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Monte Carlo simulations of lipid bilayers and lipid protein interactions in the light of recent experiments

Thomas Heimburg
2000 Current Opinion in Colloid & Interface Science  
The concept of hydrophobic matching, underlying the simulations, has experimentally been shown to be relevant for the function of membrane proteins.  ...  Statistical thermodynamics simulations in recent years have considerably altered the view of biological and model membranes.  ...  To shorten equilibration times, some authors have combined Monte-Carlo and MD simulations [20, 21] or used plain Monte-Carlo approaches on the atomistic level [22, 23] .  ... 
doi:10.1016/s1359-0294(00)00059-5 fatcat:yo4nqr7zqbcg3ji4u5orjmtf7e

Combined Monte Carlo and Molecular Dynamics Simulation of Fully Hydrated Dioleyl and Palmitoyl-oleyl Phosphatidylcholine Lipid Bilayers

S.W. Chiu, Eric Jakobsson, Shankar Subramaniam, H.Larry Scott
1999 Biophysical Journal  
We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine  ...  The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions  ...  This work was supported by National Institutes of Health Grant GM54651 (to E.J. and H.L.S.) and National Science Foundation Grant MCB 96-31050 (to E.J.).  ... 
doi:10.1016/s0006-3495(99)77082-7 pmid:10545348 pmcid:PMC1300522 fatcat:zfpa6gm6ljaw5bvuzdalypo7sy

Combined Monte Carlo and Molecular Dynamics Simulation of Hydrated Lipid-Cholesterol Lipid Bilayers at Low Cholesterol Concentration

S.W. Chiu, Eric Jakobsson, H. Larry Scott
2001 Biophysical Journal  
We have applied a hybrid equilibration and sampling procedure for the atomic level simulation of a hydrated lipid bilayer to systems consisting of dipalmitoyl phosphatidylcholine (DPPC) and cholesterol  ...  After equilibration, three separate 400-ps continuous molecular dynamics runs, separated by 10,000 configurational bias Monte Carlo steps, were carried out for each system.  ...  Early atomic level simulations of lipids and cholesterol were carried out using Monte Carlo (MC) (Scott, 1991) , and molecular dynamics (MD) (Edholm and Nyberg, 1992; Robinson et al., 1995) methods.  ... 
doi:10.1016/s0006-3495(01)76088-2 pmid:11222276 pmcid:PMC1301307 fatcat:kl5lefebwrfzvaoqpdp2gdov5y

Modeling the lipid component of membranes

H.Larry Scott
2002 Current Opinion in Structural Biology  
495 During the past several years, there have been a number of advances in the computational and theoretical modeling of lipid bilayer structural and dynamical properties.  ...  Molecular dynamics (MD) simulations have increased in length and time scales by about an order of magnitude.  ...  Acknowledgements I thank S Feller, O Edholm, M Pasenkiewicz-Gierula, B Roux and G Voth for providing preprints and reprints of their work, JF Nagle for comments on the manuscript and E Jakobsson for many  ... 
doi:10.1016/s0959-440x(02)00353-6 pmid:12163073 fatcat:hwnt7ipd7jbupdh4p65eiofkuq

Development of the CHARMM Force Field for Lipids

R. W. Pastor, A. D. MacKerell
2011 Journal of Physical Chemistry Letters  
The functions noted above are being increasingly studied by classical molecular dynamics (MD) and Monte Carlo (MC) computer simulation carried out using models of varying detail.  ...  Structural and dynamical details of lipid/lipid, lipid/protein, and lipid/ solvent interaction are presently the realm of all-atom simulations.  ...  The functions noted above are being increasingly studied by classical molecular dynamics (MD) and Monte Carlo (MC) computer simulation carried out using models of varying detail.  ... 
doi:10.1021/jz200167q pmid:21760975 pmcid:PMC3133452 fatcat:gksfhioziferxcz24rsou6qd7i

Probing the Membrane Deformations Induced by Binding of Membrane Proteins: Alpha-Synuclein and CRAC

Jonathan N. Sachs, Jason D. Perlmutter, Anthony R. Braun, Eva Sevcsik, Stephanie Tristram-Nagle, Elizabeth Rhoades
2010 Biophysical Journal  
Furthermore, this water results in significant electrostatic screening, an important consideration when building theoretical and computational models of membrane remodeling.  ...  Our results support the insertion of hydrophobic moieties as the major driving force of membrane remodeling by N-BAR domains.  ...  Using a combination of all-atom and coarse-grained molecular dynamics simulations to interpret a range of x-ray scattering experiments, we aim to understand the role of membrane deformation in the action  ... 
doi:10.1016/j.bpj.2009.12.2655 fatcat:xzizy54ysbcezn5klrqzano6zi

Cholesterol interactions with phospholipids in membranes

H Ohvo-Rekilä
2002 Progress in lipid research  
Finally, we look at the recent trends in computer and molecular dynamics simulations regarding phospholipid and cholesterol/phospholipid behavior in bilayer membranes. #  ...  We discuss the synthesis and distribution in the cell of these lipids, how they are believed to interact with each other, and what cellular consequences such interactions may have.  ...  Kulturfonden, the Oskar Ö flund Foundation, the Borg Foundation, the Walter and Lisi Wahl Foundation, and from the Å bo Akademi University is gratefully acknowledged.  ... 
doi:10.1016/s0163-7827(01)00020-0 pmid:11694269 fatcat:hlboy6ifljccflvcta52lmye5q

Structure and Dynamics of Lipid-Modified Antimicrobial Peptides in Anionic and Zwitterionic Membranes Investigated by Solid-State NMR

