1. Functional classification of IDPs Peter Tompa Institute of Enzymology Hungarian Academy of Sciences Budapest, Hungary

2. 1. Functional advantages 2. Functional classification (7 basic mechanisms) 3. Functional classification (28 partners-effects) 4. The relationship of schemes: extension of the GO system?

3. 1) Functional advantages of disorder

4. i) Entropic-chain functions

5. ii) Specificity without strong binding (reversibility, inducibility)

6. Gunasekaran (2004) JMB 341, 1327 Globular IDP iii) Large binding surfaces in complexes (specificity, multiple partners)

7. iv) Fast binding - first observed in DNA renaturation - hnRNAP A1 no protein Pontius (1990) PNAS 87, 8403

8. ”Fly-casting” model Shoemaker B. A, (2000) PNAS 8868-8873 Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

9. ”Protein fishing” model clathrin AP180

10. v) Binding promiscuity (one-to-many signaling, moonlighting)

11. Protein One (inhibitory) function Another (activatory) function Disord er IUPre d (%) PONDR ® (%) calpastatininhibition of calpainactivation of calpain * 10080.1 CFTR (R domain) inhibition of CFTRactivation of CFTR * 40.853.7 DHPR (peptide C) inhibition of RyRactivation of of RyR * 10081.1 EBV SM down-regulation of intron-containing mRNA up-regulation of intron-less mRNA 44.144.4 MDM2 (180-298) down-regulation of p21 Cip1 activation of estrogen receptor  70.0 p21 Cip1 /p27 Kip1 inhibition of Cdkactivation of Cdk * 48.261.0 PIAS1 (392-541) inhibition of activated STAT activation of p5341.340.7 PPI-2inhibition of PP1activation of PP1 * 91.777.8 ribosomal L5 inhibition of MDM2 ubiquitin ligase activation/chaperoning of ribosome * 22.330.8 securin inhibition of separase activation/chaperoning of separase * 52.054.2 thymosin-  (WH2 domain) sequestration of G- actin activation of actin polymerization, ILK kinase * 10064.3 IUPs with multiple talents: moonlighting

12. vi) Flexibility in the assembly of complexes

13. Disorder correlates with complex size Hegyi et al. (2007) BMC Struct. Biol. 7, 65 single 11-100 2-4 5-10

14. 2) Functional classification: 7 basic mechanisms 7 basic mechanisms

15. Tompa (2005) FEBS Lett. 579, 3346 Six basic mechanisms of IDPs

16. IDP I: entropic chains IDP I: entropic chains

17. cytoskeleton MTs Tubulin dimers protein 2 Microtubule-associated protein 2

18. MAP projection domain: entropic bristle Mukhopadhyay (2001) FEBS Lett. 505, 374

19. Spacing of MTs in dendrites and axons

20. V-dependent K + -channel: entropic clock

21. Titin: an entropic spring (like a piece of rubber)

22. PEVPPVRVPEVPKEVV PEKKVPAAPPKKPEVT PVKVPEAPKEVVPEKK

23. Titin PEVK domain: entropic spring

24. IDPs II: effectors IDPs II: effectors

25. FlgM: inhibitor of sigma28 transcription factor Plaxco and Gross (1997) Nature, 386, 657

26. p27: another effector, inhibitor of Cdk2

27. IDPs III: scavengers

28. Casein: rapid and high-capacity binding of Ca 3 (PO 4 ) 2 Ca 2+ + PO 4 3- Ca 3 (PO 4 ) 2

29. Salivary PRPs: high-capacity binding of tannins MLLILLSVALLALSSAQNLNEDVSQEESPSLIAGNPQGPSP QGGNKPQGPPPPPGKPQGPPPQGGNKPQGPPPPGKPQGPPP QGDKSRSPRSPPGKPQGPPPQGGNQPQGPPPPPGKPQGPPP QGGNKPQGPPPPGKPQGPPPQGDKSQSPRSPPGKPQGPPPQ GGNQPQGPPPPPGKPQGPPPQGGNKPQGPPPPGKPQGPPPQ GDKSQSPRSPPGKPQGPPPQGGNQPQGPPPPPGKPQGPPQQ GGNRPQGPPPPGKPQGPPPQGDKSRSPQSPPGKPQGPPPQG GNQPQGPPPPPGKPQGPPPQGGNKPQGPPPPGKPQGPPAQG GSKSQSARAPPGKPQGPPQQEGNNPQGPPPPAGGNPQQPQA PPAGQPQGPPRPPQGGRPSRPPQ Baxter (1997) Biochemistry 36, 5566

