Paper Citing NAMD - Abstract
Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Sekar, K.
An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II (Human): Recognition of Cofactor and Substrate to Catalytic Arg 322
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:149-158, OCT 2009
Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofactor through the catalytic D 364 and N 303. The 15 ns simulation and the water dynamics of the three different PDB structures (1B3O, 1NF7, and 1NFB) of human IMPDH by CHARMM force field have clearly indicated the involvement of three conserved water molecules (W(L), W(M), and W(C)) in the recognition of catalytic residues (R 322, D 364, and N 303) to inhibitor and cofactor. Both the guanidine nitrogen atoms (NH1 and NH 2) of the R 322 have anchored the di- and mono-nucleotide (cofactor and inhibitor) binding domains via the conserved W(C) and W(L) water molecules. Another conserved water molecule W(M) seems to bridge the two domains including the R 322 and also the W(C) and W(L) through seven centers H-bonding coordination. The conserved water molecular triad (W(C) - W(M) - W(L)) in the protein complex may thought to play some important role in the recognition of inhibitor and cofactor to the protein through R 322 residue.
