective bending rigidity than PC systems. The variation of hydrophilic groups of IPA also leads to fewer hydrogen bonds on the membrane surface and smaller electrostatic potentials for the biomimetic bilayer. The non-covalently linked head groups of IPA further decouple alkyl tilting and surface water retention. The combined results reveal the importance of hydrophilic groups of amphiphiles on modulating the membrane properties, which also provides insights for designs of biomimetic membranes.
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11
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Cordeiro RM. Molecular Structure and Permeability at the Interface between Phase-Separated Membrane Domains. J Phys Chem B 2018; 122:6954-6965. [DOI: 10.1021/acs.jpcb.8b03406] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rodrigo M. Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil
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12
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Thermal Response Analysis of Phospholipid Bilayers Using Ellipsometric Techniques. BIOSENSORS-BASEL 2017; 7:bios7030034. [PMID: 28820461 PMCID: PMC5618040 DOI: 10.3390/bios7030034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/29/2022]
Abstract
Biomimetic planar artificial membranes have been widely studied due to their multiple applications in several research fields. Their humectation and thermal response are crucial for reaching stability; these characteristics are related to the molecular organization inside the bilayer, which is affected by the aliphatic chain length, saturations, and molecule polarity, among others. Bilayer stability becomes a fundamental factor when technological devices are developed—like biosensors—based on those systems. Thermal studies were performed for different types of phosphatidylcholine (PC) molecules: two pure PC bilayers and four binary PC mixtures. These analyses were carried out through the detection of slight changes in their optical and structural parameters via Ellipsometry and Surface Plasmon Resonance (SPR) techniques. Phospholipid bilayers were prepared by Langmuir-Blodgett technique and deposited over a hydrophilic silicon wafer. Their molecular inclination degree, mobility, and stability of the different phases were detected and analyzed through bilayer thickness changes and their optical phase-amplitude response. Results show that certain binary lipid mixtures—with differences in its aliphatic chain length—present a co-existence of two thermal responses due to non-ideal mixing.
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13
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Sun L, Böckmann RA. Membrane phase transition during heating and cooling: molecular insight into reversible melting. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:151-164. [PMID: 28725998 DOI: 10.1007/s00249-017-1237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/18/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022]
Abstract
With increasing temperature, lipid bilayers undergo a gel-fluid phase transition, which plays an essential role in many physiological phenomena. In the present work, this first-order phase transition was investigated for variable heating and cooling rates for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer by means of atomistic molecular dynamics simulations. Alternative methods to track the melting temperature [Formula: see text] are compared. The resulting [Formula: see text] is shown to be independent of the scan rate for small heating rates (0.05-0.3 K/ns) implying reversible melting, and increases for larger heating (0.3-4 K/ns) or cooling rates (2-0.1 K/ns). The reported dependency of the melting temperature on the heating rate is in perfect agreement with a two-state kinetic rate model as suggested previously. Expansion and shrinkage, as well as the dynamics of melting seeds is described. The simulations further exhibit a relative shift between melting seeds in opposing membrane leaflets as predicted from continuum elastic theory.
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Affiliation(s)
- Liping Sun
- Computational Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstrasse 5, Erlangen, 91058, Germany.
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14
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Zhang T, Luo Q, Yang L, Jiang H, Yang H. Characterizing the interactions of two lipid modifications with lipid rafts: farnesyl anchors vs. palmitoyl anchors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:19-30. [PMID: 28585042 DOI: 10.1007/s00249-017-1217-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/27/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022]
Abstract
Farnesyl (Far) and palmitoyl (Pal) anchors play important roles in the traffic of many lipidated proteins. Herein, we show the distinctive interactions and influences of the two lipid modifications on lipid rafts (LRs) and non-raft-like membranes using molecular dynamics simulations. Palmitoyl anchors behave in a more ordered fashion, pack tighter with the lipids of LRs and diffuse at a slower rate than farnesyl anchors in LRs. When interacting with non-raft-like membranes these two types of anchors become less ordered, pack more loosely with lipids, and diffuse at a higher rate. By calculating both the number of contacts per chain and the number of contact atoms per carbon of the two anchors with the lipid components, we found that the palmitoyl chains preferred to associate with the saturated chains of lipids and cholesterol molecules in LRs, while farnesyl chains favored association with saturated chains and unsaturated chains. For non-raft-like membranes, these two lipid anchors had roughly the same preference for the three types of contact lipid chains. Additionally, palmitoyl anchors caused cholesterol to orient more perpendicular to the membrane surface, surrounding lipids to become more ordered, and lipid lateral fluidity to reduce significantly, compared to farnesyl anchors in LRs. By contrast, the POPE and DSPC became much less ordered, cholesterol became more tilted, and lipids became more fluid, when the two types lipid anchors were inserted in non-raft-like membranes. These findings are useful for understanding the traffic mechanisms of lipidated proteins with farnesyl and palmitoyl modifications in cell membranes.
