Application of elastic network models to proteins in the crystalline state.

ABSTRACT: Normal mode analysis using elastic network models has grown popular for probing the low-frequency collective dynamics of proteins and other biomolecular assemblies. In most previous studies, these models were validated by comparing calculated atomic fluctuations for isolated proteins with experimental temperature factors determined in the crystalline state, although there were also hints that including crystal contacts in the calculations has an impact on the comparison. In this study, a set of 83 ultra-high resolution crystal structures with experimentally determined anisotropic displacement parameters is used to evaluate several C(alpha)-based elastic network models that either ignore or treat the crystal environment in different ways; the latter include using periodic boundary condition

SUBMITTER: Riccardi D 

PROVIDER: S-EPMC2716453 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature