Functional Linkage:

1. Interacting subunits in molecular complexes

2. Signal Transduction or Metabolic pathway members

Computational Methods for Identification of Functional linkages:

1. Corrrelated Evolution (Phylogenetic profile)

Work on the assumption that proteins that travel across species together, work together

2. Gene Neighbor Analysis

3. Gene Cluster Analysis

4. Text Links

5.  Correlated Messenger RNA Expression Patterns

6.  Patterns of Domain Fusion

reviewed in: Galperin & Koonin: Who's your neighbor? New computational approaches for functional genomics.
Nat Biotechnol. 2000 Jun;18(6):609-13. [Link]

Rosetta Stone sequences - some pairs of interacting proteins have homologs in another organism fused into a single protein chain.
Frequent: 7000 in E.Coli, 19,100 in C. Elegans , 45,502  in yeast.

E.Coli gyrases A & B both in S. Cerevisiae Topoisomerase II

Purine biosynthesis proteins in RS sequences with others

Carbamoylphosphate synthase B (carB) has undergone 2 fission events

More fusion events have occured than fission. More fission in thermophiles

FusionDB: database of Rosetta Stones

Nit-Fhit protein example

Application of above methods to identification of proteins in S. Cerevisiae, H. Sapiens
 

Example 1: Yeast ORF YGR021W - member of protein family of unknown function

Application of above methods:

28 links to other yeast proteins - 18 predicted to target mitochondria, also:

YGL236C -member of gidA family - unknown function

YOLO60C - homology to C. Elegans M02F4.4 family

1 link to human TP1 triose phosphate isomerase - human deficiency causes grossly-altered mitochondrial structure

These findings indicate YGR021W family involved in mitochondrial protein synthesis

Example 2: yeast prion Sup35

- normal function translation release factor, interacts with ribosome to release new peptide chain

Links to protein sorting & targeting proteins - consistent with accessory role in guiding nascent proteins to final destinations. Also correlated evolution & correlated mRNA expression with a yeast chaperonin system - aids folding of new proteins.

above analysis suggests links to many proteins involved in protein synthesis

Example 3:  MHS6: DNA mismatch repair system. Mutation associated with most human heredtary nonpolyposis colorectal cancers.

Links to:

sequence - unrelated PMS1 DNA mismatch repair protein family - mutations in human colorectal cancer

purine biosynthetic pathway

2 RNA modification enzymes

uncharacterized protein family - related to DNA repair?

Example 4:  Application to tuberculosis: 6 drugs in use, how to find others?

                                                                        filter
TB genome: 3924 proteins --------> 100,000 links ------> 12 reduced side - effect targets

- 2 known drug targets

- 10 good new targets?

- known penicillin targets
 

Post - genomic view of protein function is therefore definition not by individual activity
 
 

but by context of interactions:

References:
 

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. and Yeates, T. O. Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles,. PNAS 96:4285-4288 1999

Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D A combined algorithm for genome-wide prediction of protein function. Nature 1999 Nov 4;402(6757):83-6

Detecting Protein Function and Protein-Protein Interactions from Genome Sequences, by Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T., & Eisenberg, D.  Science (1999) 285:751-753

Gene fusion/fission method also reported for E.Coli, M. Jannaschii and H. Influenzae in:

Enright AJ, Illiopoulos I, Kyrpides NC and Ouzounis A Protein interaction maps for complete genomes based on gene fusion events
Nature 1999 Nov 4;402(6757):86-90

Schwikowski, B et al. A network of protein-protein interactions in yeast. Nature Biotech. (2000) 18: 1257-61.

 RESOURCES

Combined approaches:

Prolinks - a database of protein functional linkages derived from coevolution.

Predictome

EXAMPLE:

To what other proteins are the E.Coli K12 proteins mure and carB, and S. Cerevisiae proteins Sup35 and YER133W functionally linked?

What organisms have Rosetta Stone proteins encoding the above ?

PROTEIN-PROTEIN INTERACTIONS:

A. DATABASES

The Database of Interacting Proteins (DIP) - a database that documents experimentally determined protein-protein interactions.

PIMRider - Protein Interaction Database and Tools for H. Pylori, HCV and HIV

Reference: The protein-protein interaction map of H. Pylori. Rain et al. Nature 2001, 211-215

BIND - Database of Bimolecular Interactions

BRITE: Biomolecular Relations in Information Transmission and Expression

MINT - Molecular Interactions

Associative Database of Protein Sequences (ADOPS) and other programs

Eragen - commercial database & software for protein sequences, domains, phylogenies etc
 

EXAMPLE:

What proteins do the human Heat Shock Protein 90 alpha and the aryl hydrocarbon receptor Ahr complex with?

Lecture and Resources - Amit Singh in Stanford Course Biochem 218:  http://cmgm.stanford.edu/biochem218/Dock.html

Protein Interactions - Lectures at Chemistry Department, University of Cambridge, 2003. includes link to above

Introduction to Structural Bioinformatics Course

MinimotifMiner:  analyzes protein queries for the presence of short functional motifs that, in at least one protein, has been demonstrated to be involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules, or proteins trafficking.

Compendium of Docking sites

AutoDock Web site- examples and movies

Dock Web site

Accelerys Insight

FlexX(Tripos)
 

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