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Comparison of two force fields in MD‐simulations of α‐helical structures in keratins
Author(s) -
Knopp Birgitta,
Jung Bernd,
Wortmann FranzJosef
Publication year - 1996
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/mats.1996.040050511
Subject(s) - force field (fiction) , molecular dynamics , helix (gastropod) , hydrogen bond , chemistry , crystallography , monomer , protein filament , chemical physics , computational chemistry , molecule , physics , polymer , quantum mechanics , ecology , biochemistry , organic chemistry , snail , biology
Molecular dynamic (MD) simulations based on two different force fields, CVFF and CFF91, were carried out in order to check their feasibility for the structural investigation of the wool intermediate filament (IF) monomeric unit. Selecting an ideal α‐helix as start conformation, all MD‐simulations with CVFF in vaccum show the α‐helix to be unstable. Independently of the amino acid sequence of the α‐helix, a new helical structure with a larger diameter arises during the MD‐simulation, due to a shift of the intrahelical hydrogen bonds. However in simulations with surrounding water the α‐helix remains stable throughout the simulations with the CVFF force field. In contrast to this, MD‐simulations in vaccume based on the CFF91 force field are able to determine different stabilities for the α‐helical start conformation of various IF‐segments, that agree well with secondary structure predictions. The simulation results obtained with CFF91 in vacuum can like wise be verified using an explicit water environment. We found that higher partial charges attributed to the atoms of the amide groups that form the intrahelical hydrogen bonds are the reason for the superiority of the CFF91 force field.