5Proteomics to studygenes and genomescompiler: Yashgin Hassanzadeh
Introduction oLarge-scale DNA sequencing has transformed biomedicalresearch in a short span of time. With the discovery of mosthuman genes, it is now apparent that a ‘factory approach’to address biological problems is desirable if we are to gaina comprehensive understanding of complex biologicalprocesses. In this seminar we will review how proteomics issimilarly making a crucial contribution to our understandingof biology and medicine through the global analysis of geneproducts.
Defining proteomicsLarge-scale study of proteins, usually by biochemical methods.It is dates back to the late 1970s.In 1990s, biological mass spectrometry emerged as a powerfulanalytical method that removed most of the limitation ofprotein analysis.Today, the term proteomics covers much of the functionalanalysis of gene products, including large-scale identification orlocalization studies of proteins.
Why is proteomics necessary?With the accumulation of vast amounts of DNA sequences in databases,researchers are realizing that merely having complete sequences of genomesis not sufficient to elucidate biological function.There is no strict linear relationship between genes and the proteincomplement. ORF in genomic data does not necessarily imply the existenceof a functional gene so it is still difficult to predict genes accurately fromgenomic data.Modification of proteins such as isoforms and post-translationalmodifications, can be determined only by proteomic methodologies. Thelocalization of gene products, which is difficult to predict from the sequence,can be determined experimentally and so on.
Identification and analysis of proteinsProtein preparation methodsMass spectrometric identification of proteinsPost –translational modifications
Figure 1. A strategy for mass spectrometric identification of proteins and post-translational modification.(Akhilesh Pandey and Matthias Mann)
Differential-display proteomicsThe two-dimensional gel approachProtein chips Figure 2. A schematic showing the two- dimensio nal gel approach. (Akhilesh Pandey and Matthias Mann)
Figure 3. A schematic showinguse of arrays for proteomicsanalysis.
Protein-protein interactionsPurification of protein complexesYeast two-hybrid system Figure 4. A schematic strategy to isolate interacting proteins.
Questions• What is mass spectrometry method?• Why we use peptides instead of proteins in MALDI?• Why we use SDS-page in second steps of electrophoresis?• What is the name of staining method for electrophoresis gel?• Why we should study proteomics?
ReferencePandey, A. ,Mann, M. (2000). Proteomics to study genesand genomes. Nature 405: 837-846. Thank you