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Proteomics

All proteins are formed from 20 different common amino acids that are joined by the hundreds in various combinations to form long beaded chains that are twisted into thousands of unique shapes. The amino acid sequence of a protein is specified by the nucleotide sequence of the gene that encodes it. The amino acid sequence of a protein ultimately dictates its three-dimensional (3D) structure, which influences its biomolecular interactions and specialized functions. As a consequence of decades of careful research, the appearance of certain common patterns of short amino acid sequence motifs can now be used to predict the general functions of many proteins. Moreover, the 3D structures of thousands of proteins have now been deduced by x-ray crystallographic studies and other methods.

Knowledge of the primary structure of a given protein predicted from its gene sequence can provide some clues as to its specific function. However, protein function is not only dictated by its shape, but also the context in which the protein must work. The same protein may have multiple functions that depend upon which other interacting proteins are also present. These other proteins may serve as regulators or targets for functional expression of the protein. Thus it is of great importance to track the wide scale distribution of proteins to hone in on their cell-specific functions. This underlies the importance of systems biology approaches to the investigation of proteins.

With only a few exceptions (e.g. germ-line cells, red blood cells and tumour cells), almost all of the two hundred or so different specialized types cells in the human body share the same genes. However, they differ profoundly with respect to which of these genes are actively turned on to produce proteins. The term "proteome" has been adopted to specifically describe the unique complement of proteins that reside in a cell.
Mapping the proteomes of humans and other organisms will be several orders of magnitude more difficult than sequencing their genomes. More than a third of all the genes may be actively expressed in a typical cell. Many genes can specify the synthesis of multiple proteins through alternative splicing to generate slightly different mRNA copies during gene transcription. Furthermore, most proteins subsequently undergo extensive post-translational modifications. Several hundred different type of covalent modifications of proteins have been discovered, including phosphorylation, glycosylation, sulphation, methylation, acetylation, myristoylation, palmitoylation, and isoprenylation. These covalent modifications can have profound effects on the activities, functional interactions and locations of proteins within cells. It is likely that, on average, each gene may specify a hundred or more protein variants that arise from alternative splicing and covalent modification. Therefore, the number of potentially distinct protein entities in the human proteome is probably in the several millions. Apart from the staggering multitude of different potential proteins species within any cell, another major issue is the very dynamic nature of the proteome. A cell's protein composition markedly varies with cell type, gender, age, health and environmental conditions. Consequently, the goal to identify specific biomarkers of human disease is extremely challenging and requires very broad based screening approaches.

Antibodies have proven to be the most specific and reliable probes available to track the expression and covalent modifications of proteins. Kinexus has screened over 6000 of the world’s best commercial antibodies and incorporated them into its proteomics services to permit the broad analysis of signal transduction protein levels and phosphorylation. In addition, Kinexus has developed over 700 of its own antibodies to support these research efforts.
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