Role of the N-terminal part of the coat protein in the assembly of cowpea chlorotic mottle virus: A 500 MHz proton nuclear magnetic resonance study and structural calculations

Abstract

The interaction of the oligonucleotides (Ap) 8A and (A-T) 5 with empty capsids of the coat protein of cowpea chlorotic mottle virus (CCMV) has been studied with 500 MHz 1H nuclear magnetic resonance. It is found that these oligonucleotides specifically bind to the arginine and lysine residues of the N-terminal arm of the protein. Upon this binding, immobilization of part of the N-terminal arm occurs. In addition, secondary structure predictions and energy calculations have been performed on the N-terminal arm. These calculations were carried out as a function of the charges on the arginine and lysine side-chains. For free coat protein, where the arginine and lysine side-chains are charged, the arm is found in a random-coil conformation. In the neutralized state, as for the coat protein in the virus, the arm adopts an α-helical conformation. The results support a previously published model for the assembly of CCMV, in which a random-coil to α-helix conformational transition, induced by neutralizing the arginine and lysine side-chains, plays an essential role.