Interaction between Capsid Coat Protein and MS2 Bacteriophage SSRNA with Different Loop Motif for Virus Assembly Process

Abstract

In MS2 bacteriophage single-stranded RNA virus, the genomic RNA plays vital roles in the virus assembly process. Multiple dispersed RNA sequence/structure motifs are central recognition motif to specific interact with capsid protein in an assembly process referred to as packaging signal (PS) mediated assembly. The identification of these PSs was based on bioinformatics, geometric approaches and sophisticated experimental protocols. We deal this problem by an altogether different approach, using a large-scale quantitative ab initio methodology centered on critical aspects of the consensus PS recognition motif. DFT calculations are carried out on four nucleoprotein complexes (PDB IDs: 1ZDI, 1ZDH, 5MSF and 6MSF respectively) that are representative of the phage MS2 PSs. The calculated partial charge distribution of individual protein and RNA residues, as well as the calculated strength of the hydrogen bonding (HB) configurations between them, enabled us to locate the exact binding sites of both nucleoprotein, corresponding to the sites exhibiting the strongest HBs. The formation of strong HBs can be traced to the change in the sequence of the ssRNA, leading to an information for PSs between the amino acids and nucleobases. The specific interatomic HBs between atoms in the amino acids of the coat protein and the ssRNA are explored and quantified. Moreover, NAMD simulation provided quantitative information on the strength of electrostatic interactions and the change in free energies between the four types of the capsid protein-RNA, exemplifying the role that modern computational techniques can play in further advancing the field of physical virology.