6533b874fe1ef96bd12d615d
RESEARCH PRODUCT
Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance
Luca MaraglianoGiovanni CiccottiLorenzo CordoneGrazia Cottonesubject
Models MolecularMean squareSurface (mathematics)Hot TemperatureTime FactorsNitrogenProtein ConformationMolecular ConformationBiophysicsBiophysical Theory and ModelingMeasure (mathematics)Protein Structure SecondaryMolecular dynamicsBacterial ProteinsStatistical physicsProbabilityThermostabilityAnalysis of VarianceQuantitative Biology::BiomoleculesModels StatisticalChemistryProteinsModels TheoreticalCrystallographyDistribution functionSolventsProbability distributionAnalysis of varianceAlgorithmsdescription
AbstractInformation 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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2004-05-01 |