Paper Citing NAMD - Abstract
Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Sekarz, K.
Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 26:497-507, FEB 2009
The IMPDH (Inosine monophosphate dehydrogenase)-II is largely produced in cancer cells. Extensive MD-simulation (2 ns) of the 11330, 1NFB, 1NF7, 1LRT, and I MEW PDB-structures revealed the presence of a conserved water molecule, which is H-bonded and stabilized by the surrounding ribose hydroxyl (O2) of inhibitor, nitrogen (NN) of cofactor, carboxyl oxygen (OD2) and amide nitrogen atoms of the active site Asp 364 and Asn 303 of human. These water-mediated interaction are partially supported in the solvated and X-ray structures. The stereochemistry of the four- centered H-bonds around the conserved water center may be exploited to design a better model inhibitor for IMPDH-II.
