Progress in analyzing protein-protein interactions Chia Jer-ming Prasanna R Kolatkar LinKui(BNU)

1. Progress in analyzing protein-protein interactions Chia Jer-ming Prasanna R Kolatkar LinKui(BNU)

2. Paaventhan Palasingam Jeremiah S Joseph Structure guys

3. Protein Functional Dbase Protein Interactions “Rosetta Stone” Text Information/Dbase MS/yeast two-hybrid

6. Protein-Protein Interaction Database (PPiDB v 1.0)

7. Protein-Protein Interaction Queries •    Query Interactions • by Species • by Protein • by Text Search engine.

8. [ P | [ V ] PROTEIN KINASE 1 [ PKGA ] <- P34101Also called EC 2.7.1.-, FRAGMENT.From Dictyostelium discoideum.Interacting domain: Eukaryotic protein kinase domain.

9. Information of Eukaryotic protein kinase domain • DB links: | Pfam | PubMed | Swissprot | PDB | Genbank | DIP | • Interacting with [ 55 ] domains: • Actin • Adenylate and Guanylate cyclase catalytic domain • Ank repeat • BTK motif • C2 domain • CNH domain • Cadherin domain • Cyclic nucleotide-binding domain • Death domain • DnaJ domain • Double-stranded RNA binding motif • EF hand • EGF-like domain • F5/8 type C domain • FHA domain • Fes/CIP4 homology domain • Fibronectin type III domain • Furin-like cysteine rich region • GAF domain • Guanylate kinase • Hr1 repeat motif • IPT/TIG domain • IQ calmodulin-binding motif • Immunoglobulin domain • LIM domain containing proteins • Lectin (probable mannose binding) • Leucine Rich Repeat • Leucine rich repeat C-terminal domain • Leucine rich repeat N-terminal domain • Myosin head (motor domain) • Octicosapeptide repeat • P21-Rho-binding domain • PAS domain • PDZ domain (Also known as DHR or GLGF). • PH domain • POLO box duplicated region. • PQQ enzyme repeat • Phorbol esters/diacylglycerol binding domain (C1 domain) • Phytochrome region • Plexin repeat • Raf-like Ras-binding domain • Receptor L domain • Receptor family ligand binding region • Regulator of G protein signaling domain • Response regulator receiver domain • SAM domain (Sterile alpha motif) • SH3 domain • SPRY domain • Sema domain • Src homology domain 2 • TNFR/NGFR cysteine-rich region • UBA domain • WD domain, G-beta repeat • Zinc finger, C3HC4 type (RING finger) • Zn-finger in ubiquitin-hydrolases and other proteins

10. Interacting domains: Eukaryotic protein kinase domain <=> Death domain • Shared proteins: • death-associated protein kinase 1, alsoEC 2.7.1.-, DAP KINASE 1, fromHomo sapiens • probable serine/threonine protein kinase pelle, alsoEC 2.7.1.37, fromDrosophila melanogaster • serine/threonine protein kinase rip, alsoEC 2.7.1.-, CELL DEATH PROTEIN RIP, RECEPTOR INTERACTING PROTEIN, fromMus musculus • serine/threonine protein kinase rip, alsoEC 2.7.1.-, CELL DEATH PROTEIN RIP, RECEPTOR INTERACTING PROTEIN, fromHomo sapiens • Protein pairs: • Species: Bovine - Bos taurus • activin receptor type i precursor <=> fasl receptor precursor • activin receptor type ii precursor <=> fasl receptor precursor • angiopoietin 1 receptor precursor <=> fasl receptor precursor

11. [ P | [ V ] PROTEIN KINASE 1 [ PKGA ] <- P34101Also called EC 2.7.1.-, FRAGMENT.From Dictyostelium discoideum.Interacting domain: Eukaryotic protein kinase domain.

