Protein Interaction (domain domain interaction)

Bioinformatics in Biosophy

Park, Jong Hwa

MRC-DUNN Hills Road Cambridge

CB2 2XYEngland

1

Next:02/06/2001

What is protein interaction?

http://www.biochem.ucl.ac.uk/bsm/PP/server/

Any direct and indirect interaction between proteins.Infinite kinds of interaction.We are interested in structural interactions usually.

Analytical Ultracentrifuge Titration Calorimetry Optical Biosensors

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

Fusion of domains1. Certain protein domains occur

intermolecularly in one genome. The same domains occur intra-molecularly in some other genomes. Fusion detectable at sequence level.

2. It is supposed that enzymes are more likely to have fusion events.

3. It is difficult to detect fusion if there is an intermediate domain between any 2 domains.

How many possible fusion events?

Protein Structural Domain Interaction

PSIMAP:

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

Literature contains very big amount of interaction info.

If a protein name A occurs with protein name B, it is likely thatThere is some kind of relationship between them. Hopefully an interaction.

Natural language parsing.Grammar

http://www.binddb.org/

• Mass spec.– One of the surest technologies to detect protein

interaction.– Especially for complexes.– Quantification is possible.– The sensitivity is limited.

Experimental Technology

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

2d gel

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

SPR: kRU Concentration for different proteins

Very large scale protein interaction detection

Peptide level interaction detection is now automated.

Protein Chip

Ciphergen• System OverviewThe 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.

• Yeast 2 hybrid system

The two-hybrid system and other similar genetic screens in yeast involve the use of two different plasmids in a single yeast cell.

1. One plasmid often contains a cloned gene or DNA sequence

2. while the other plasmid contains a library of genomic or cDNA.

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