Protein Interaction (domain domain interaction)

1. 1 Protein Interaction (domain domain interaction) Park, Jong Hwa MRC-DUNN Hills Road Cambridge CB2 2XY England Bioinformatics in Biosophy Next: 02/06/2001

2. Any direct and indirect interaction between proteins. Infinite kinds of interaction. We are interested in structural interactions usually. What is protein interaction? Optical Biosensors Titration Calorimetry Analytical Ultracentrifuge http://www.biochem.ucl.ac.uk/bsm/PP/server/

4. Detecting Interaction • Using pure sequence  Fusion • Using pure structure  PDB • Using literature  Text parsing • Using experimental technology • Mass spec • Yeast 2 hybrid system • Membrane 1 hybrid system (G protein alpha subunit) • Protein chip

5. Fusion of domains • Certain protein domains occur intermolecularly in one genome. The same domains occur intra-molecularly in some other genomes.  Fusion detectable at sequence level. • It is supposed that enzymes are more likely to have fusion events. • It is difficult to detect fusion if there is an intermediate domain between any 2 domains.

6. How many possible fusion events?

7. Protein Structural Domain Interaction

8. PSIMAP: Park, J., Lappe, M. & Teichmann, S.A. Mapping protein family interactions: intra- and intermolecular interaction repertoires. J. Mol. Biol. 307, 929-939 (2001).

9. Literature contains very big amount of interaction info. If a protein name A occurs with protein name B, it is likely that There is some kind of relationship between them. Hopefully an interaction. Natural language parsing. Grammar

17. http://www.binddb.org/

18. Experimental Technology • Mass spec. • One of the surest technologies to detect protein interaction. • Especially for complexes. • Quantification is possible. • The sensitivity is limited.

19. http://www-lecb.ncifcrf.gov/2dwgDB/

20. 2d gel

21. Biacore (surface plasmon resonance (SPR)-based pharmacoproteomics assay)

24. SPR: kRU  Concentration for different proteins

25. Protein Chip Very large scale protein interaction detection Peptide level interaction detection is now automated.

26. Ciphergen • System Overview The Ciphergen ProteinChip System (series PBS II) is comprised of a ProteinChip Reader integrated with ProteinChip Software and a PC to analyze proteins captured on Ciphergen’s ProteinChip Arrays. With state-of-the-art ion optic and laser optic technologies, the ProteinChip System detects proteins ranging from small peptides of less than 1000 Da up to proteins of 300 kilodaltons or more and calculates the mass based on time-of-flight. The ProteinChip Reader and PC fit easily into almost any lab space, allowing researchers direct assess to precision mass analysis of important biological samples.

28. Yeast 2 hybrid system

29. The two-hybrid system and other similar genetic screens in yeast involve the use of two different plasmids in a single yeast cell. • One plasmid often contains a cloned gene or DNA sequence • while the other plasmid contains a library of genomic or cDNA.

30. Protein-protein interactions detected by assaying colonies for beta-galactosidase activity: y2h