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Affiliation(s)
- Tao Zhang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qichao Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linlin Yang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, 450001, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaiyu Yang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China.
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15
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Lopez H, Brandt EG, Mirzoev A, Zhurkin D, Lyubartsev A, Lobaskin V. Multiscale Modelling of Bionano Interface. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:173-206. [PMID: 28168669 DOI: 10.1007/978-3-319-47754-1_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a framework for coarse-grained modelling of the interface between foreign nanoparticles (NP) and biological fluids and membranes. Our model includes united-atom presentations of membrane lipids and globular proteins in implicit solvent, which are based on all-atom structures of the corresponding molecules and parameterised using experimental data or atomistic simulation results. The NPs are modelled by homogeneous spheres that interact with the beads of biomolecules via a central force that depends on the NP size. The proposed methodology is used to predict the adsorption energies for human blood plasma proteins on NPs of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the NP, which can be used for predicting the composition of the NP-protein corona for the corresponding material. We also show how the model can be used for studying NP interaction with a lipid bilayer membrane and thus can provide a mechanistic insight for modelling NP toxicity.
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Affiliation(s)
- Hender Lopez
- School of Physics, Complex and Adaptive Systems Lab, University College Dublin, Belfield, Dublin 4, Ireland
| | - Erik G Brandt
- Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden
| | - Alexander Mirzoev
- Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden
| | - Dmitry Zhurkin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden
| | - Alexander Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden
| | - Vladimir Lobaskin
- School of Physics, Complex and Adaptive Systems Lab, University College Dublin, Belfield, Dublin 4, Ireland.
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16
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Pagoto A, Stefania R, Garello F, Arena F, Digilio G, Aime S, Terreno E. Paramagnetic Phospholipid-Based Micelles Targeting VCAM-1 Receptors for MRI Visualization of Inflammation. Bioconjug Chem 2016; 27:1921-30. [DOI: 10.1021/acs.bioconjchem.6b00308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Amerigo Pagoto
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
| | - Rachele Stefania
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
| | - Francesca Garello
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
| | - Francesca Arena
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
| | - Giuseppe Digilio
- DISIT,
Università
del Piemonte Orientale “A. Avogadro”, Via T. Michel 11, 15121 Alessandria, Italy
| | - Silvio Aime
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
| | - Enzo Terreno
- Molecular & Preclinical Imaging Centers, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126-Torino, Italy
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17
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Kim S, Chang R. Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Seonghan Kim
- Department of Chemistry; Kwangwoon University; Seoul 01897 Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry; Kwangwoon University; Seoul 01897 Republic of Korea
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18
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Uppulury K, Coppock PS, Kindt JT. Molecular Simulation of the DPPE Lipid Bilayer Gel Phase: Coupling between Molecular Packing Order and Tail Tilt Angle. J Phys Chem B 2015; 119:8725-33. [PMID: 26109479 DOI: 10.1021/acs.jpcb.5b05720] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural properties and thermal stability of dipalmitoylphosphatidylethanolamine (DPPE) in the ordered gel phase have been studied by molecular dynamics simulation using two force fields: the Berger united-atom model and the CHARMM C36 atomistic model. As is widely known, structural features are sensitive to the initial preparation of the gel phase structure, as some degrees of freedom are slow to equilibrate on the simulation time scale of hundreds of nanoseconds. In particular, we find that the degree of alignment of the lipids' glycerol backbones, which join the two hydrocarbon tails of each molecule, strongly affects the tilt angle of the tails in the resulting structures. Disorder in the backbone correlates with lower tilt angles: bilayer configurations initiated with aligned backbones produced tilt angles near 21° and 29° for the Berger and C36 force fields, respectively, while structures initiated with randomized backbone orientations showed average tilt angles of 7° and 18°, in closer agreement with the untilted structure observed experimentally. The transition temperature for the Berger force field gel bilayer has been determined by monitoring changes in width of gel phase stripe domains as a function of temperature and is 12 ± 5 K lower than the experimental value.
