Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution

The 'loop' involving residues 98-110 in Bacillus stearothermophilus lactate dehydrogenase (BSLDH) is of great interest as substrate-induced 'loop' closure is thought to be rate-limiting and essential in catalyzing the reaction and in determining substrate specificity. Consequently, we have explored the mechanism underlying 'loop' opening in BSLDH through a molecular dynamics simulation at high temperature (1000 K) in the presence of explicit solvent, starting from the X-ray structure of BSLDH complexed with the co-enzyme NAD+ and oxamate at 2.5 A. During the simulation, a significant conformational change occurred, as evidenced by sharp dihedral angle transitions, hydrogen bond breaking and formation and large root mean square deviations from the starting structure; these changes define the criteria for 'loop' opening. The mechanical elements responsible for 'loop' opening, i.e. 'loop' hinges and flap, are defined through a combination of order parameters, dihedral angle changes and their correlations and the dynamical cross-correlation map of atomic displacements for the 'loop' residues. The results indicate that the 'loop' consists of two flexible hinge regions on either side of a relatively rigid three-residue segment that undergoes a significant spatial displacement during 'loop' opening. 'Loop' opening is made possible through an array of correlated dihedral angle changes and intra-'loop' rearrangements of hydrogen-bond interactions. The present findings are compared to previous work related to 'loop' opening and site-directed mutagenesis experiments.