1. Quantitative analysis of domain interactomes Jason Lee Capstone presentation Sp `07

2. Protein domain Domain architecture of proteins A protein with three domains Protein PKC Each domain carries out certain function Modular nature confers protein a capability to compose domains to effect desired functions

3. Domain interaction Ex) Pkinase domain Different interfaces mediating domain- domain interaction –distinct ways of interaction Possible units of interaction (a) pdb_1ung: cell division kinase 5 and CDK5 activator

4. Domain interaction (cont’d) (b) pdb_1buh: CDK2 and CKSHS1 (c) pdb_1b6c: TGF-beta receptor R4 and FK506 binding protein

5. Purpose and pertinence of current study Characterize domain interactions Characterize protein interactions that are mediated by domain interaction Use domain interaction information to predict protein interactions Gain evolutionary perspective

6. Data and methods Databases: ipfam, BIND BIND: a compilation of known protein interactions Ipfam: known domain interactions obtained from structural information Five species were examined: human, mouse, fruit fly, yeast and E. coli 49043 protein interactions among 26313 proteins Take intersection between ipfam and BIND: compile protein interactions that involve known ipfam pair HumanMouseFruit flyYeastE. ColiTotal proteins7915364377644885210626313 interaction115504029218729870172249043

7. Example Protein TGFBR1 interacts with 132 other proteins according to BIND Domains activin_recp and pkinase comprise TGFBR1 Each BIND interaction is checked to see if it involves any of ipfam DDI pairs 44 protein interactions are found to have ipfam pair TGFBR1+GI13786127 – Pkinase+PBD TGFBR1+GI4503725 - Pkinase+FKBP_C TGFBR1+GI4507465 - Activin_recp+TGF_beta …

8. Obtained domain interactions 1884 domain-domain interactions among 1587 domains HumanMouseFruit flyYeastE. Coli Domains469212159328419 Interaction586251160394493

9. Low coverage of DDI over PPI 1650 PPI in human involve known domain pairs, while 9900 did not 14.29% of total human protein interactions From 5 species, 4604 PPI’s involve at least one domain pair, while 44439 did not have any 9.39% of total interactions HumanMouseFruit flyYeastE. coliTotal Ipfam intrn.165086640767610054604 Non-ipfam intrn. 9900316321465919471744439 %14.2921.491.866.8558.369.39 Total intrn.115504029218729870172249043

10. Possible explanations of low coverage of DDI High FP rate in PPI data Incomplete coverage of ipfam DDI data Many PPI’s are not mediated by DDI Possible expedience of protein interactions –Domain interaction may be too restricting to answer all physiological and molecular demands from organisms

11. Domain interaction graph (H. sapiens) Entire domain interactome

12. Protein interaction graph (H. sapiens) Many subgraphs, only the largest subgraph is shown

13. Comparison of node degree distribution Both show power-law distribution

14. Comparison of graph topologies Both domain and protein interaction graphs show scale- free property Domains on average interacts with half the number of partners a protein interacts with PPIDDI Subgraphs3853261 Avg. node degree3.29701.7655 Avg. node degree (excl. single partner nodes) 5.4756 2.6934 Largest subgraph5422 (68.50)71 (15.14) Nodes7915469

15. Phylogenetic tree of five species Human a Mouse E. coli Fruit fly Yeast Mammal Multi-cellularEukaryotes Prokaryote single-cell

16. Measuring commonality of domain composition and interactomes between species Inner product of domains and domain pairs between two species S and T IP_domain =|Common_domains| / sqrt (|Domains_S| * |Domains_T|) IP_pair = |Common_domain_pairs| / sqrt (|Domains_pairs_S| *|Domains_pairs_T|)

17. Evolutionary consideration Common domains Common domain pairs HumanMouseFruit flyYeastE. coli Human10052.46544.85340.43424.083 Mouse52.46510046.58530.22112.371 Fruit fly44.85346.58510040.53513.887 Yeast40.43430.22140.53510028.785 E. Coli24.08312.37113.88728.785100 HumanMouseFruit flyYeastE. coli Human10049.54138.53735.17121.954 Mouse49.54110042.41526.3939.950 Fruit fly38.53742.41510031.86311.750 Yeast35.17126.39331.86310024.278 E. Coli21.9549.95011.75024.278100 Common domains and domain pairs reflect evolutionary relationship

18. Ontological characterization Use GO controlled vocabulary and compare physiological reflection of domain compositions of species Correlation between physiology and domain composition Differential domains – domains that are present exclusively in one lineage or species and not in the other Multi-cellularsingle-cell Response to stimulus 103 Cell communication105 Regulation of cellular process 84 Signal transducer113 Enzyme regulator92 transport1729

19. Ontological characterization (cont’d) Categories of other differential domains unique to multicellular species –Cell adhesion (2) –Regulation of biological processes (2) –Cell differentiation (1) –Cell death (1) –Cell homeostasis (1) –Coagulation (1) Domains involved in multi-cellularity are conspicuous

20. Domain node degree and DomainDegreeInstances (copy number) Occur. in intrn. (interaction frequency) Associativity RAS172572412 Pkinase1396459245 RNA_pol_RPB1_ 5 891425 Ubiquitin8894215 RNA_pol_RPB2_ 6 75117 Trypsin7167736 AAA71436512 RNA_pol_L611152 GTP_EFTU655326 SNARE641523 Ten domains with largest degrees

21. Correlation among node degree, copy number, etc. (all five species) Correlation between DDI node degree and interaction frequency: 0.3399 Correlation between DDI node degree and number of instances: 0.2093 When RNA polymerase domains are excluded –Degree and interaction frequency: 0.3753 –Degree and number of instances: 0.2380 Associativity: number of domains a domain appears together in peptide sequences –Ex) domain pkinase associates with 45 domains Node degree and associativity: 0.1179 Having a large number of domain partners does not mean a domain mediates many protein interactions nor it is associated with many other domains

22. Interaction propensity Between a pair of domains Only hetero-domain pairs are considered due to possible crystallization artifacts of homo-domain pairs Interaction propensity = |pair_occurrences| / ( |domain_0| * |domain_1| ) Domain0Domain1Pairs| Domain_0 || Domain_1|i-prop (%) Cyclin_NPkinase65314420.4743 AnkPkinase24814420.0670 PHRas191241150.1332 Cyclin_CPkinase16194420.1905 FGFIG13172200.3476 ANKTIG1381240.6687 ANKRHD1381170.9441 SH2STAT_bind11156170.4148 Sufficient selectivity can be encoded at the molecular level onto domain interaction Protein interactions mediated by domain interactions are very specific

23. Discussion A domain on average has a smaller number of interaction partners than proteins Only small number of protein interactions are mediated by domain interactions Domain composition and domain interactomes reflect evolutionary relationship between species Correlation among domain node degree, domain copy number, occurrences in interaction and number of associated domains were all very low Domain interaction is a scaffold and specificity is tuned up by atomic and residue level coding

24. Acknowledgement Prof. Sun Kim Prof. Haixu Tang Prof. Predrag Radivojac Prof. Mehmet Dalkilic Dr. John Colburne Prof. Marty Siegel Linda Hostetter