Literature DB >> 20515115

An implicit solvent coarse-grained lipid model with correct stress profile.

Alex J Sodt1, Teresa Head-Gordon.   

Abstract

We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20515115      PMCID: PMC2887916          DOI: 10.1063/1.3408285

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  50 in total

1.  Intermediates and the folding of proteins L and G.

Authors:  Scott Brown; Teresa Head-Gordon
Journal:  Protein Sci       Date:  2004-04       Impact factor: 6.725

2.  Influence of denatured and intermediate states of folding on protein aggregation.

Authors:  Nicolas L Fawzi; Victor Chubukov; Louis A Clark; Scott Brown; Teresa Head-Gordon
Journal:  Protein Sci       Date:  2005-04       Impact factor: 6.725

3.  Fluid vesicles with viscous membranes in shear flow.

Authors:  Hiroshi Noguchi; Gerhard Gompper
Journal:  Phys Rev Lett       Date:  2004-12-13       Impact factor: 9.161

4.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Authors:  Jeffery B Klauda; Bernard R Brooks; Alexander D MacKerell; Richard M Venable; Richard W Pastor
Journal:  J Phys Chem B       Date:  2005-03-24       Impact factor: 2.991

5.  Mode excitation Monte Carlo simulations of mesoscopically large membranes.

Authors:  Oded Farago
Journal:  J Chem Phys       Date:  2008-05-14       Impact factor: 3.488

6.  Computer simulations of self-assembled membranes.

Authors:  J M Drouffe; A C Maggs; S Leibler
Journal:  Science       Date:  1991-11-29       Impact factor: 47.728

7.  Factors governing the foldability of proteins.

Authors:  D K Klimov; D Thirumalai
Journal:  Proteins       Date:  1996-12

8.  Tunable generic model for fluid bilayer membranes.

Authors:  Ira R Cooke; Kurt Kremer; Markus Deserno
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-07-26

9.  Elastic curvature constants of lipid monolayers and bilayers.

Authors:  Derek Marsh
Journal:  Chem Phys Lipids       Date:  2006-09-06       Impact factor: 3.329

10.  Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints.

Authors:  Teemu Murtola; Emma Falck; Mikko Karttunen; Ilpo Vattulainen
Journal:  J Chem Phys       Date:  2007-02-21       Impact factor: 3.488

View more
  12 in total

1.  Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field.

Authors:  Zun-Jing Wang; Markus Deserno
Journal:  New J Phys       Date:  2010-09-01       Impact factor: 3.729

2.  Determining the Gaussian curvature modulus of lipid membranes in simulations.

Authors:  Mingyang Hu; John J Briguglio; Markus Deserno
Journal:  Biophys J       Date:  2012-03-20       Impact factor: 4.033

3.  A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.

Authors:  Anand Srivastava; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

Review 4.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

5.  Normal vibrations of ternary DOPC/DPPC/cholesterol lipid bilayers by low-frequency Raman spectroscopy.

Authors:  Dmitry V Leonov; Sergei A Dzuba; Nikolay V Surovtsev
Journal:  RSC Adv       Date:  2019-10-25       Impact factor: 3.361

6.  COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

Authors:  Casey T Andrews; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2014-10-07       Impact factor: 6.006

7.  Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure.

Authors:  Saeed Mortezazadeh; Yousef Jamali; Hossein Naderi-Manesh; Alexander P Lyubartsev
Journal:  PLoS One       Date:  2019-04-05       Impact factor: 3.240

8.  Coarse-Grained Models for Protein-Cell Membrane Interactions.

Authors:  Ryan Bradley; Ravi Radhakrishnan
Journal:  Polymers (Basel)       Date:  2013       Impact factor: 4.329

Review 9.  Atomistic Monte Carlo simulation of lipid membranes.

Authors:  Daniel Wüstner; Heinz Sklenar
Journal:  Int J Mol Sci       Date:  2014-01-24       Impact factor: 5.923

10.  The power of coarse graining in biomolecular simulations.

Authors:  Helgi I Ingólfsson; Cesar A Lopez; Jaakko J Uusitalo; Djurre H de Jong; Srinivasa M Gopal; Xavier Periole; Siewert J Marrink
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-05
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.