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Proteomics to study genes and genomes

compiler: Yashgin Hassanzadeh

oIntroduction

Large-scale DNA sequencing has transformed biomedical research in a short span of time. With the discovery of most human genes, it is now apparent that a ‘factory approach’ to address biological problems is desirable if we are to gain a comprehensive understanding of complex biological processes. In this seminar we will review how proteomics is similarly making a crucial contribution to our understanding of biology and medicine through the global analysis of gene products.

Defining proteomics

Large-scale study of proteins, usually by biochemical methods.It is dates back to the late 1970s.

In 1990s, biological mass spectrometry emerged as a powerful analytical method that removed most of the limitation of protein analysis.

Today, the term proteomics covers much of the functional analysis of gene products, including large-scale identification or localization 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 genomes is not sufficient to elucidate biological function.

There is no strict linear relationship between genes and the protein complement. ORF in genomic data does not necessarily imply the existence of a functional gene so it is still difficult to predict genes accurately from genomic data.

Modification of proteins such as isoforms and post-translational modifications, can be determined only by proteomic methodologies. The localization of gene products, which is difficult to predict from the sequence, can be determined experimentally and so on.

Identification and analysis of proteins

Protein preparation methods

Mass spectrometric identification of proteins

Post –translational modifications

Figure 1. A strategy for mass spectrometric identification of proteins and post-translational modification.(Akhilesh Pandey and Matthias Mann)

Differential-display proteomics

The two-dimensional gel approach

Protein chips

Figure 2. A schematic showing the two-dimensional gel approach.

(AkhileshPandey and Matthias Mann)

Figure 3. A schematic showing use of arrays for proteomics analysis.

Protein-protein interactions

Purification of protein complexes

Yeast two-hybrid system

Figure 4. A schematic strategy to isolate interacting proteins.

Figure 5. The yeast two-hybrid system.

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?

Reference

Pandey, A. ,Mann, M. (2000). Proteomics to study genes

and genomes. Nature 405: 837-846.

Thank you