Molecular Dynamics Study on Conformational Sampling of Triosephosphate Isomerase

Abstract

Triosephosphate Isomerase (TIM) is a glycolytic enzyme catalyzing the interconversion of Dihydroxyacetone phosphate (DHAP) to Glyceraldehyde-3-phosphate (GAP). TIM is a non-allosteric dimeric enzyme with three distinct loops (loop-6, 7 & loop-8) enveloping the active site. Loop-6 acts as a lid on the active site and residues from loop-7 and loop-8 stabilize the substrate in the active site. Depending on the orientation of loop-6 and loop-7, TIM can be classified into various conformational states. These different conformations of TIM suggest that for each task i.e. substrate binding, catalysis and product release, the protein adopts to a specific conformation suited for that particular task. Various NMR, X-ray and MM experiments have studied the conformational flexibility of loop-6 in presence or absence of natural substrates, various inhibitors and have suggested that the conformational exchange rate of loop-6 is similar to the catalytic rate of the enzyme (104/s). These studies have provided glimpses of individual events of what essentially is a dynamic process.We study the sequence of events from the binding of the ligand to the release of the product by molecular dynamics simulations. Our simulations revealed that loop-6 opens and closes in both apo and holo enzymes at microsecond time scale and also that N-termini (168P-169V-170W) and C-termini (176K-177V-178A) hinges of the loop-6 move independently which was also reported by Berlow et.al [Biochemistry 46 2007 6001]. Loop-7 on the other hand samples the closed state only when the active site is occupied by the ligand or an inhibitor. It was also observed that the conformational preference of loop-6 and loop-7 is independent of the conformation of the other.