Deciphering of packing signal hypothesis in bacterophage RNA recognition by the MS2 capsid protein in virus assembly

Abstract

MS2 is a classical example of a single-stranded RNA virus for which the genomic RNA plays pivotal roles in the virus assembly process. Multiple dispersed RNA se quence/structure motifs, packaging signals (PSs) varying around a central recognition motif, interact with capsid protein in a process referred to as packaging signal me diated assembly. While the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimen tal protocols, we approach this problem by an altogether different philosophy, 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 nucleopro tein complexes (PDB IDs: 1ZDI, 1ZDH, 5MSF and 6MSF) that are representative of the phage MS2 PSs. We have calculated atomic partial charge in the models using ab initio DFT based OLCAO method. The calculated partial charge distribution of individual protein and RNA residues indicates that the gross features is the same in CP because they have identical sequences, but there are some important minor differences due to the different RNAs to which they bind. It shows that CP is lost and ssRNA is gained charge in all models. The loss of charge by CP in order of 6MSF>5MSF>1ZDI>1ZDH in CP-RNA complex. We have also calculated strength of the interfacial hydrogen bonding (HB) configurations between protein and RNA. The interfacial HBs enable us to locate the exact binding sites of both nucleoprotein, corresponding to the sites exhibiting the strongest interfacial HBs, here identified to be (TYR85-U⁻⁵) in 1ZDI and LYS43 A⁻⁴ in 1ZDH, 5MSF and 6MSF. The formation of stronger HBs can be traced to the change in the sequence of the mutated RNA, and three-base loop motif leading to more pronounced HB fit between the amino acids and nucleobases. We have quantify HB with a physical quantum quantity of bond order (BO) and summed up all BO values of interfacial HBs as a total bond order (TBO). This is very important quantum quantity for strength of binding between CP and ssRNA. We found that he interfacial TBO are in order of 6MSF>1ZDI>5MSF>1ZDH. The binding between CP with RNA is higher in three-base loop motif than tetra-base loop motif and the mutate form of RNA has higher binding than wild type RNA. Moreover, simulation provided quantitative information on the strength of CP-RNA interactions with respect to RNA sequences. Finally, our study exemplifying the role that modern computational techniques can play in further advancing the field of physical virology.