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

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?

1) Functional advantages of disorder

i) Entropic-chain functions

ii) Specificity without strong binding (reversibility, inducibility)

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

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

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

”Protein fishing” model clathrin AP180

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

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

vi) Flexibility in the assembly of complexes

Disorder correlates with complex size Hegyi et al. (2007) BMC Struct. Biol. 7, 65 single

2) Functional classification: 7 basic mechanisms 7 basic mechanisms

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

IDP I: entropic chains IDP I: entropic chains

cytoskeleton MTs Tubulin dimers protein 2 Microtubule-associated protein 2

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

Spacing of MTs in dendrites and axons

V-dependent K + -channel: entropic clock

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

PEVPPVRVPEVPKEVV PEKKVPAAPPKKPEVT PVKVPEAPKEVVPEKK

Titin PEVK domain: entropic spring

IDPs II: effectors IDPs II: effectors

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

p27: another effector, inhibitor of Cdk2

IDPs III: scavengers

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

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

IDPs IV: assemblers 45

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

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

IDPs V: display sites

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

cAMP-response element binding protein (CREB) activation

The ELM server

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

IDPs VI: chaperones

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

Disorder is involved in chaperone function

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

IDPs VII: prions

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

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

Prion form of Sup35: translation read-through

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

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

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

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

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

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

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

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

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

4) Extension of the GO scheme ?

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