Advanced sampling simulations of coupled folding and binding of phage P22 N-peptide to boxB RNA.

ABSTRACT: Protein-RNA interactions are crucially important for numerous cellular processes and often involve coupled folding and binding of peptide segments upon association. The Nut-utilization site (N)-protein of bacteriophages contains an N-terminal arginine-rich motif that undergoes such a folding transition upon binding to the boxB RNA hairpin loop target structure. Molecular dynamics free energy simulations were used to calculate the absolute binding free energy of the N-peptide of bacteriophage P22 in complex with the boxB RNA hairpin motif at different salt concentrations and using two different water force field models. We obtained good agreement with experiment also at different salt concentrations for the TIP4P-D water model that has a stabilizing effect on unfolded protein structures. It

SUBMITTER: Vollmers L 

PROVIDER: S-EPMC11480772 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature