32.20: Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics describing it as the ‘PROTein complement expressed by a genOME.’
As proteomics often complements genomics, it is useful when scientists want to test their research hypotheses. Even though all the cells in a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different because it is dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins). Also, many proteins modify themselves after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate studying proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Because of this, there are different types of proteomics, such as expression, structural and functional, which help study various aspects of the proteins.
The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as analyzing the genome requires basic DNA sequencing technique, proteomics requires techniques for protein analysis. The basic technique for protein analysis is mass spectrometry that identifies and determines a molecule's characteristics. Advances in spectrometry have allowed researchers to analyze very small protein samples. X-ray crystallography, for example, enables scientists to determine a protein crystal's three-dimensional structure at atomic resolution. Nuclear magnetic resonance uses atoms' magnetic properties to determine the protein's three-dimensional structure in an aqueous solution. Scientists have also used protein microarrays to study protein interactions. Large-scale adaptations of the basic two-hybrid screen have provided the basis for protein microarrays. Scientists use computer software to analyze the vast amount of data for proteomic analysis.
