RICIN A-CHAIN STRUCTURAL DETERMINANT FOR BINDING SUBSTRATE-ANALOGS - A MOLECULAR-DYNAMICS SIMULATION ANALYSIS

Ricin A-chain is a cytotoxic protein that attacks ribosomes by hydroly zing a specific adenine base from a highly conserved, single-stranded rRNA hairpin containing the tetraloop sequence GAGA. Molecular-dynamic s simulation methods are used to analyze the structural determinant fo r three substrate analogues bound to the ricin A-chain molecule. Simul ations were applied to the binding of the dinucleotide adenyl-3',5'-gu anosine employing the x-ray crystal structure of the ricin complex and a modeled CGAGAG hexanucleotide loop taken from the NMR solution stru cture of a 29-mer oligonucleotide hairpin. A third simulation model is also presented describing a conformational search of the docked 29-me r structure by using a simulated-annealing method. Analysis of the str uctural interaction energies for each model shows the overall binding dominated by nonspecific interactions, which are mediated by specific arginine contacts hom the highly basic region on the protein surface. The tetraloop conformation of the 29-mer was found to make specific in teractions with conserved protein residues, in a manner that favored t he GAGA sequence. A comparison of the two docked loop conformations wi th the NMR structure revealed significant positional deviations, sugge sting that ricin may use an induced fit mechanism to recognize and bin d the rRNA substrate. The conserved Tyr-80 may play an important confo rmational entropic role in the binding and release of the target adeni ne in the active site. Proteins 27:80-95 (C) 1997 Wiley-Liss, Inc.