Rob Russell Cell Networks University of Heidelberg

2. Putting it all together to answer a “real” question Rob Russell Cell Networks University of Heidelberg

3. Domains assemble to form higher-order structures Pawson & Nash, Science, 2003

4. Case study 1: GabaB R1/R2 • Family 3 GPCRs • Subunit R1 binds ligands, R2 signals, but not vice versa • Why?

5. Analysis of intrinsic features Signal peptide Transmembrane helices Low complexity Coiled coil region PFAM analysis >gi|3776094|emb|CAA09940.1| GABAB receptor, subunit 1b [Homo sapiens] MGPGAPFARVGWPLPLLVVMAAGVAPVWASHSPHLPRPHSRVPPHPSSERRAVYIGALFPMSGGWPGGQACQPAVEMALEDVNSRRDILPDYELKLIHHDSKCDPGQATKYLYELLYNDPIKIILMPGCSSVSTLVAEARMWNLIVLSYGSSSPALSNRQRFPTFFRTHPSATLHNPTRVKLFEKWGWKKIATIQQTTEVFTSTLDDLEERVKEAGIEITFRQSFFSDPAVPVKNLKRQDARIIVGLFYETEARKVFCEVYKERLFGKKYVWFLIGWYADNWFKIYDPSINCTVDEMTEAVEGHITTEIVMLNPANTRSISNMTSQEFVEKLTKRLKRHPEETGGFQEAPLAYDAIWALALALNKTSGGGGRSGVRLEDFNYNNQTITDQIYRAMNSSSFEGVSGHVVFDASGSRMAWTLIEQLQGGSYKKIGYYDSTKDDLSWSKTDKWIGGSPPADQTLVIKTFRFLSQKLFISVSVLSSLGIVLAVVCLSFNIYNSHVRYIQNSQPNLNNLTAVGCSLALAAVFPLGLDGYHIGRNQFPFVCQARLWLLGLGFSLGYGSMFTKIWWVHTVFTKKEEKKEWRKTLEPWKLYATVGLLVGMDVLTLAIWQIVDPLHRTIETFAKEEPKEDIDVSILPQLEHCSSRKMNTWLGIFYGYKGLLLLLGIFLAYETKSVSTEKINDHRAVGMAIYNVAVLCLITAPVTMILSSQQDAAFAFASLAIVFSSYITLVVLFVPKMRRLITRGEWQSEAQDTMKTGSSTNNNEEEKSRLLEKENRELEKIIAEKEERVSELRHQLQSRQQLRSRRHPPTPPEPSGGLPRGPPEPPDRLSCDGSRVHLLYK Homology to known structure can be used to create model

6. Family III GPCRs Ligand binding domain R1 cut EC2 EC1 EC3 1 2 3 4 5 6 7 dimerisation IC2 IC1 IC3 Cterm - - - G-protein

7. R1 binds ligand R2 signals Robbins et al, J. Neurosci, 21, 8043, 2001

8. GabaB R1/R2 Ligand binding domain R2 R1 (none) EL2 EL1 EL3 EL2 EL1 EL3 1 2 3 4 5 6 7 1 2 3 4 5 6 7 - IL2 IL2 IL1 IL1 - - - IL3 Cterm IL3 Cterm blocked - - - G-protein

9. Case study 2: Human RYKan inactive tyrosine kinase

10. Human RYK model Human RYK (model) Insulin receptor YK (template) Katso, Russell, Ganesan, Mol Cell Biol, 19, 6427, 1999

11. Case study 3: What are phosphorylation sites doing? Van Noort et al, Mol Sys Biol, 2012

12. MPN134 is phosphorylated at Serine 392 Katso, Russell, Ganesan, Mol Cell Biol, 19, 6427, 1999

13. What do modifications do to interfaces? From polar to negatively charged From positively charged to polar Modelled MPN134 homodimer: From a polar-polar interaction to a pair of negative charges in proximity Van Noort et al, Mol Sys Biol, 2012

14. Homology modelling algorithm +

15. Homology modelling steps • Identify the homologue of known structure • Get the best alignment of your sequence to the structure • Model building • Side-chain replacement • Loop building • Optimisation/relaxation/minimisation

17. Problem with loops Two subtilisin-like serine proteases