MODELING OF THE 3-DIMENSIONAL STRUCTURE OF LUFFIN-ALPHA AND ITS SIMULATED REACTION WITH THE SUBSTRATE OLIGORIBONUCLEOTIDE GAGA

A fundamental problem in biochemistry and molecular biology is underst anding the spatial structure of macromolecules and then analyzing thei r functions. In this study, the three-dimensional structure of a ribos ome-inactivating protein luffin-alpha was predicted using a neural net work method and molecular dynamics simulation. A feedforward neural ne twork with the backpropagation learning algorithm were trained on mode l class of homologous proteins including trichosanthin and alpha-momor charin. The distance constraints for the C alpha atoms in the protein backbone were utilized to generate a folded crude conformation of luff in-alpha by model building and the steepest descent minimization appro ach. The crude conformation was refined by molecular dynamics techniqu es and a simulated annealing procedure. The interaction between luffin -alpha and its analogous substrate GAGA was also simulated to understa nd its action mechanism.