30. IDPs IV: assemblers 45

31. p27 Kip1 IA 3 FnBP Tcf3 CycA Cdk2 fibronectin  -catenin Asp prot. Fibronectin binding protein

32. High-affinity binding to fibronectin, tethering bacteria to host Schwarz-Linek (2004) JBC 279, 39017

33. IDPs V: display sites

34. CREB KID phosphorylation induces binding to CBP KIX domain Radhakrishnan (1997) Cell 91, 741 CREB KID Ser 133 PKA

35. cAMP-response element binding protein (CREB) activation

36. The ELM server http://elm.eu.org/

37. ELMs and local disorder Fuxreiter et al (2006) Bioinformatics, 23, 950

38. IDPs VI: chaperones

39. Prediction: very high level of disorder in chaperones regulatory signaling RNA chaperones protein chaperones

40. Disorder is involved in chaperone function

41. Tompa and Csermely (2004) Faseb J., 18, 1170-1175 The entropy-transfer model of disordered chaperones binding S transfer misfolded folded IUP

42. IDPs VII: prions

43. Patholopgical prion: structure of PrP C (PHGGGWGQ) 5 A 127 GAAA*AGAVVGGLGG 133 GPI * * * * * * * * * P107L * P102L Amyloid: mad-cow disease

44. Physiological prion: Sup35p, eukaryotic translation release factor3 MSNPQDQLSNDLANASISGDQSKQPQQQQPQQQQPY FNPNQAQAFVPTGGYQQFQPQQQQQYGGYQQNYTQY QAGGYQQNYNNRGGYQQNYNNRGGYQQNYNNRGGYQ QQQQQQYQAYNPNQQYGGYQAYNPQQQQQQQTQSQG MSLADFQKQKAEQQASLNKPAVKKTLKLASSSGIKL ANATKKVDTAKPAASKEASPAPKDEEASAEPEAKKE STPVPASSSPAPAAADSTPAPVKKESTPTPSVASKS APVSASASVVTADALAKEQEDEVDEEVVKDMFGGKD HVSIIFMGHVDA........

45. Prion form of Sup35: translation read-through

47. 3) Functional classification: 28 partners-effects 28 partners-effects

48. Functional classification of IDPs, Dunker 2002 protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown

49. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone Functional classification of IDPs, Dunker 2002

50. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain Functional classification of IDPs, Dunker 2002

51. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain prion Functional classification of IDPs, Dunker 2002

52. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain prion scavenger Functional classification of IDPs, Dunker 2002

53. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain prion scavenger display site Functional classification of IDPs, Dunker 2002

54. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain prion scavenger display site chaperone ? effector ? Functional classification of IDPs, Dunker 2002

55. protein-protein binding protein-DNA binding protein-rRNA binding protein-tRNA binding protein-mRNA binding protein-genomic RNA binding protein-lipid interaction flexible linkers/spacers entropic spring entropic bristle entropic clock structural mortar protein detergent self-transport through channel polymerization substrate/ligand binding cofactor/heme binding metal binding acetylation fatty acylation (myristoyl/palmitoyl) glycosylation methylation phosphorylation ADP-ribosylation DNA unwinding DNA bending reg. of proteolysis in vivo autoregulatory not essential/unknown assembler effector chaperone entropic chain prion scavenger display site effector chaperone ? effector ? Functional classification of IDPs, Dunker 2002

56. 4) Extension of the GO scheme ?

57. The Gene Ontology (GO) scheme Three ontologies mol. function biol. process cellular component MAP2