Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations.

ABSTRACT: Protein-RNA interactions are important for many cellular processes. The Nut-utilization site (N)-protein of bacteriophages contains an N-terminal arginine-rich motif that undergoes a folding transition upon binding to the boxB RNA hairpin loop target structure. Molecular dynamics simulations were used to investigate the dynamics of the P22 N-peptide-boxB complex and to elucidate the energetic contributions to binding. In addition, the free-energy changes of RNA and peptide conformational adaptation to the bound forms, as well as the role of strongly bound water molecules at the peptide-RNA interface, were studied. The influence of peptide amino acid substitutions and the salt dependence of interaction were investigated and showed good agreement with available experimental results. Several

SUBMITTER: Bahadur RP 

PROVIDER: S-EPMC2793363 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature