The document discusses functional proteomics, defined as the study of protein interactions and expression at various levels, initiated by the term 'proteome' coined by Marc Wilkins in 1994. It outlines key methodologies and tools used in proteome analysis, such as 2D polyacrylamide gel electrophoresis and mass spectrometry, alongside the applications and limitations of functional proteomics. The conclusion emphasizes its importance in understanding biological processes and enhancing system biology.

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
1. Protein Expression comparison
2. Structural Proteomics
3. 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:
1. Sample collection, handling and storage.
2. Separation of individual proteins by 2-D polyacrylamide gel
electrophoresis (2-D PAGE).
3. Identification by mass spectrometry or N-terminal sequencing of
individual proteins recovered from the gel.
4. Protein characterization.
5. 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. 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. APLLICATIONS
Protein-Protein
Interactions
Protein Post-
Translational
Modification
Protein
Expression
Studies
Protein
Localization
&
Compartment
alization
Protein
Function
Protein
identification

22. Lack of general
techniques for
absolute quatitation
of proteins
COMPLEXITY- some
proteins have > 1000
variants
Limited throughput of
todays proteomic
platforms
Need for a general
technology for
targeted manipulation
of gene expression
LIMITATIONS

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

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