Intrinsically disordered proteins:

drug development and the most interesting examples

Peter Tompa

Institute of EnzymologyHungarian Academy of Sciences

Budapest, Hungary

• IDPsIDPs:: in vitroin vitro evidence andevidence and in vivoin vivo considerationsconsiderations

• nnotot RC RC, tran, transient ordersient order

• ffuncunctional advantagestional advantages (specifi (specificity without city without excessive excessive binding strengthbinding strength, , fast bindingfast binding, , one-one-to-many to-many signalingsignaling))

• prevalentprevalent, , frequency increases from frequency increases from prokaryotes to prokaryotes to eukareukaryotesyotes

• funfunctional importancectional importance (regulatory, (regulatory, transcription, transcription, cytoskeletalcytoskeletal))

• involvement in diseaseinvolvement in disease (cancer-associated, (cancer-associated, neurodegenerative)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

http://iupred.enzim.hu

Dosztányi (2005) J. Mol. Biol. 347, 827

TAD DBD TD RD AAPPVAPAPAAPTPAAPAPAP

AAPPVAPAPAAPTPAAPAPAP

p53

p53 binding partners (MoRE, SLM)

Oldfield et al. (2005) Biochemistry 44, 12454

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

PDBSwissProt

signalinghuman 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

PEVPPVRVPEVPKEVVPEKKVPAAPPKKPEVTPVKVPEAPKEVVPEKK

PEVK domain of titin: entropic spring

cytoskeleton

MTs

Tubulin dimers

PKA RII

MAP2: entropic bristle

Mukhopadhyay (2001) FEBS Lett 505, 374

MAP2: entropic bristle

“Dynamic” spacing of MTs in axons and dendrites

Ca2+ + PO4

3-

Ca3(PO4)

2

Casein: scavenger in milk

FlgM: disorder in vivo

Plaxco and Gross (1997) Nature, 386, 657

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-s28 structure

Sorensen et al. (2004) Mol. Cell 14, 127

C y cA

C d k 2

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 The securin storystory

normal chromosome segregation

Inhibition of separase expression

Waizenegger (2002) Curr. Biol. 12, 1368

The securin The securin storystory

Jallepalli (2001) Cell 105, 445

- 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 Entropic gating in nuclear porepore

Patel (2007) Cell 129, 83

...SVFSFSQPGFSSVPAFGQPASSTPTSTSGSVFGAASSTSSSSSFSFGQSSPNTGGGLFGQSNAPAFGQSPGFGQGGSVFGGTSAATTTAATSGFSFCQASGFGSSNTGSVFGQAASTGGIVFGQQSSSSSGSVFGSGNTGRGGGFFSGLGGKPSQDAANKNPFSSASGGFGSTATSNTSNLFGNSGAKTFGGFASSSFGEQKPTGTFSSGGGSVASQGFGFSSPNKTGGFGAAPVFGSPPTFGGSPGFGGVPAFGSAPAFTSPLGSTGGKVFGEGTAAASAGGFGFGSSSNTTSFGTLASQNAPTFGSLSQQTSGFGTQSSGFSGFGSGTGGFSFGSNNSSVQGFGGWRS

350 AAsF: 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 homeodom

ain

Nuclear receptor

co-activator binding

Nuclear receptor interactio

nZinc

binding domain

CBP KIX-CREB KID

Dyson and Wright (2005) Nat. Rev. MCB 6, 197

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