Paper Citing NAMD - Abstract
Ierich, Jessica C. M.; Oliveira, Guedmiller S.; Vig, Ana C. A.; Amarante, Adriano M.; Franca, Eduardo F.; Leite, Fabio L.; Mascarenhas, Yvonne P.
A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:1702-1709, AUG 2015
A combined molecular modeling and molecular dynamics simulation was carried out to obtain an improved description of the yeast acetohydroxyacid synthase (AHAS) in aqueous solution. After a thorough homology modeling, the AHAS catalytic dimer was subjected to a molecular dynamics (MD) simulation to analyze its behavior and optimize its geometry. The AHAS 3D molecular structure was analyzed according to the number of salt bridges and hydrogen bonds formed. During 20 ns of MD simulation, an average fluctuation of 3.9 angstrom was obtained. The cofactor thiamine diphosphate makes a relevant contribution to the system stability; this hypothesis was confirmed by the decrease in the average fluctuation of 0.3 angstrom. Moreover, the Ramachandran plot revealed no denaturation framework during the time of the simulation.