Holger A. Scheidt, Alexander Vogel
2011 Biophysical Journal  
The capabilities of this combination are demonstrated on a model system composed of palmitoyl oleoyl phosphatidylcholine, sphingomyelin and ceramide.  ...  Reports on phase coexistence regimes and directions of tie lines of ternary lipid mixtures are often controversial.  ...  Monte Carlo (MC) simulations.  ... 
doi:10.1016/j.bpj.2010.12.1170 fatcat:iga3w64w3jhfbjjqmaio4mz4ve

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools [chapter]

S.W. Leong, T.S. Lim, Y.S. Choong
2016 Bioinformatics - Updated Features and Applications  
Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems.  ...  The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules.  ...  Mori and colleagues proposed a more sophisticated method for calculating the APL using Voronoi tessellation and Monte Carlo simulation [80] .  ... 
doi:10.5772/62576 fatcat:wdswubhlabb4djyo7bnjoedr5u

Structure and Dynamics of Lens Lipid Membranes Derived from a Single Porcine Donor: High Field EPR Study

Laxman Mainali, Jason W. Sidabras, Theodore G. Camenisch, Marija Raguz, James S. Hyde, Witold Subczynski
2014 Biophysical Journal  
compared by taking into account the chemical and molecular structure of the lipids and the drug.  ...  lipids, namely DPPS (dipalmitoyl phosphatidyl serine), and cholesterol.  ...  We compare our experimental findings with results of Monte Carlo simulations of Brownian hard needles in 2D. [1] A. Czogalla, E. P. Petrov, D. J. Kauert, V. Uzunova, Y. Zhang, R. Seidel, and P.  ... 
doi:10.1016/j.bpj.2013.11.3881 fatcat:ejvyyvmsbncdjmtpgkjned35ze

Modelling of the Interaction between Cationic Lipid Dlin-Kc2-Dma (XTC2) and Anionic Lipid Distearoylphosphatidylserine (DSPS)

Mohammad Ashtari, D. Peter Tieleman, Linda Wang, Jenifer Thewalt, Peter R. Cullis
2014 Biophysical Journal  
They are widely used to study the effects of curvature on the mechanics of lipid bilayers and proteo-lipid interactions.  ...  It also provides a clue to understanding an efficient and effective reaction by the DNA-binding proteins in bacterial cells. Membrane nanotubes (NT) are cylinders made of a lipid bilayer.  ...  We compare our experimental findings with results of Monte Carlo simulations of Brownian hard needles in 2D. [1] A. Czogalla, E. P. Petrov, D. J. Kauert, V. Uzunova, Y. Zhang, R. Seidel, and P.  ... 
doi:10.1016/j.bpj.2013.11.3876 fatcat:dbezs4bq2fburhb36p7ftfl3qe

Membrane Physical Properties Influence Transmembrane Helix Formation

Francisco N. Barrera, Justin Fendos, Donald M. Engelman
2013 Biophysical Journal  
In order to investigate the presence of pi-cation interactions between PI-PLC tyrosines and Cho in lipid headgroups, we performed a 500 nanoseconds-long molecular dynamics (MD) simulation of PI-PLC anchored  ...  Interaction free energies that have been determined from these measurements have been used in Monte Carlo simulations to quantify the distribution of the peptides between liquid-ordered and liquid-disordered  ... 
doi:10.1016/j.bpj.2012.11.2965 fatcat:6ayl3ahhjfc7rheaddoxz4ndqu

Theory of phase equilibria and critical mixing points in binary lipid bilayers

Jens Risbo, Maria M. Sperotto, Ole G. Mouritsen
1995 Journal of Chemical Physics  
Results are presented from mean-field calculations and Monte Carlo simulations on a statistical mechanical model in which the interaction between lipid acyl chains of different length is formulated in  ...  The part of the free energy necessary to derive phase equilibria is determined from the simulations using distribution functions and histogram techniques, and the nature of the phase equilibria is determined  ...  NUMERICAL SIMULATION METHODS A. Monte Carlo techniques The Monte Carlo simulations are carried out on finite lattices subject to periodic boundary conditions.  ... 
doi:10.1063/1.470041 fatcat:ow6gvtpf7rdvtlpid7lnxija2i

Computational predictions on the interactions of parabens with a dipalmitoylphosphatidylcholine lipid bilayer and the human serum albumin protein

Diego Masone, F´elix Rubio Dalmau
2016 Interdisciplinary Journal of Chemistry  
tprotein, was assessed using extensive atomistic molecular dynamics simulations.  ...  Simulation results show that among the paraben ligands studied, methyl, propyl and butyl parabens penetrate more easily the bilayer and show higher binding affinity to human serum albumin in terms of their  ...  Declaration of conflicting interests DM and FRD declared no conflicting interests with respect to the research, authorship and publication of this article.  ... 
doi:10.15761/ijc.1000104 fatcat:wevt4ym76zchdd6m4v3t7nebre

X-Ray Scattering from Gold Labeled Supported Membranes

Curt M. DeCaro, Laurence B. Lurio, Justin Berry, Sunil K. Sinha, Gang Chen, Atul Parikh, Adrian Brozell
2010 Biophysical Journal  
Molecular dynamics (MD) simulations with this new force field, referred to as CHARMM36 (C36), resulted in a significant improvement to the S CD 's and water hydration for DPPC lipid bilayers.  ...  A Monte Carlo algorithm is used to calculate headgroupheadgroup interactions and network energies in both dipole and point-charge approximations.  ... 
doi:10.1016/j.bpj.2009.12.1538 fatcat:pdmxcul6vner3c2fjnwhobqs7e
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