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Affiliation(s)
- Karthik Uppulury
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick S Coppock
- 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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19
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Zhang H, Li F, Xiao Q, Lin H. Conformation of Capping Ligands on Nanoplates: Facet-Edge-Induced Disorder and Self-Assembly-Related Ordering Revealed by Sum Frequency Generation Spectroscopy. J Phys Chem Lett 2015; 6:2170-6. [PMID: 26266587 DOI: 10.1021/acs.jpclett.5b00717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Surface-curvature-amplified conformational disorder in alkyl capping ligands has been observed previously when the nanoparticle radii approach the ligand length. Herein, sum frequency generation studies on oleic-acid-capped nanoplates show that even on faceted surfaces with dimensions tens of times greater than the ligand length a significant proportion of gauche defects exist in the capping layer. The molecular disorder on the nanosized facets is attributed to a facet-edge effect, which is diminished when increasing the facet size or assembling the nanofacets side to side. This feature is further explored to probe the self-assembly dynamics of nanoplates.
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Affiliation(s)
- Hao Zhang
- †i-LAB, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou 215123, P. R. China
- ‡School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, P.R. China
| | - Fujin Li
- †i-LAB, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Qingbo Xiao
- †i-LAB, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Hongzhen Lin
- †i-LAB, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou 215123, P. R. China
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20
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Marquardt D, Geier B, Pabst G. Asymmetric lipid membranes: towards more realistic model systems. MEMBRANES 2015; 5:180-96. [PMID: 25955841 PMCID: PMC4496639 DOI: 10.3390/membranes5020180] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/28/2015] [Indexed: 01/23/2023]
Abstract
Despite the ubiquity of transbilayer asymmetry in natural cell membranes, the vast majority of existing research has utilized chemically well-defined symmetric liposomes, where the inner and outer bilayer leaflets have the same composition. Here, we review various aspects of asymmetry in nature and in model systems in anticipation for the next phase of model membrane studies.
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Affiliation(s)
- Drew Marquardt
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, NAWI Graz, Humboldtstr 50/III, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, 8010, Austria.
| | - Barbara Geier
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, NAWI Graz, Humboldtstr 50/III, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, 8010, Austria.
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, NAWI Graz, Humboldtstr 50/III, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, 8010, Austria.
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21
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Yang L, Kindt JT. Simulation study of the permeability of a model lipid membrane at the fluid-solid phase transition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2187-2195. [PMID: 25621817 DOI: 10.1021/la504269t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
When a range of lipid bilayers are melted to the disordered fluid phase from the (much less permeable) ordered gel phase, their permeability to a variety of permeants shows a peak at the transition temperature and drops off with increasing temperature, rather than just rising as melting proceeds. To explore this anomalous behavior, a simulated coarse-grained lipid membrane model that exhibits a phase transition upon expansion or compression was studied to determine how the permeation rate of a simple particle depends on the phase composition in the two-phase region and on particle size. The permeation rate and each phase's area fraction and area density could be directly calculated, along with the probability that the permeant would cross in either phase or in interfacial regions. For large permeants and system sizes, conditions could be found where permeability increases upon compression of the bilayer. Permeation was negligible in the gel phase and, in contrast to the predictions of the "leaky interface" hypothesis, was not enriched in interfacial regions. The anomalous effect could instead be attributed to an increase in the area per lipid of fluid-phase domains. This result motivated a model for the decrease in effective permeability barrier through fluid-phase domains arising from a decrease in the length of the gel/fluid interface at the midpoint of a permeation event.
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Affiliation(s)
- Lewen Yang
- Emory University , 1515 Dickey Drive, Atlanta, Georgia 30033, United States
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22
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Wang H, Ren X, Meng F. Molecular dynamics simulation of six β-blocker drugs passing across POPC bilayer. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1008470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Ferraro M, Masetti M, Recanatini M, Cavalli A, Bottegoni G. Modeling lipid raft domains containing a mono-unsaturated phosphatidylethanolamine species. RSC Adv 2015. [DOI: 10.1039/c5ra02196k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An advanced coarse-grained model for “atypical” lipid rafts was built and validated to be employed in studies of membrane-protein interactions.
