An efficient method for sampling the essential subspace of proteins.
A method is presented for a more efficient sampling of the configurational space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conformational changes in proteins revealed by the "essential dynamics" analysis. A form of constrained dynamics is performed, forcing the system to move along some of the essential coordinates. This results in a broader sampling of the essential subspace than in a comparable conventional molecular dynamics simulation without constraints. The new sampling method (essential dynamics sampling) was applied to the histidine-containing phosphocarrier protein HPr. The results indicate that the essential dynamics sampling method produces physically allowed structures, as estimated by the evaluation of many geometrical properties. In addition, a study of the motions in the essential subspace reveals a diffusion-like behavior.
Amadei
A
A
Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, the University of Groningen, The Netherlands.
Linssen
A B
AB
de Groot
B L
BL
van Aalten
D M
DM
Berendsen
H J
HJ
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry; D006860:Hydrogen Bonding; D008432:Mathematical Computing; D008958:Models, Molecular; D010750:Phosphoproteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents; D013816:Thermodynamics
D001426:Bacterial Proteins; D010750:Phosphoproteins; D012997:Solvents