Using structural information to predict protein-protein interaction and enyzme specificity

Structure, interaction and peptide specificity Using Structural Information To Predict Protein-Protein Interaction And Enzyme Specificity Neil Saunders , Thomas Huber, Bostjan Kobe School of Molecular and Microbial Sciences The University of Queensland http://predikin.biosci.uq.edu.au

Structure, interaction and peptide specificity Peptide specificity of protein kinases CK-2 PKA MAPK kinase ATP protein OH + protein O-P i kinase ADP +

Structure, interaction and peptide specificity Structural basis for peptide specificity PKA surface + heptapeptide RRA S IHD Schematic of heptapeptide + PKA SDRs

Structure, interaction and peptide specificity 1. Identify key sequence residues reference *->Yellkkl GkG aFGkVylardkktgrlv AiK vik..........eril Y+++k+lG+G+FGkV+la+++ tg++vA+K+i+++ +++ + ri+ query 55 YQIVKTL GE GS F GKVKLAYHTTTGQKV ALK IINkkvl aks dmqGRIE 101 -1 +2 X 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 Q FS T VKG E QF S TVK R SV S EAA R SG S SPN R HD S GLD R RM S DEF A RG S FDA Query kinase kinases substrates sites

Structure, interaction and peptide specificity 3. Build scoring matrices from peptides; score query substrates Score all XXX[STY]XXX kinase substrate score NP_001547 1 COA1 80 SSM S GLH 85.49 NP_001269 1 COA1 80 SSM S GLH 85.49 XP_042066 1 COA1 80 SSMSGLH 75.77 XP_001128827 1 COA1 80 SSMSGLH 75.77 NP_001013725 1 COA1 80 SSMSGLH 74.72 NP_004064 1 COA1 80 SSMSGLH 73.84 NP_006613 1 COA1 80 SSMSGLH 73.84 NP_001778 1 COA1 80 SSMSGLH 72.21 XP_001128005 1 COA1 80 SSMSGLH 72.21 NP_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 α/β

Experimental evidence (Bruce Kemp)

Structure, interaction and peptide specificity 4. Evaluate scores serine/threonine CMGC Predikin (SDR) 0.86 (0.04) 0.93 (0.02) GPS 0.83 0.94 KinasePhos 0.78 0.95 NetPhosK 0.90 0.57 PPSP 0.92 0.95 Scansite 0.95 0.94 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 Less visual inspection More computed analyses Queries Predictions Protein-peptide structures Define key contacts Database Models

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 chains 29 390 + >= 2 protein entities 8 306 + <= 2.5 Å 5 137 + > 90% non-redundant 1 168

Structure, interaction and peptide specificity 3. Data curation and visualisation Model organisms kinases substrates sites queries visualisation prediction annotation

Structure, interaction and peptide specificity Summary & Acknowledgements