Proteomic Variations in Herpesvirus Structural Proteins

Abstract

Abstract

In all pathogens, the biological processes of living cells are orchestrated in an organised system. Most viral cellular processes are synthesised by structural proteins. The proteome is the set of proteins that are expressed within a cell, tissue or viral particle, and whose composition functions to control or interact with other molecules to facilitate infection. This study aimed to evaluate the mass spectrometry (MS) analysis of bovine herpesvirus 1 (BoHV-1) and herpes simplex virus (HSV-1) from previously published and unpublished data to map variations in the C-capsid and mature virion proteins of these viruses and to identify novel peptides. We report that when the BoHV-1 and HSV-1 gene products were quantified using MaxQuant and the intensity-based absolute quantification (iBAQ) value, their abundance was comparable to that of the expected viral proteins. Next, we searched for potential novel peptides in these viruses from the full-length six frame translations (6FTs) of the entire viral genome. This allowed us to identify novel viral gene products on the basis of peptides that did not map to canonical viral proteins. Further study of the physicochemical properties and prediction of the secondary structures of all novel proteins using tools, such as PSIPRED and JPred4, indicated that the α-helices and β-sheets had little-to-no sequence similarity. However, using the AlphaFold2 algorithm to analyse all the identified novel proteins showed that the secondary structure of proteins is noteworthy. The AlphaFold2 (“Ranked_1.pdb”) output was then imported to a three-dimensional (3D) view in PyMOL and mapped with the highest confident score prediction of the nuclear localisation signal (NLS) sequence. This study adds insight to the protein composition of BoHV-1 and HSV-1 and provides evidence of the utility of MS for accurate and sensitive quantitation of viral proteins. This work also aids in identifying and annotating potential novel viral proteins in pathogenic viruses, such as BoHV-1 and HSV-1.