Water-Intake and Water-Molecule Paths to the Active Site of Secretory Phospholipase A 2 Studied Using MD Simulations and the Tracking Tool AQUA-DUCT

• Published in: The journal of physical chemistry. B Vol. 124; no. 10; pp. 1881 - 1891
• Main Authors: Tjørnelund, Helena D, Madsen, Jesper J, Peters, Günther H J
• Format: Journal Article
• Language: English
• Published: United States 12-03-2020
• Subjects: Catalytic Domain; Hydrolysis; Liposomes; Phospholipases A2, Secretory - metabolism; Water
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.9b10837

Secretory phospholipases A
(sPLA
s) are a subclass of enzymes that catalyze the hydrolysis at the sn-2 position of glycerophospholipids, producing free fatty acids and lysophospholipids. In this study, different phospholipids with structural modifications close to the scissile sn-2 ester bond were studied to determine the effect of the structural changes on the formation of the Michaelis-Menten complex and the water entry/exit pathways using molecular dynamics simulations and the computational tracking tool AQUA-DUCT. Structural modifications include methylation, dehydrogenation, and polarization close to the sn-2 scissile bond. We found that all water molecules reaching the active site of sPLA
-IIA pass by the aromatic residues Phe
and Tyr
and enter the active site through an active-site cleft. The relative amount of water available for the enzymatic reaction of the different phospholipid-sPLA
complexes was determined together with the distance between key atoms in the catalytic machinery. The results showed that (
)-unsaturated phospholipid is a good substrate for sPLA
-IIA. The computational results are in good agreement with previously reported experimental data on the ability of sPLA
-IIA to hydrolyze liposomes made from the different phospholipids, and the results provide new insights into the necessary active-site solvation of the Michaelis-Menten complex and can pave the road for rational design in engineering applications.