scholarly journals Molecular dynamics simulations of membrane proteins

2012 ◽  
Vol 4 (3) ◽  
pp. 271-282 ◽  
Author(s):  
Turgut Baştuğ ◽  
Serdar Kuyucak
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

Molecular Dynamics Simulations of Membrane Proteins

2013 ◽  
pp. 85-101 ◽  
Author(s):  
Kristyna Pluhackova ◽  
Tsjerk A. Wassenaar ◽  
Rainer A. Böckmann
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 644a
Author(s):  
Shahidul M. Islam ◽  
Giacomo Florin ◽  
Yifei Qi ◽  
Rong Shen ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Spin Label ◽  
Structural Function ◽  
Function Study ◽  
Dynamics Simulations

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

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