Molecular Modelling Studies on the Catalytic Mechanism of Candida Rugosa Lipase

Quantum chemical and molecular dynamics investigations have been performed on model systems for Candida rugosa lipase (CRL) to study mechanistic and conformational features of the catalytic hydrolysis. Based on X-ray data, a simplified model of the CRL substrate complex was created for the PM3 and ab initio calculations, including the amino acid residues both of the catalytic triad and the oxyanion hole.The energetic and structural properties of significant species along the pathway of the hydrolysis of the model substrate acetic acid methyl ester have been calculated. By modifications of the residues of the oxyanion hole as well as the catalytic triad, the influence of these parts of the active site on the pathway of the reaction was analysed in more detail.Moreover, molecular dynamics simulations have been carried out on CRL adducts with (±)-cis-4-acetamido-cyclopent-2-ene-1-carboxylic esters with different lengths of their alkyl chain and their absolute configuration as substrates. For the MD simulations using the AMBER program, all amino acid residues and water molecules with a cut-off radius less than 1500 pm from the substrate were taken into account. From the analysis of the trajectories and histograms for significant hydrogen bonds in the active site of the enzyme adducts, some hints were obtained for the enantiodifferentiation and the chain dependence of the esters in catalytic hydrolysis by CRL.Electronic Supplementary Material available.