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 ch[orotic mottle virus has been studied with five molecular dynamics simulation s of 2.0 ns each. This 25-residue peptide (pep25) is highly charged: i t contains six Arg and three Lys residues. An alpha-helical fraction o f the sequence is stabilized in vitro by salts. The interaction of mon ophosphate (Pi) ions with pep25 was studied, and it was found that onl y two Pi ions are bound to pep25 on average, but water-mediated intera ctions 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 magneti c resonance experiments.