13.   Interactions: • P34101[protein kinase 1] • <=> Q02158[1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase] • <=> P05987[camp-dependent protein kinase regulatory chain] • <=> P08796[contact site a protein precursor] • <=> P34125[myosin heavy chain kinase] • <=> P42527[myosin heavy chain kinase a] • <=> P90648[myosin heavy chain kinase b] • <=> P22467[myosin ia heavy chain] • <=> P34092[myosin ib heavy chain] • <=> P42522[myosin ic heavy chain] • <=> P34109[myosin id heavy chain] • <=> Q03479[myosin ie heavy chain] • <=> P54695[myosin if heavy chain] • <=> P54696[myosin ih heavy chain] • <=> P08799[myosin ii heavy chain, non muscle] • <=> P54697[myosin ij heavy chain] • <=> P13833[myosin regulatory light chain] •   Interactions: • P34101[protein kinase 1] • <=> Q02158[1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase] • <=> P05987[camp-dependent protein kinase regulatory chain] • <=> P08796[contact site a protein precursor] • <=> P34125[myosin heavy chain kinase] • <=> P42527[myosin heavy chain kinase a] • <=> P90648[myosin heavy chain kinase b] • <=> P22467[myosin ia heavy chain] • <=> P34092[myosin ib heavy chain] • <=> P42522[myosin ic heavy chain] • <=> P34109[myosin id heavy chain] • <=> Q03479[myosin ie heavy chain] • <=> P54695[myosin if heavy chain] • <=> P54696[myosin ih heavy chain] • <=> P08799[myosin ii heavy chain, non muscle] • <=> P54697[myosin ij heavy chain] • <=> P13833[myosin regulatory light chain] • Interactions • P34101[protein kinase 1] • <=> Q02158[1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase] • <=> P05987[camp-dependent protein kinase regulatory chain] • <=> P08796[contact site a protein precursor] • <=> P34125[myosin heavy chain kinase] • <=> P42527[myosin heavy chain kinase a] • <=> P90648[myosin heavy chain kinase b] • <=> P22467[myosin ia heavy chain] • <=> P34092[myosin ib heavy chain] • <=> P42522[myosin ic heavy chain] • <=> P34109[myosin id heavy chain] • <=> Q03479[myosin ie heavy chain] • <=> P54695[myosin if heavy chain] • <=> P54696[myosin ih heavy chain] • <=> P08799[myosin ii heavy chain, non muscle] • <=> P54697[myosin ij heavy chain] • <=> P13833[myosin regulatory light chain]

14. Scoring System Computational Identification [Weak] Same keywords [Moderate] Experimental evidence from DIP or elsewhere [Good] References in literature relating names of proteins [Good] More than 1+ support [Strong]

15. PPDB Current Status Putative Filtered 753508 350819

16. Christian von Mering*, Roland Krause†, Berend Snel*, Michael Cornell‡, Stephen G. Oliver‡, Stanley Fields§ & Peer Bork* NATURE |VOL 417 | 23 MAY 2002 |

17. Evolutionary Relationships Functional Relationships Putative Drug Targets

18. Current BIND Database Statistics DatabaseRecord Count Interaction Database 20000+ Biomolecular Pathway Database 8 Molecular Complex Database 851 Organisms represented 12 GI Database 4651 DI Database 0 Publication Database 428

19. BIND Interactions RAS-GTP active form of RAS bound to GTP RAF Y2H Homo sapiens

20. DIPDATABASE STATISTICS Number of proteins 6963 Number of organisms 113 Number of interactions 18059

21. Integrating high quality structural data Separating interaction categories Decreasing false positives Improving Quality

22. 3-D data from PDB (Thornton,Ofran and Rost) Inter-domain interactions distances and comparison between sequence separation Also do for inter-protein interactions Using 3-D data

23. Careful analysis of the structural data needed Transient,Permanent,homo-oligomers,hetero-oligomers ML could be highly useful with better categorization Better structural analysis

24. Sarah Teichman – domains separated by 30 residues are the ones that have interaction

25. Testing the rule: Need a good data set to test the rule

26. Structural Information important for detailed and mechanistic understanding Least populated data Highly useful when merged with lots of functional information X-ray crystallography

28. Pseudo H-type topology D E B A G F C C'

29. PFAM/PDB Single chain with multiple domains including complexes Only use non-redundant chains calculate distances between the domains

30. Criteria 6A Number of contacts you can choose Between domains If xtal contact omit

31. What did we see with the 1273 chains Teichman rule basically obeyed Exceptions Binding proteins SH3 proteins

33. PPDB can be used to predict a set of interacting proteins. Intersection with Y2H studies and other methods Help direct structural genomics of complexes and improve PPDB Applying PPDB

34. Great model to look at a large set of complexes Will be useful for looking at interactions in other systems Can be used to build a database of interacting motifs Thermatoga structural genomics

35. Crystallized several hundred and scores of structures Initial Yeast two hybrid data Large scale-up facilities Thermatoga current state

36. 15% overlap Improving Thermatoga Y2H vs PPDB

37. Stem Cell totipotency TFs Hep B TFs ER TFs TFs

38. Mass Spec MA Structure Other info Support

39. Careful genomic data analysis can greatly accelerate discovery (i.e regulatory networks) Genomic analysis

40. Pombe kinase What are the possible interactions?

44. Strong et al …Eisenberg Dec 15 NAR Functional linkage M. Tuberculosis Giot et al….Rothberg Dec 5 Science Drosophila Y2H Which way is right?