1. Intrinsically disordered proteins: drug development and the most interesting examples Peter Tompa Institute of Enzymology Hungarian Academy of Sciences Budapest, Hungary

2. IDPs: in vitro evidence and in vivo considerations IDPs: in vitro evidence and in vivo considerations not RC, transient order not RC, transient order functional advantages (specificity without excessive binding strength, fast binding, one-to-many signaling) functional advantages (specificity without excessive binding strength, fast binding, one-to-many signaling) prevalent, frequency increases from prokaryotes to eukaryotes prevalent, frequency increases from prokaryotes to eukaryotes functional importance (regulatory, transcription, cytoskeletal) functional importance (regulatory, transcription, cytoskeletal) involvement in disease (cancer-associated, neurodegenerative) involvement in disease (cancer-associated, neurodegenerative) IUPs

3. 1)Involvement in disease and drug development 2)Most interesting examples

4. p53 tumor supressor Levine (1997) Cell 88, 323

5. Prediction of disorder: IUPred http://iupred.enzim.hu Dosztányi (2005) J. Mol. Biol. 347, 827 TADDBDTDRD AAPPVAPAPAAPTPAAPAPAP p53

6. p53 binding partners (MoRE, SLM) Oldfield et al. (2005) Biochemistry 44, 12454 MDM2 DNA S100B p53

7. p53 binding DNA

8. Breast cancer-associated BRCA1: intrinsic disorder Mark et al. (2005) JMB 345, 275

9. BRCA1: intrinsic disorder Mark et al. (2005) JMB 345, 275

11. PDB SwissProt signaling human cancer

13. New molecules approved by FDA

14. Partners of MoRFs: druggable targets

15. Inhibition of p53-MDM2 interaction by small-molecule antagonists Vassilev et al. (2004) Science 303, 844

16. In vivo activation of p53 by small- molecule antagonists of MDM2 Vassilev et al. (2004) Science 303, 844

17. PEVPPVRVPEVPKEVV PEKKVPAAPPKKPEVT PVKVPEAPKEVVPEKK

18. PEVK domain of titin: entropic spring

19. cytoskeleton MTs Tubulin dimers PKA R II MAP2: entropic bristle

20. Mukhopadhyay (2001) FEBS Lett 505, 374 MAP2: entropic bristle

21. “Dynamic” spacing of MTs in axons and dendrites

22. Ca 2+ + PO 4 3- Ca 3 (PO 4 ) 2 Casein: scavenger in milk

23. FlgM: disorder in vivo Plaxco and Gross (1997) Nature, 386, 657

24. FlgM: disorder in vivo

25. NMR secondary chemical shifts: transient ordering in FlgM Daughdrill et al. (2004) Biochemistry 37, 1082

26. FlgM-s 28 structure Sorensen et al. (2004) Mol. Cell 14, 127

27. Inhibition of Cdks in cell-cycle regulation

28. Structural ensemble of p27 KID (NMR, MD) Sivakolundu et al. (2005) JMB 353, 1118

29. Lacy et al. (2005) NSMB 11, 358 P27 KID binding: molecular staple mechanism

31. Sheaff et al. (2000) Mol. Cell. 5, 403 p21 turnover w/o ubiquitination

32. Proteasomal degradation requires unstructured initiation site Prakash et al. (2000) NSB 11, 830

33. Endoproteolytic activity of proteasome Liu et al. (2003) Science 299, 408

34. Mitosis

35. The securin story normal chromosome segregation Inhibition of separase expression Waizenegger (2002) Curr. Biol. 12, 1368

36. The securin story Jallepalli (2001) Cell 105, 445 - securin knockout -

37. Human full-length securin is IDP Sánchez-Puig et al. (2005) Prot. Sci. 14, 1410

38. Separase-securin complex by cryoEM Viadiu et al. (2005) NSMB 12, 552

39. Separase-securin complex reconstruction Viadiu et al. (2005) NSMB 12, 552

40. Entropic gating in nuclear pore Patel (2007) Cell 129, 83

41. ...SVFSFSQPGFSSVPAFGQPASSTPTSTSGSVFGAASSTSSSS SFSFGQSSPNTGGGLFGQSNAPAFGQSPGFGQGGSVFGGTSAATT TAATSGFSFCQASGFGSSNTGSVFGQAASTGGIVFGQQSSSSSGS VFGSGNTGRGGGFFSGLGGKPSQDAANKNPFSSASGGFGSTATSN TSNLFGNSGAKTFGGFASSSFGEQKPTGTFSSGGGSVASQGFGFS SPNKTGGFGAAPVFGSPPTFGGSPGFGGVPAFGSAPAFTSPLGST GGKVFGEGTAAASAGGFGFGSSSNTTSFGTLASQNAPTFGSLSQQ TSGFGTQSSGFSGFGSGTGGFSFGSNNSSVQGFGGWRS 350 AAs F: 13% G: 23% S+T: 31%

42. Long-range repulsion and entropic exclusion Lim (2006) PNAS 103, 9512

43. CREB-binding protein (CBP) Dyson and Wright (2005) Nat. Rev. MCB 6, 197 Histone acetyl transferase Transcriptional adaptor zinc finger 1 Plant homeodomain Nuclear receptor co- activator binding Nuclear receptor interaction Zinc binding domain

44. CBP KIX-CREB KID Dyson and Wright (2005) Nat. Rev. MCB 6, 197

45. CBP TAZ1-HIF1a/CITED2 HIF1  : hypoxia factor

46. Dyson and Wright (2005) Nat. Rev. MCB 6, 197 CBP bromo-p53 AcLys

47. Dyson and Wright (2005) Nat. Rev. MCB 6, 197 CBP NCBD-ACTR ACTR: activator for thyroid hormone and retinoid receptor