Viral proteomics

Abstract

Viruses have long been studied not only for their pathology and associated disease but also as model systems for molecular processes and as tools for identifying important cellular regulatory proteins and pathways. Recent advances in mass spectrometry methods coupled with the development of proteomic approaches have greatly facilitated the detection of virion components, protein interactions in infected cells, and virally induced changes in the cellular proteome, resulting in a more comprehensive understanding of viral infection. In addition, a rapidly increasing number of high-resolution structures for viral proteins have provided valuable information on the mechanism of action of these proteins as well as aided in the design and understanding of specific inhibitors that could be used in antiviral therapies. In this paper, we discuss proteomic studies conducted on all eukaryotic viruses and bacteriophages, covering virion composition, viral protein structures, virus-virus and virus-host protein interactions, and changes in the cellular proteome upon viral infection.

FIG. 1.

Analysis of virion composition by mass spectrometry. Typical approaches for analyzing virion protein composition by MALDI-TOF mass spectrometry (MS) and LC-MS/MS are shown. 1D, one dimensional.

FIG. 2.

Viral protein structures in the PDB. The numbers of protein structures from eukaryotic viruses (black) and phages (gray) are shown according to the year deposited in the PDB.

FIG. 3.

Proteomic methods for protein-protein interactions. Schematic representation of the yeast-based two-hybrid screen (A), affinity column profiling (B), and TAP tagging (C) are shown. IgG, immunoglobulin G; TEV, tobacco etch virus protease site; CBP, calmodulin binding protein.

FIG. 4.

Methods for comparative proteomics. Schematic representations for the 2D DIGE, ICAT, and SILAC methods used to compare the relative abundance of individual proteins in two samples are shown.