Protein structural variation in computational models and crystallographic data.
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational flexibility. Normal modes from four simple elastic network model potentials and from the CHARMM force field are calculated for a data set of 83 diverse, ultrahigh-resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, all-atom potentials have a clear edge at prediction of directionality, and the CHARMM potential has the highest prediction quality. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity.
Kondrashov
Dmitry A
DA
Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706, USA. dkon@biochem.wisc.edu <dkon@biochem.wisc.edu>
Van Wynsberghe
Adam W
AW
Bannen
Ryan M
RM
Cui
Qiang
Q
Phillips
George N
GN
D016880:Anisotropy; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
D011506:Proteins