2. Proteomics
• The term ‘’Proteome’’ and ‘’Proteomics’’ is coined by Marc Wilkins and colleagues in early 1990s
• Proteomics has been developed from genomics
• Difference between studying a single protein and proteome
Protein chemistry Proteomics
Individual protein Complex mixture of proteins
Complete sequence analysis Partial sequence analysis
Emphasis on structure and function Emphasis on identification
Structural biology Systems biology
4. Sequence and structural proteomics
• Primary databases for nucleic acid sequence: GenBank, EMBL, DDBJ
• Protein databases: Swissprot, Uniprot
• Structural database: PDB
• String database for protein-protein interaction
5. Tools of Proteomics
• Principle of Proteomics analysis: relies on identification of peptides, a 6-amino acid peptide
maps to a single gene product
6. Tools of Proteomics
• Separating proteins before digestion:
• 1D Gel electrophoresis
• 2D Gel electrophoresis
• IEF
• The protein mixture is separated in fractions before digestion
1D Gel Electrophoresis
• 1D Gel electrophoresis separates proteins according to molecular weight
• Discontinuous gel electrophoresis system
• Polyacrylamide gel: extent of crosslinking varies 5-15%, lower degree of crosslinking allows
easier passage of large proteins
7.
8. Tools of Proteomics
2D Gel Electrophoresis
• 1D Gel electrophoresis separates proteins in two dimensions: isoelectric point and molecular
weight
• The protein in first loaded to immobilized pH gradient (IPG) strips for isoelectric focusing and
then run on SDS-PAGE
• The problem with 2D Gel electrophoresis is : 1. lack of reproducibility, 2. many hydrophobic
proteins are incompatible with IEF, 3. suitable for detecting highly abundant proteins
9.
10. Section of a 2D gel depicting “smearing” of protein
in the IEF (horizontal) direction
Section of a 2D gel depicting “spot trains” due to
differently modified/charged forms of the same protein
11. Reference books:
1. R.M. Twyman ; Principles of Proteomics, Bioscientific Publishers
2. Daniel C. Liebler, Introduction to Proteomics: Tools for the New Biology, Humana Press
3. T. A. Brown , Genomes 3, John Wiley & Sons
