Phylogenetic analysis and Molecular Dynamics Simulation of a new secretory Phospholipase A2 from Glycine max Soybean

MARIANI, M.E., ; VILLARREAL M.A.,; MADOERY, R.; FIDELIO G.D.

Salta

Congreso; Latin American Protein Society Meeting and XXXIX Argentinean Biophysical Society (SAB); 2010

SAB and Latin American Protein Society Meeting and XXXIX Argentinean Biophysical Society

SUMMARY

                The Phospholipase A₂ superfamily is a broad and growing group of enzymes that stereospecifically catalyze the cleavage of the sn-2 acyl ester union of diacyl-phospholipids and liberate 1-acyl-2-lysophospholipids and free fatty acids. Two structural characteristics of any sPLA₂ are of high functional interest: the catalytic site and the interfacial recognition surface (IRS). All sPLA₂s have the same architecture at the catalytic site level (His-Asp) but differ on the aminoacid residues that compose the IRS. A TBLASTN search of  the Glycine max genome mRNA database  using Arabidopsis thaliana, Oryza sativa and Zea mays sPLA₂s as templates, showed the existence of five putative sPLA₂s isoenzymes, denoted as GmsPLA₂-I,GmsPLA₂-II, GmsPLA₂-III, GmsPLA₂-IV and GmsPLA₂-V. The five sPLA₂s sequences contained a conserved PA2c domain having the Ca^2+- binding loop (YGKYCGxxxxGC) and the active site motif (DACCxxHDxC) and the His/Asn, His or Ser dyad. A phylogenetic tree of Glycine max sPLA₂s was proposed after sequence alignment. The sequences were grouped in two categories (known as group XIA and XIB) on the basis of their differences in molecular weight and deviating sequences especially in the N- and C- terminal regions of the proteins. Enzymes of these groups differ in the third Ca²⁺ coordinating amino acid and the amino acid composition of the “dyad”. Homology Modeling and Molecular Dynamics generated on the basis of the known crystal structure of Rice isoform II, allowed first insights into the three-dimensional structure of the protein GmsPLA₂-I in solution and at the membrane.