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Affiliation(s)
- M. Ferraro
- D3 Compunet
- Istituto Italiano di Tecnologia
- Genova
- Italy
| | - M. Masetti
- Department of Pharmacy and Biotechnology
- Alma Mater Studiorum – Università di Bologna
- Bologna
- Italy
| | - M. Recanatini
- Department of Pharmacy and Biotechnology
- Alma Mater Studiorum – Università di Bologna
- Bologna
- Italy
| | - A. Cavalli
- D3 Compunet
- Istituto Italiano di Tecnologia
- Genova
- Italy
- Department of Pharmacy and Biotechnology
| | - G. Bottegoni
- D3 Compunet
- Istituto Italiano di Tecnologia
- Genova
- Italy
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24
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Zhuo H, Li Q, Li W, Cheng J. Non-additivity between substitution and cooperative effects in enhancing hydrogen bonds. J Chem Phys 2014; 141:244305. [DOI: 10.1063/1.4904294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Laner M, Horta BAC, Hünenberger PH. Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2014; 55:48-64. [PMID: 25437095 DOI: 10.1016/j.jmgm.2014.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events.
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Affiliation(s)
- Monika Laner
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Bruno A C Horta
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland; Dpto. de Engenharia Elétrica, PUC-Rio, Rio de Janeiro, Brazil; Dpto. de Ciências Biológicas, UEZO, Rio de Janeiro, Brazil.
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26
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Feng JW, Ding HM, Ma YQ. Controlling water flow inside carbon nanotube with lipid membranes. J Chem Phys 2014; 141:094901. [DOI: 10.1063/1.4893964] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:517-44. [DOI: 10.1007/s00249-014-0982-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/16/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
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28
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Pentak D. Physicochemical properties of liposomes as potential anticancer drugs carriers. Interaction of etoposide and cytarabine with the membrane: spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 122:451-460. [PMID: 24326261 DOI: 10.1016/j.saa.2013.11.061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/05/2013] [Accepted: 11/10/2013] [Indexed: 06/03/2023]
Abstract
The interactions between etoposide, cytarabine and 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine bilayers were studied using differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR). These techniques have proven to be a very powerful tool in studying the structure and dynamics of phospholipid bilayers. In particular, DSC can provide information on the phase transition temperature and cooperativity of the lipid molecules in the absence and presence of the drug. Vibrational spectroscopy is well suited to the study of drug-lipid interactions, since it allows for an investigation of the conformation of phospholipid molecules at different levels in lipid bilayers and follows structural changes that occur during the gel to liquid-crystalline phase transition. NMR supported the determination of the main phase transition temperatures (TC) of 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine (DPPC). The main phase transition temperature (TC) determined by (1)H NMR is comparable with values obtained by DSC for all studied liposomes. The location of cytarabine and etoposide in liposomes was also determined by NMR. Atomic force microscopy (AFM) images, acquired immediately after sample deposition on a mica surface, revealed the spherical shape of lipid vesicles.
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Affiliation(s)
- Danuta Pentak
- Department of Materials Chemistry and Chemical Technology, Institute of Chemistry, University of Silesia, 40-006 Katowice, Poland.
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29
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Kong X, Qin S, Lu D, Liu Z. Surface tension effects on the phase transition of a DPPC bilayer with and without protein: a molecular dynamics simulation. Phys Chem Chem Phys 2014; 16:8434-40. [DOI: 10.1039/c3cp55524k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A coarse-grained molecular dynamics simulation was applied to illustrate the phase transition behavior of the pure DPPC bilayer and aquaporin-embedded DPPC bilayer under different surface tensions.
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Affiliation(s)
- Xian Kong
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Shanshan Qin
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084, P. R. China
| | - Diannan Lu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Zheng Liu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
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30
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Bennett WD, Tieleman DP. Computer simulations of lipid membrane domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1765-76. [DOI: 10.1016/j.bbamem.2013.03.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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31
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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32
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Diggins P, Deserno M. Determining the bending modulus of a lipid membrane by simulating buckling. J Chem Phys 2013; 138:214110. [DOI: 10.1063/1.4808077] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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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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34
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Kuo AT, Chang CH, Shinoda W. Molecular dynamics study of catanionic bilayers composed of ion pair amphiphile with double-tailed cationic surfactant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8156-8164. [PMID: 22564043 DOI: 10.1021/la300651u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The physical stability of catanionic vesicles is important for the development of novel drug or DNA carriers. For investigating the mechanism by which catanionic vesicles are stabilized, molecular dynamics (MD) simulation is an attractive approach that provides microscopic structural information on the vesicular bilayer. In this study, MD simulation was applied to investigate the bilayer properties of catanionic vesicles composed of an ion pair amphiphile (IPA), hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS), and a double-tailed cationic surfactant, ditetradecyldimethylammonium chloride (DTDAC). Structural information regarding membrane elasticity and the organization and conformation of surfactant molecules was obtained based on the resulting trajectory. Simulation results showed that a proper amount of DTDAC could be used to complement the asymmetric structure between HTMA and DS, resulting in an ordered hydrocarbon chain packing within the rigid membrane observed in the mixed HTMA-DS/DTDAC system. The coexistence of gel and fluid phases was also observed in the presence of excess DTDAC. MD simulation results agreed well with results obtained from experimental studies examining mixed HTMA-DS/DTDAB vesicles.
