1. John Mitchell Bioinformatics Chemoinformatics Computational Chemistry Theoretical Chemistry

2. 2 Mitchell group – BSRC & EaStCHEM School of Chemistry Purdie Building rooms 150 &152 Lazaros Mavridis Ava Sih-Yu Chen Rosanna Alderson Neetika Nath James Mc Donagh Luna De Ferrari

3. MACiE Mechanism, Annotation and Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ MACiE Database

4. Enzyme Nomenclature and Classification EC Classification Class Subclass Sub-subclass Serial number

5. The EC Classification  Reaction direction arbitrary  Cofactors and active site residues ignored  Doesn’t deal with structural and sequence information  However, it was never intended to do so  Deals with overall reaction, not mechanism

6. A New Representation of Enzyme Reactions?  Should be complementary to, but distinct from, the EC system  Should take into account:  Reaction Mechanism  Structure  Sequence  Active Site residues  Cofactors  Need a database of enzyme mechanisms

7. MACiE Mechanism, Annotation and Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ MACiE Database

10. EC is not Everything Different mechanisms can occur with exactly the same EC number. MACiE has six beta-lactamases, all with different mechanisms but the same overall reaction.

12. EC Coverage of MACiE Representative – based on a non-homologous dataset, and chosen to represent each available EC sub-subclass. Structures exist for: 6 EC 1.-.-.- 61 EC 1.2.-.- 204 EC 1.2.3.- 1776 EC 1.2.3.4 MACiE covers: 6 EC 1.-.-.- 57 EC 1.2.-.- 183 EC 1.2.3.- 321 EC 1.2.3.4

13. Coverage of MACiE Representative – based on a non-homologous dataset, and chosen to represent each available EC sub-subclass.

14. Repertoire of Enzyme Catalysis G.L. Holliday et al., J. Molec. Biol., 372, 1261-1277 (2007) G.L. Holliday et al., J. Molec. Biol., 390, 560-577 (2009)

15. Repertoire of Enzyme Catalysis Enzyme chemistry is largely nucleophilic

16. Repertoire of Enzyme Catalysis

17. Protontransfer Ad N 2 E1 SN2SN2SN2SN2E2 RadicalreactionTautom.Others Repertoire of Enzyme Catalysis

20. We do see a few steps corresponding to well- known organic reactions; but these are the exception.

21. Residue Catalytic Propensities

22. Residue Catalytic Functions

23. Predicting Enzyme Function … … and Mechanism L. De Ferrari et al. BMC Bioinformatics 2012, 13:61

24. 24 Data sources EnzML: Multi-label prediction of enzyme classes using InterPro signatures, L. De Ferrari et al. BMC Bioinformatics 2012, 13:61

25. 25 Data schema (1,108 Uniprot proteins)

26. 26 Predicting enzyme mechanism from Sequence M0243 pyridoxine 5'-phosphate synthase (EC 2.6.99.2) M0243 pyridoxine 5'-phosphate synthase (EC 2.6.99.2)

27. Predicting enzyme mechanism from Structure

28. Moonlighting: A starting point for evolving a new catalytic function! Main reaction Minor side reaction Enzyme Evolution

29. Investigating the apparent independent evolutionary origins of the B1 & B3 metallo- beta- lactamases at the chemical catalytic level

30. Numbers of Mechanisms for Folds of Different Ages

31. Protein-Ligand Affinity Prediction: Scoring Functions

32. Prediction of Off-target Activities and Side Effects Phospholipidosis; hERG blockade; Doping in sport; Polypharmacology

33. ACKNOWLEDGEMENTS Cambridge Overseas Trust