Paper Citing NAMD - Abstract
Xu, Wei; Cai, Ping; Yan, Ming; Xu, Lin; Ouyang, Ping-kai
Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
CHINESE JOURNAL OF CHEMICAL PHYSICS, 22:467-472, OCT 27 2009
The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 us by NAMD2.5. The radius of gyration (R(g)), subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148; 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loop-helix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The R(g) of catalytic domain at 360 K shows 0.16 angstrom higher than that at 300 K, but R(g) of small C-terminal domain has no obvious difference. The results indicate that enhanced R(g) of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at, subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
