Elucidation of Active Site Protective Residues in Rhizomucor miehei Lipase by Targeted Molecular Dynamics Approach

Rhizomuor miehei Lipase (RmL) is a type of lipase that has a single lid segment playing important role in its catalytic activity. RmL lid segment is a long helical chain located at residues 85 to 92 acting as a gate to mediate substrate binding and product releasing by making open and close dynamics movement. In the present study, we were interested to evaluate the molecular mechanism of opening RmL lid segment from its closed state in aqueous solvent by using targeted molecular dynamics (TMD) approach. The external forces about 0.125 kcal/(mol.Å) was applied in TMD to push the closed state of RmL lid toward the targeted open state. The results showed that RmL lid was fail to reach the targeted structure, in which the final structure was stacked at about 65% opening. The comparative structural analysis between the partially and fully open states revealed the caused of the sterical hindrance preventing the lid segment to reach the fully open state. Strong hydrophobic interactions among Trp88 with the surrounding non-polar residues in the active site was the major caused for the sterical hindrance. This restriction will protect the active site of the enzyme to be fully exposed to the solvent, thereby minimizing the accessibility of non-substrate molecules into the active site.