Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions.

The RNA-binding N-terminal arm of the coat protein of cowpea chlorotic mottle virus has been studied with five molecular dynamics simulations of 2.0 ns each. This 25-residue peptide (pep25) is highly charged: it contains six Arg and three Lys residues. An alpha-helical fraction of the sequence is stabilized in vitro by salts. The interaction of monophosphate (Pi) ions with pep25 was studied, and it was found that only two Pi ions are bound to pep25 on average, but water-mediated interactions between pep25 and Pi, which provide electrostatic screening for intrapeptide interactions, are abundant. Shielding by the Pi ions of repulsive electrostatic interactions between Arg sidechains increases the alpha-helicity of pep25. A hydrogen bond at the N-terminal end of the alpha-helix renders extension of the alpha-helix in the N-terminal direction impossible, in agreement with evidence from nuclear magnetic resonance experiments.