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Affiliation(s)
- An-Tsung Kuo
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
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35
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King DT, Warren DB, Pouton CW, Chalmers DK. Using molecular dynamics to study liquid phase behavior: simulations of the ternary sodium laurate/sodium oleate/water system. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:11381-11393. [PMID: 21838286 DOI: 10.1021/la2022903] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The prediction of surfactant phase behavior has applications in a wide range of areas. An accurate modeling of liquid phase behavior can aid our understanding of colloidal process or be used to design phases that respond in a defined way to their environment. In this work, we use molecular dynamics to model the phase behavior of the ternary sodium laurate/sodium oleate/water system and compare the simulation results to experimental data. Simulations were performed with the GROMOS 53A6 united-atom force field and cover the entire ternary phase diagram, producing micellar, hexagonal, and lamellar phases. The aggregate simulation time for the 33 simulations performed during this study is 4.4 μs. We find that the simulations were able to model the experimentally observed liquid phase behavior accurately, showing that the carboxylate and lipid parameters of the 53A6 force field give very good quality results for the in silico prediction of liquid system phase behavior.
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Affiliation(s)
- Dylan T King
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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36
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Hall K, Lee TH, Aguilar MI. The role of electrostatic interactions in the membrane binding of melittin. J Mol Recognit 2011; 24:108-18. [PMID: 21194121 DOI: 10.1002/jmr.1032] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The binding of melittin and the C-terminally truncated analogue of melittin (21Q) to a range of phospholipid bilayers was studied using surface plasmon resonance (SPR). The phospholipid model membranes included zwitterionic dimyristylphosphatidylcholine (DMPC) and dimyristylphosphatidylethanolamine (DMPE), together with mixtures DMPC/dimyristylphosphatidylglycerol (DMPG), DMPC/DMPG/cholesterol and DMPE/DMPG. Melittin bound rapidly to all membrane mixtures, whereas 21Q, which has a reduced charge, bound much more slowly on the DMPC and DMPC/DMPG mixtures reflecting the role of the initial electrostatic interaction. The loss of the cationic residues also significantly decreased the binding of 21Q with DMPC/DMPG/Cholesterol, DMPE and DMPE/DMPG. The role of electrostatics was also highlighted with NaCl in the buffer, which affected the way melittin bound to the different membranes, causing a more uniform, concentration dependant increase in response. The biosensor results were correlated with the conformation of the peptides determined by circular dichroism analysis, which indicated that high α-helicity was associated with high binding affinity. Overall, the results demonstrate that the positively charged residues at the C-terminus of melittin play an essential role in membrane binding, that modulation of peptide charge influences selectivity of binding to different phospholipids and that manipulation of the cationic regions of antimicrobial peptides can be used to modulate membrane selectivity.
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Affiliation(s)
- Kristopher Hall
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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37
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Kindt JT. Atomistic simulation of mixed-lipid bilayers: mixed methods for mixed membranes. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.561434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Coppock PS, Kindt JT. Determination of Phase Transition Temperatures for Atomistic Models of Lipids from Temperature-Dependent Stripe Domain Growth Kinetics. J Phys Chem B 2010; 114:11468-73. [DOI: 10.1021/jp104529m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick S. Coppock
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - James T. Kindt
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
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39
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Wu FG, Wang NN, Yu JS, Luo JJ, Yu ZW. Nonsynchronicity Phenomenon Observed during the Lamellar−Micellar Phase Transitions of 1-Stearoyllysophosphatidylcholine Dispersed in Water. J Phys Chem B 2010; 114:2158-64. [DOI: 10.1021/jp9107014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Fu-Gen Wu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Nan-Nan Wang
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Ji-Sheng Yu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jun-Jie Luo
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wu Yu
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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