This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Maragliano, L. Articles by Ciccotti, G. Search for Related Content PubMed PubMed Citation Articles by Maragliano, L. Articles by Ciccotti, G.

Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance

Luca Maragliano ^*, Grazia Cottone , Lorenzo Cordone  and Giovanni Ciccotti ^*

^* National Institute for the Physics of Matter and Physics Department, University of Rome, La Sapienza, 00185 Rome, Italy; and National Institute for the Physics of Matter and Department of Physical and Astronomical Sciences, University of Palermo, 90123 Palermo, Italy

Correspondence: Address reprint requests to Luca Maragliano, National Institute for the Physics of Matter National Research Center on nanoStructures and bioSystems at Surfaces (S3), Physics Dept., University of Modena, via Campi 213/A, 41100 Modena, Italy. Tel.: +39-059-205-5323; Fax: +39-059-367-488; E-mail: maragliano.luca{at}unimo.it.

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.

This article has been cited by other articles:

				C. Scharnagl, M. Reif, and J. Friedrich Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c Biophys. J., July 1, 2005; 89(1): 64 - 75. [Abstract] [Full Text] [PDF]