ESSENTIAL DYNAMICS OF LIPASE BINDING-SITES - THE EFFECT OF INHIBITORSOF DIFFERENT CHAIN-LENGTH

The biochemical activity of enzymes, such as lipases, is often associa ted with structural changes in the enzyme resulting in selective and s tereospecific reactions with the substrate. To investigate the effect of a substrate and its chain length on the dynamics of the enzyme, we have performed molecular dynamics simulations of the native Rhizomucor miehei lipase (Rml) and lipase-dialkylphosophate complexes, where the length of the alkyl chain ranges from two to 10 carbon atoms. Simulat ions were performed in water and trajectories of 400 ps were used to a nalyse the essential motions in these systems. Our results indicate th at the internal motions of the Rml and Rml complexes occur in a subspa ce of only a few degrees of freedom. A high flexibility is observed in solvent-exposed segments, which connect beta-sheets and helices. In p articular, loop regions Gly35-Lys50 and Thr57-Asn63 fluctuate extensiv ely in the native enzyme. Upon activation and binding of the inhibitor , involving the displacement of the active site loop, these motions ar e considerably suppressed. With increasing chain length of the inhibit or, the fluctuations in the essential subspace increase, levelling off at a chain length of 10, which corresponds to the size of the active- site groove.