Atomic mean-square displacements in proteins by molecular dynamics: a case for analysis of variance.
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.
Maragliano
Luca
L
National Institute for the Physics of Matter and Physics Department, University of Rome, La Sapienza, 00185 Rome, Italy. maragliano.luca@unimo.it
Cottone
Grazia
G
Cordone
Lorenzo
L
Ciccotti
Giovanni
G
D000465:Algorithms; D000704:Analysis of Variance; D001426:Bacterial Proteins / Q000737:chemistry; D006358:Hot Temperature; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009584:Nitrogen / Q000737:chemistry; D011336:Probability; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013997:Time Factors
D001426:Bacterial Proteins; D011506:Proteins; D012997:Solvents; D009584:Nitrogen