Functional proteomics, methods and tools

INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION

1. FUNCTIONAL PROTEOMICS By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )

2. SYNOPSIS INTRODUCTION HISTORY DEFINITION PROTEOMICS FUNCTIONAL PROTEOMICS PROTEOMICS SOFTWARE PROTEOMICS ANALYSIS TOOLS FOR PROTEOM ANALYSIS DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS APLLICATIONS LIMITATIONS CONCLUSION

3. INTRODUCTION Proteome is a relatively new term that defines the complete set of proteins expressed during a cell’s entire lifetime. In a narrower sense, it also describes the set of proteins expressed in a cell at a given time. Proteomics is the study of proteins that are generated from the genetic code of an organism.

4. HISTORY Marc Wilkins coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy.

5. DEFINITION PROTEOMICS Protein Expression comparison Structural Proteomics Functional Proteomics

6. DEFINITION FUNCTIONAL PROTEOMICS The core of Functional Proteomics is the study of direct interactions on the molecular scale. So, either we detect interactions between; Pairs of proteins {Binary Interactions}, or Multiple proteins of a complex {Complex Interactions}

7. PROTEOMICS SOFTWARE Proteomics software provides scientists with the ability to conduct database searches of known protein sequences utilizing batch or real time processing.

8. PROTEOME ANALYSIS There are five main steps in proteome analysis: Sample collection, handling and storage. Separation of individual proteins by 2-D polyacrylamide gel electrophoresis (2-D PAGE). Identification by mass spectrometry or N-terminal sequencing of individual proteins recovered from the gel. Protein characterization. Storage, manipulation, and comparison of data using bioinformatics.

9. TOOLS FOR PROTEOME ANALYSIS DNA microarray technology can be used to this because mRNA and protein concentrations are often correlated. It can measure even poorly expressed genes, ensuring a comprehensive assessment of which genes are expressed in which tissue Microarrays

10. MASS SPECTROMETRY APPROACH

11. PROTEIN-PROTEIN INTERACTIONS Protein-protein interactions are at the heart of most cellular processes, including carbohydrate and lipid metabolism, cell-cycle regulation, protein and nucleic acid metabolism, and cellular architecture.

12. 1.Domain fusion DIFFERENT METHODS FOR ANALYSIS OF FUNCTIONAL PROTEOMICS Based on the theory that protein domains are structurally and functionally independent units that can operate either as discrete polypeptides or as part of the same polypeptide chain.

13. 2. Conservation of gene position Genes of related function are often adjacent in the genome-especially in prokaryotic operons . Besides co-transcription regulation, this is also likely to be an effects of horizontal transfer-probability of co- transfer is higher for linked genes, so linkage of interacting proteins is useful if horizontal transfer rates are appreciable .

14. 3.Phylogenetic Profiling Method For instance, the conservation of 3 or 4 uncharacterized genes in 20 aerobic bacteria and their absence in 20 anaerobic bacteria might indicate that their products are required for aerobic metabolism .

15. 4.Affinity Based Biochemical Method In this, prot X is immobilized on a Sephadex matrix, and a complex mixture of proteins is passed through the column under controlled conditions.

16. 5.Immunoprecipitation The affinity-based isolation of interacting proteins can also be achieved in solution by techniques such as immunoprecipitation .

17. 6.Physical Methods Many methods of PI studies, exploits the principle of physics, like XRD and NMR. They generate data about the relative spacing of atoms, and high resolution models of proteins, protein complexes and proteins interacting with various ligands and cofactors.

18. Binding Domain Activation Domain Binding Domain Activation Domain Transcription factor Yeast Two-Hybrid Analysis

19. Binding Domain Activation Domain Binding Domain Prot1 Activation Domain Prot2 Yeast 2-hybrid system Binding Domain Activation Domain Transcription factor

20. Binding Domain Activation Domain Binding Domain Prot1 Activation Domain Prot2 Reporter Gene Promoter Region Binding Domain Prot1 Activation Domain Prot2 mRNA Yeast 2-hybrid system If Prot1 and Prot2 interact: Binding Domain Activation Domain Transcription factor

21. CONCLUSION Proteomics is extremely valuable for understanding biological processes and advancing the field of system biology.

22. REFERENCES Principles of Gene Manipulation and Genomics; by primrose & Twyman Bioinformatics : C.S.V. Murthy (first edition 2003) www.wikipedia.com