New Insights Into the Effect of Residue Mutation on the Rotavirus VP1 Function Using Molecular Dynamic Simulations

Abstract

Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanently emergence of new genotypes puts the potential effectiveness of vaccines under serious question. Thirteen VP1 mutants were analyzed using molecular dynamic simulations and the results were combined with the experimental findings, reported previously. The results revealed structural fluctuations and secondary structure change of VP1 protein that may alter its function during viral replication/transcription. Altogether, the structural analysis of VP1 may boost efforts to develop antivirals, as they might complement the available vaccines. IntroductionRotavirus A (RVA) is a double-stranded RNA (dsRNA) virus of the Reoviridae family. It is a significant cause of childhood gastroenteritis and accounts for ~450,000 deaths annually, most occurring in developing countries [1]. RVA causes also great economic loss to livestock industry worldwide, and again mostly in the developing countries [2,3]. The structural analysis of RVA proteins upon mutations may enhance our ability to better understand their role in viral replication.We focus in the present study on rotavirus RNA-directed RNA polymerase (RdRp), named VP1 protein and coded by VP1 gene, as one of the most important proteins in the viral replication; it is involved in both transcription and genome replication/packaging [4,5] in the presence of other proteins, such as VP2 protein; its N-terminal tether domain extends around VP1 and forms cradle that helps stabilize the enzyme in position [6], suggesting to regulate VP1 transitions between transcription and replication states [7].From the structural point of view, VP1 protein is organized as three distinct domains: an Nterminal domain (residues 1 to 332); a central polymerase domain with canonical fingers (residues 333 to 488 and residues 524 to 595), palm (residues 489 to 523 and residues 596 to 685), and thumb subdomains (residues 686 to 778); and a C-terminal "bracelet" domain (residues 779 to 1089) [8].Together, the N-and C-terminal domains enclose the central polymerase domain to create a cagelike enzyme with a buried active site. Although the crystal structures of the RVA VP1 have been determined and fitted into their capsid structures [7][8][9], the structures of the viral particle-associated VP1 and cofactor proteins, such as NSP2, NSP5 and VP3, are still unknown.The importance of amino acid residues that affect the activity of VP1 protein has been demonstrated [7,10-12] and mutant VP1 proteins in specific positions were engineered in order to assess their capacity to synthesize dsRNA in vitro [10,11]. Authors reported that, based on their effect on the replication level, the induced mutations can be classified into three groups: (i) mutations with no significant effect on replication level; (ii) mutations significantly lower levels of dsRNA product; and (iii) mutation that enhanced the initiation capacity and product elongation rate of VP1 protein. In addition, temperature-sensitive (ts) mutant mapped t...

New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations

“…We acknowledge Cineca and ELIXIR-IIB for computing resources. This manuscript has been released as a preprint at BiorXiv () …”