Outline of talk

Introduction to protein kinases

Prediction of substrate specificity

Predikin and PredikinDB

Evaluation

Neil SaundersSchool of Molecular and Microbial SciencesUniversity of Queensland

Introduction to protein kinases

kinaseATPprotein

OH

+

protein

OPi

kinaseADP+

Biochemistry

Two major (eukaryotic) types: (1) Ser/Thr; (2) Tyr

~ 2% of human genes encode a protein kinase

At least 30-50% of human proteins phosphorylated

Regulate essentially every cellular process

Complex signalling networks

How do protein kinases find their targets?

Kinase specificity substrate recruitment

Remenyi et al. (2006)Docking interactions in protein kinaseand phosphatase networks.Curr Opin Struct Biol 16: 676-685

LOCATE calcium/calmodulin-dependent protein kinase IV

Substrate recruitment

Any process that brings substrate to kinase

- docking

- binding to scaffolding protein(s)

- colocalisation

- coregulation

Docking interactions

Colocalisation

Kinase specificity - peptide specificity

Amino acid frequency in substrate sequences at X{7}[ST]X{7} sites

CK-2

PKA

MAPK

Structural basis for peptide specificity

Substrate heptapeptide binding to protein kinase A

PKA surface + heptapeptide RRASIHD

Schematic of heptapeptide + PKA SDRs

Accurate location of key residues using HMMER

*->YellkklGkGaFGkVylardkktgrlvAiKvik..........eril Y+++k+lG+G+FGkV+la+++ tg++vA+K+i+++ +++ + ri+snf1p 55 YQIVKTLGEGSFGKVKLAYHTTTGQKVALKIINkkvlaksdmqGRIE 101

rEikiLkk.dHPNIVkLydvfed.dklylVmEyceGdlGdLfdllkkrgr rEi+ L+ +HP+I+kLydv+ ++d++ +V Ey+++ +Lfd++++r +snf1p 102 REISYLRLlRHPHIIKLYDVIKSkDEIIMVIEYAGN---ELFDYIVQRDK 148

rglrkvlsE.earfyfrQilsaLeYLHsqgIiHRDLKPeNiLLds..hvK +sE+ear++f+Qi+sa+eY+H+++I+HRDLKPeN+LLd++ +vKsnf1p 149 ------MSEqEARRFFQQIISAVEYCHRHKIVHRDLKPENLLLDEhlNVK 192

laDFGlArql......ttfvGTpeYmAPEvl...gYgkpavDiWSlGcil +aDFGl+ ++++++ +t +G+p+Y APEv++++ Y +p+vD+WS+G+ilsnf1p 193 IADFGLSNIMtdgnflKTSCGSPNYAAPEVIsgkLYAGPEVDVWSCGVIL 242

yElltGkpPFp..qldlifkkig..........SpeakdLikklLvkdPe y +l+++ PF+++ + ++fk+i ++ ++ ++ Sp a Lik++L ++P snf1p 243 YVMLCRRLPFDdeSIPVLFKNISngvytlpkflSPGAAGLIKRMLIVNPL 292

kRlta.eaLedeldikaHPff