Spontaneous lid closure and substrate-induced lid opening dynamics of human pancreatic lipase-related protein 2: A computational study

Abstract

Pancreatic lipases are essential dietary enzymes with a well-conserved catalytic triad covered by a lid. Unlike classical lipases, pancreatic lipase-related proteins 2 (PLRP2) are active in aqueous medium without any colipase. As their substrate accessibility is controlled by the lid in N-terminal domain, we investigated the lid dynamics of human PLRP2 (HPLRP2) in its closed and open conformational states using molecular dynamics (MD) simulation. The free energy landscape constructed from the MD trajectory of HPLRP2 in the open conformation suggests that the well-conserved W254 along with the hydrophobic region G256-V261 on the lid, which differs from the classical lipases, show larger conformational changes during the lid closure pathway of HPLRP2. Further, HPLRP2 in the closed conformation could attain the open state only after introducing a double mutation D251S/E255C and upon the addition of substrate molecules, tributyrin (Tbt). This initially disrupted the stable interactions between the lid and β6 loop, and the lid opening movement was further facilitated by the interactions of Tbt with β8 and β9 loops. Tbt also bound to C-terminal domain and significantly altered its orientation. The lid opening pathway of HPLRP2 was found to be distinct from its closing trajectory and tributyrin could access the active site even when the lid did not attain its fully-extended open conformation. The results indicate that the lid dynamics of HPLRP2 is different from the classical lipases and facilitates its function in the absence of any colipase.