Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid

Protein–ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil–water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.