Correlative motions and memory effects in molecular dynamics simulations of molecules: principal components and rescaled range analysis suggest that the motions of native BPTI are more correlated than those of its mutants.
In this work MD simulations of the native bovine pancreatic trypsin inhibitor (BPTI) and 16 mutants were done in vacuum in order to study memory effects in the mutants using principal component analysis (PCA) and the rescaled range analysis (Hurst exponents). Both PCA and the rescaled range analysis support our previous proposition, based on PCA of lysozyme, that the motions of a native protein are more correlated than those of mutants. The methods are compared, the nature and applications of the rule and the role of the long-range correlations in MD time series (i.e. memory) are discussed in the context of collective motions.
Saarela
Janne T A
JT
Department of Chemistry, University of Kuopio, P.O. Box 1627, FIN-70211, Kuopio, Finland
Tuppurainen
Kari
K
Peräkylä
Mikael
M
Santa
Harri
H
Laatikainen
Reino
R
D000465:Algorithms; D007611:Aprotinin / Q000737:chemistry* / Q000235:genetics*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004735:Energy Transfer; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry; D011487:Protein Conformation; D013816:Thermodynamics
D007611:Aprotinin; D009113:Muramidase