Paper Citing NAMD - Abstract
Zhang Yue-Bin; Cheng Ying-Kun; Lue Ming; Zhang Hua-Li; Li Zheng-Qiang
Function of the Hydrogen-bonding Network Between the Y-S-R Motif and the Heme Propionate Groups in sGC-HNOX Domain
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 31:1039-1044, MAY 10 2010
Molecular dynamics methods were implemented to investigate the functions of hydrogen-bonding network between the conserved Y-S-R motif and the heme propionate groups in sGC-HNOX domain. The RMSD analysis reveals that the hydrogen-bonding network can stabilize the conformation of sGC-HNOX domain conspicuously during our simulation. The secondary structure, radius of gyration and solvent-accessible surface area of sGC-HNOX domain are not disturbed by the restraint hydrogen-bonding network. The principal component analysis on trajectory data and the heme configuration analysis indicate that the essential function of hydrogen-bonding network is to stabilize the binding of 4-E motif to 7-H motif, which is related to the structural integrity of sGC-HNOX domain.
