Proteomics takes into consideration the synthesis and identification of protein products of genomic genes for their possible exploitation in clinical therapeutics and pharmacy and indeed other areas of biotechnology. These may go far beyond therapeutics and may dabble into areas of relevant research into the functions of biological proteins and the analysis of their properties. But by far the most important areas of the utilization of proteomic information would be in therapeutics and clinical pharmacy. While genomics studies the genome which is the totality of all DNA in an organism, proteomics studies the proteome, which is the totality of all proteins in the cell (Wilkins et al 1996; Dhinga et al 2005; Rogers et al 2008; Klopfleisch et al 2010).
Proteins from the cells undergo modifications to mark them biologically active. Thus we have phosphorylation and ubiquitination. Yet others include methylation, acetylation, glycosylation, oxidation and nitrosylation. Enzymes like E3 ubiquitin ligases help to add a small protein called ubiquitin and can be helpful in determining sets of ligases from a particular cell. Phosphoproteomics and glycoproteomics help to study posttranslational genomics. Proteomics gives a better explanation of the substances in tissue than genomics.
Complexity of proteomics
Genomics is a straight forward discipline than preotomics. While the genome of a cell is constant, the proteome of cell varies depending on many factors. That is to say not only proteins are translated from mRNA and therefore the proteome of a cell differs from that of another in the same species or individual, even though the genome is always constant. Even the amount of mRNA does not correlate with the level of protein in a single cell.
Post translational modification is not constant. Proteins differ in their posttranslational modifications and these modifications are not always the same; they vary and therefore allow very many types of chemical modifications of the protein.
Phosphorylation is one of the commonest post-translational modifications in proteins. It is caused by various protein kinases in the body, most especially the ones that attach phosphate to amino acids such as serine and threonine and sometimes tyrosine, called serine kinase, threonine kinase and tyrosine kinase respectively.
Another type of chemical modification after translation is ubiquitination performed by E3 ubiquitin ligases, which attach a small molecule ubiquitin to protein after translation.
Proteins are now identified as biomakers for certain diseases. They can be used as diagnostic tools in the future for many diseases. The FDA defines a biomarker as Ďa characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic interventioní.
Techniques like western blot, immunohistochemical staining and ELISA (enzyme linked immunosorbent assay and mass spectrometry can be used to identify these biomakers and make diagnoses of diseases. Also computational methods are becoming increasingly popular for studying biomakers.
Studying post translational modifications
Proteins that have been post translationally modified can be studied and identified by various methods
Antibody method: Antibodies can be raised against postranslational proteins. Phosphospecific antibodies can be raised to detect tyrosine phosphorylated proteins. Lectins can identify glycosylated proteins.
Two dimensional electrophoresis
This can be used to identify posttranslational proteins. It exaggerates differences between modified and unmodified proteins in mixture.
This method is relatively new. It combines SDS-polyacrilamide gel electrophoresis with shotgun proteomics, to determine posttranslational modifications.
Other methods of studying proteins in proteomics include ELISA, MALDI (matrix-assisted laser desorption/ionization and electrospray ionization).
Protein kinases and rDNA pharmaceutical products
An example of rDNA products in biology would be protein kinases which exist in 60 different rDNA products
A protein kinase modifies other protein by adding phosphate groups through phosphorylation which changes target protein by altering enzyme activity, association with other proteins and even cellular location. They affect signal transduction and have up to 500 protein kinase genes.
The human protein kinase family can be divided into classes as follows
∑ Serine/threonine-specific protein kinases
∑ Tyrosine-specific protein kinases
∑ Receptor tyrosine kinases
∑ Receptor-associated tyrosine kinases
∑ Histidine-specific protein kinases
∑ Mixed kinases
Strategies for rDNA pharmaceutical products through exploitation of genome/proteome information
Modern rDNA pharmaceuticals recognize the production of these premier rDNA drugs
∑ Factor VIII for treatment of hemophilia
∑ Insulin for treatment of insulin dependent diabetes mellitus
∑ Tissue plasminogen activator (activase- a clot dissolving agent)
Interferons are known to
∑ Decrease symptoms of hepatitis
∑ Decrease spread of herpes zoster
∑ Shrink certain tumours
o α-IFN (α-interferon) for the treatment of certain leuakemias, Kaposiís sarcoma, malignant melanoma, multiple myeloma and some kidney cancers.
o β-IFN-1b- multiple sclerosis
o Epogen for the stimulation of red cell production
o Neupogen for stimulation of white cells
o Interleukin 2- which is a T cell growth factor
o Monoclonal antibodies against cell-surface tumour antigens can be used for diagnosis and immunotherapy.
o Monoclonal antibodies can be conjugated to toxins or radioactive isotypes to kill tumour cells. They are then called immunotoxins.
o Monoclonal antibodies- human for immunotherapy of cancer
o Colony stimulating factors