Structure, interaction and peptide specificity

Using Structural Information To Predict Protein-Protein Interaction And Enzyme Specificity

Neil Saunders, Thomas Huber, Bostjan KobeSchool of Molecular and Microbial SciencesThe University of Queensland

http://predikin.biosci.uq.edu.au

Structure, interaction and peptide specificity

Peptide specificity of protein kinases

CK-2

PKA

MAPK

kinaseATPprotein

OH

+

protein

O-Pi

kinaseADP+

Structure, interaction and peptide specificity

Structural basis for peptide specificity

PKA surface + heptapeptide RRASIHD

Schematic of heptapeptide + PKA SDRs

Structure, interaction and peptide specificity

1. Identify key sequence residues

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

-1 +2X X X [ST] X X X

Prediction of peptide specificity from sequence

kinase

substrate

Structure, interaction and peptide specificity

2. Query a database for similar protein kinases

kinasessubstratessites

Query kinaseQFSTVKGEQFSTVKRSVSEAARSGSSPNRHDSGLDRRMSDEFARGSFDA

Structure, interaction and peptide specificity

3. Build scoring matrices from peptides; score query substrates

kinase substrate scoreNP_001547 1 COA1 80 SSMSGLH 85.49NP_001269 1 COA1 80 SSMSGLH 85.49XP_042066 1 COA1 80 SSMSGLH 75.77XP_001128827 1 COA1 80 SSMSGLH 75.77NP_001013725 1 COA1 80 SSMSGLH 74.72NP_004064 1 COA1 80 SSMSGLH 73.84NP_006613 1 COA1 80 SSMSGLH 73.84NP_001778 1 COA1 80 SSMSGLH 72.21XP_001128005 1 COA1 80 SSMSGLH 72.21NP_277021 1 COA1 80 SSMSGLH 72.21

Kinases for acetyl CoA carboxylase

Known phosphorylation site on S80

Phosphorylated in AMPK knockout mice

Suggested alternate kinases: IKK /

Experimental evidence (Bruce Kemp)

Score all XXX[STY]XXX

Structure, interaction and peptide specificity

4. Evaluate scores

serine/threonineCMGCPredikin (SDR)0.86 (0.04)0.93 (0.02)GPS0.830.94KinasePhos0.780.95NetPhosK0.900.57PPSP0.920.95Scansite0.950.94

ROC curve, CMGC kinases, Predikin SDR

AROC values, Predikin v. competition

Structure, interaction and peptide specificity

5. Publish!

Nucleic Acid Res. 36: W286-W290 (2008)

BMC Bioinformatics 9: 245 (2008)

Structure, interaction and peptide specificity

Where next for this approach?

Automated pipelines

Application to other types of interaction

Data curation and visualisation

Structure, interaction and peptide specificity

1. A more automated workflow

Protein-peptidestructuresDefine key contactsLess visual inspection

More computed analyses

Queries

Predictions

DatabaseModels

Structure, interaction and peptide specificity

2. Application to other systems?

Other examples of protein - peptide recognition?

- SH2, SH3, PDZ...

Sufficient structural information?

- the PDB is not so comprehensive as you might think

Integrate contextual information?

- peptide specificity may be only ~ 40% of the story

Query# structures-53 103>= 2 chains29 390+ >= 2 protein entities 8 306+ 90% non-redundant 1 168

Structure, interaction and peptide specificity

3. Data curation and visualisation

Model organismskinasessubstratessitesqueriesvisualisation

predictionannotation

Structure, interaction and peptide specificity

Summary & Acknowledgements

University of Queensland

Bostjan Kobe & group

Thomas Huber & group

St. Vincent's Institute

Bruce Kemp, SVI Melbourne

Predikin testing and usage

Mark Guthridge, IMVS Adelaide

Paul Shannon, Institute for Systems Biology

Annabel Todd, EBI

Funding

ARC FF0561371; B. Kobe

NHMRC 395522; B. Kobe, B. Kemp