Water-Intake and Water-Molecule Paths to the Active Site of Secretory Phospholipase A2 Studied Using MD Simulations and the Tracking Tool AQUA-DUCT

Helena D. Tjørnelund, Jesper J. Madsen, Günther H.J. Peters*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Secretory phospholipases A2 (sPLA2s) 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 sPLA2-IIA pass by the aromatic residues Phe5 and Tyr51 and enter the active site through an active-site cleft. The relative amount of water available for the enzymatic reaction of the different phospholipid-sPLA2 complexes was determined together with the distance between key atoms in the catalytic machinery. The results showed that (Z)-unsaturated phospholipid is a good substrate for sPLA2-IIA. The computational results are in good agreement with previously reported experimental data on the ability of sPLA2-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.
Original languageEnglish
JournalJournal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical
Volume124
Issue number10
Pages (from-to)1881-1891
ISSN1520-6106
DOIs
Publication statusPublished - 2020

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