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Atomic mean-square displacements in proteins by molecular dynamics: a case for analysis of variance.

ABSTRACT: Information on protein internal motions is usually obtained through the analysis of atomic mean-square displacements, which are a measure of variability of the atomic positions distribution functions. We report a statistical approach to analyze molecular dynamics data on these displacements that is based on probability distribution functions. Using a technique inspired by the analysis of variance, we compute unbiased, reliable mean-square displacements of the atoms and analyze them statistically. We applied this procedure to characterize protein thermostability by comparing the results for a thermophilic enzyme and a mesophilic homolog. In agreement with previous experimental observations, our analysis suggests that the proteins surface regions can play a role in the different thermal behavior.

SUBMITTER: Maragliano L

PROVIDER: S-EPMC1304147 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature

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Atomic mean-square displacements in proteins by molecular dynamics: a case for analysis of variance.

Maragliano Luca L Cottone Grazia G Cordone Lorenzo L Ciccotti Giovanni G

Biophysical journal 20040501 5

Information on protein internal motions is usually obtained through the analysis of atomic mean-square displacements, which are a measure of variability of the atomic positions distribution functions. We report a statistical approach to analyze molecular dynamics data on these displacements that is based on probability distribution functions. Using a technique inspired by the analysis of variance, we compute unbiased, reliable mean-square displacements of the atoms and analyze them statistically ...[more]

PMID: 15111395

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