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

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

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

p53 tumor supressor Levine (1997) Cell 88, 323

Prediction of disorder: IUPred Dosztányi (2005) J. Mol. Biol. 347, 827 TADDBDTDRD AAPPVAPAPAAPTPAAPAPAP p53

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

p53 binding DNA

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

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

PDB SwissProt signaling human cancer

New molecules approved by FDA

Partners of MoRFs: druggable targets

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

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

PEVPPVRVPEVPKEVV PEKKVPAAPPKKPEVT PVKVPEAPKEVVPEKK

PEVK domain of titin: entropic spring

cytoskeleton MTs Tubulin dimers PKA R II MAP2: entropic bristle

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

“Dynamic” spacing of MTs in axons and dendrites

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

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

FlgM: disorder in vivo

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

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

Inhibition of Cdks in cell-cycle regulation

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

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

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

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

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

Mitosis

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

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

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

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

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

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

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

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

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

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

CBP TAZ1-HIF1a/CITED2 HIF1  : hypoxia factor

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

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