Proteomics; Just another name for biochemistry?

Dr Pamela Greenwell

Molecular and Medical Microbiology Research Group

School of Biosciences

University of Westminster

115, New Cavendish Street

London W1 W6UW.

Email: greenwp@wmin.ac.uk

The growth of the “omics”  technologies has many people imaging we are just giving “sexy” names for boring, old-fashioned technology. Who would dispute that genomics is just genetics and molecular biology, “glycomics” is the study of glycosylation or that “metabolomics “ is simply the study of  metabolic pathways? Surely then, proteomics is just biochemistry.  Indeed, I have told my students that we are studying proteomics as they turn off  at the mere mention of the word  biochemistry.  But is proteomics simply biochemistry?

The answer is a resounding NO!  Proteomics is a mixture of traditional biochemistry and the use of web based bioinformatics tools.  It enables us to understand and visualise protein structure, function, interaction and expression.  This is really the traditional biochemistry aspect. However, in addition, it gives us the opportunity, using bioinformatics, to predict the biochemical properties, structure and functions of proteins that have been derived from translation of the cloned nucleotides or PCR products.  Indeed, the output of most genome projects has been random gene sequences whose function and identity has been derived using bioinformatics tools.

So what can I do? If we go to Genome Japan (http://www.genome.ad.jp) and open BLAST (Basic Local Alignment Search Tool) . We can then take a small segment of DNA or protein sequence we have isolated and compare that to every one of the billions of known sequences lodged  in databases worldwide. The results are available within minutes! Analysis of homology with other proteins will then help us identify our protein. If we then go to the Expasy Proteomics Server (http://us.expasy.org/), simply by typing the name of the protein of interest we can access the TrEBML data set for the protein in which you can find links to the protein sequence, the nucleotide sequences with any known variants, function, subcellular location, tissue specificity, polymorphisms, disease associations, similarities to other proteins and, for some proteins their web site, for example www.albumin.org . Scrolling down reveals access to projected 2D PAGE analysis, 3D structures, domain structure, post-translational modifications, the protein sequence, every known variant  with references, the ability to calculate pI and mass and access to BLAST which allows you to compare this protein to every other protein known.

Now is the stage at which to point out that it isn’t always so simple. In some organisms, there are genes and proteins that have no significant homology to any other protein identified. For these, we can ask questions, via web based tools as to whether the sequence is likely to be membrane bound, does it have motifs like any other type of protein.  However, there are some proteins whose properties and functions will only be known when they are purified and assayed by traditional technology.  Nevertheless, you should go to the Expasy Server and see what is available,  I hope it will amaze you. Be warned, it is addictive and you can spend many happy hours at your computer rather than at the bench.

So, what else is available?  If you teach, the KEGG: Kyoto Encyclopedia of Genes and Genomes available at Genome Japan  gives links to the  KEGG protein network which in turn links to  metabolic pathways, regulatory pathways, molecular complexes, network-network relations, network-environment relations and diseases. The metabolic pathway pages alone are fascinating, allowing you to explore generic pathways and then the same pathway in your organism of choice, highlighting the differences. A visit to the Human Protein Reference Database (http://www.hprd.org/) will allow you, ultimately, to find information on every known human protein, protein localisation and tissue specific expression. A simple click will then take you to all the known information on that protein. This site is still collating information, but, even now it is an impressive resource.  Protein   microarray databases are now available at the European Bioinformatics Institute http://www.ebi.ac.uk/Databases/microarray.html and here you can visualise some of the many available microarray datasets. There are also pages with links to all the important databases, for example http://www.biol.rug.nl/mbp/ListDatabases.htm#PD. The internet also has allows access to on-line tutorials that will help you realise the potential of proteomics (see footnote)

Proteomics and bioinformatics are being used extensively by pharmaceutical  companies interested in drug targets and modelling potential protein-drug interaction. Microarray technology is proving to be a fast primary screen for drugs and ligands. In vaccinology, potential targets are being found using a combination of traditional biochemistry and proteomics.  Modelling studies are allowing refinements of drugs and ligands to improve binding characteristics.  Protein microarrays are also finding a place in the analysis of antibodies in a variety of context, for example in the understanding of antibody-antigen binding, analysis of antibody variants to determine and improve specificity and   in auto-immune disease for the identification of antigen targets.

In microbiology, comparative genome analysis (http://www.webact.org/)  allows us to visualise potential areas associated with pathogenicity by comparing pathogenic and non-pathogenic strains.

In the hunt for surrogate disease markers of cancer, a range of traditional biochemical techniques, such as chromatography and 2D PAGE  can allow us to determine whether the production  of individual  proteins are up or down regulated, whether some proteins are not expressed post mutation or whether there are  novel proteins associated                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Will proteomics replace “wet “ science. The answer must be no, as the databases are reliant on information produced by the traditional “wet” approach.  There are also drawbacks to predicting structure, pI and mass as if your protein is heavily glycosylated for example, the real values will not reflect those obtained for the simple polypeptide chain. However, proteomics will enhance “wet” science, providing rapid assessments, screening and novel technologies. In my opinion, now is the time to start exploring!

If you would like to run through tutorials, access references or attend courses or meetings on proteomics, information can be obtained by going to our proteomics tutorial website. http://www.mydocsonline.com/pub/greenwp/proteomics