Methodology

In recent years, the range and sophistication of protein analysis tools have exploded and only a few can be mentioned here. The study of virus structural proteins traditionally required the purification of virions from infected cells or infected-cell supernatants, free from contaminating host (or nonstructural) proteins. This can be achieved by a series of differential centrifugation steps, followed by sucrose gradient-density centrifugation (centrifugation through a sucrose gradient usually results in a sharp band of virus at a specific location on the gradient). The most commonly used technique to study virus proteins is SDS–polyacrylamide gel electrophoresis (separation based on size),  usually accompanied by either Western blotting or immunoprecipitation (both require the binding of virus proteins by highly specific antibodies).

The location of virus nonstructural proteins within cells is a useful indicator of their possible function, and many methods are used to detect proteins within cells, primarily differential staining, immunofluorescence,   and   confocal microscopy techniques. These techniques visualize, microscopically, the distribution within infected cells of fluorescent stains or fluorescence-labeled antibodies bound specifically to virus proteins. Other tools that can help characterize protein function include pulse–chase experiments (to determine when proteins are made in cells), protease or glycosylation inhibitors (to indicate how proteins are processed), and co-immunoprecipitation (to determine if individual proteins interact with others).

Bioinformatics (the prediction of amino acid sequences from gene sequencing) is commonly used now to infer virus protein structure and function, including the identification of probable functional domains within proteins. While not  exhaustive (or all inclusive), there are  recognizable amino acid  sequences (motifs) that carry  key functions such as sites for protease cleavage, motifs for spanning membranes, for the addition of modifications (e.g. glycosylation) or for targeting the  protein to specific cellular locations or for secretion from  the  cell entirely. Bioinformatic comparison of conserved motifs in genes (and proteins) has led to an understanding of the relatedness of proteins from different viruses and even cells, often revealing a close association and co-evolution of a virus and its host. With the development of gene sequencing and cloning, and of highly efficient protein expression systems, individual proteins can now be examined in isolation by cloning of their gene sequences. Often, the cloning steps include addition of extra amino acids that serve as a tag, to aid in purification or detection of the protein.