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.
Table of Contents
Introduction -- The structure and assembly of icosahedral viruses -- Simulation theory and packages -- Computational modeling and methods -- Results and discussion -- Final remarks and future works -- Appendix A. VASP input files -- Appendix B.Supporting tables and figures -- Appendix C. Abbreviations
Degree
Ph.D.