A unique structural feature of a phospholipase A2 is probed by molecular dynamics.
The unusual catalytic network, revealed by the crystal structure of one of the two phospholipases A2 (PLA2) from the venom of the crotalid A.p.piscivorus has been probed using molecular dynamics. The catalytic network has been remodeled to a conformation similar to that found in all other PLA2, and the modeled structure has been submitted to energy minimization and molecular dynamics simulation, to explore the conformational space of the network. The calculations have yielded a large reorganization of the catalytic network, which gets a conformation close to that of the crystal structure. These results suggest that the unusual catalytic network observed in the studied PLA2 is a structural feature of the protein and not a crystal artifact.
Demaret
J P
JP
Laboratoire de Biochimie (CNRS URA 240), Ecole Polytechnique, Palaiseau, France.
Brunie
S
S
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010741:Phospholipases A / Q000737:chemistry*; D054467:Phospholipases A2; D011487:Protein Conformation; D012984:Software; D013816:Thermodynamics
D010741:Phospholipases A; D054467:Phospholipases A2