Catalytic activity of D49- versus K49-phospholipase A₂: Molecular Dynamics reveals. a new hypothesis

Martins, N.F.(1), Cartier, A.(2), Brown, D.(3), Maigret, B.(2,3)

(1)Laboratório de Bioinformática - Embrapa - Recursos Genéticos e Biotecnologia, Brasília, Brasil. (2)Laboratory of Theoretical Chemistry, UMR CNRS/UHP 756, Université Henri Poincaré, France, (3)Laboratory of Organic Materials, Université Savoie, France and Instituto de Química, UnB, Brasil.

Secreted PLA2s (sPLA2) are subdivided in two classes, I (pancreas, lung, spleen and cobra) and class II (crotalid and viper venoms and human non-pancreatic secretory PLA2s) which is subdivided into two classes: D49 and K49. K49 myotoxins are distinct and form a highly conserved protein family but in addition to the substitution at position 49, the K49 have other invariant residues not found in the D49 molecules. The D49 enzymes are high catalytic activity on artificial phospholipid but K49 has a few or no hydrolytic activity on artificial membranes. The modeling procedure of K49 enzyme from Bothrops godmani itself was initiated from the 1GOD and 1PIR structures. After preliminary calculations the whole system was relaxed until a stable energy minimum. Next 1 ns of Molecular Dynamics (MD) was recorded. All calculations were performed with ddgmq domain-decomposition parallel MD software. For each trajectory a conformation was recorded each 4 psand  250 conformations were analyzed. Our calculations demonstrate that the calcium ion and the imidazole side chain are on opposite side of the conserved helix and the polarization of water by calcium is not sufficient to be translated so far from the polarization site. This means that another proposition has to be found to explain the lack of activity of K49 PLA2. Our calculations clearly reveal the role of Tyr69 in the activation of the catalytic water molecule and strongly suggest that the calcium ion is no more stabilized around the protein, moving from its starting location to the bulk. This simulation proves that calcium ions will not be anchored to another site on K49 PLA2.

CORRESPONDENCE TO:

Bernard Maigret, R. 9 Norte Bloco 4 ap. 1202, Aguas Claras, Brasília, DF, 70000-000, Brasil, Email: maigret@unb.br