Dynamics of proteins in crystals: comparison of experiment with simple models.
The dynamic behavior of proteins in crystals is examined by comparing theory and experiments. The Gaussian network model (GNM) and a simplified version of the crystallographic translation libration screw (TLS) model are used to calculate mean square fluctuations of C(alpha) atoms for a set of 113 proteins whose structures have been determined by x-ray crystallography. Correlation coefficients between the theoretical estimations and experiment are calculated and compared. The GNM method gives better correlation with experimental data than the rigid-body libration model and has the added benefit of being able to calculate correlations between the fluctuations of pairs of atoms. By incorporating the effect of neighboring molecules in the crystal the correlation is further improved.
Kundu
Sibsankar
S
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
Melton
Julia S
JS
Sorensen
Dan C
DC
Phillips
George N
GN
D055592:Biophysical Phenomena; D001703:Biophysics; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D015233:Models, Statistical; D016011:Normal Distribution; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins