DIMACS, 13 June 2005 vladimir.sobolev@weizmann.ac.il

1. AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases Vladimir Sobolev Weizmann Institute of Science DIMACS, 13 June 2005 vladimir.sobolev@weizmann.ac.il

2. AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 1. Approach to molecular docking and definition of surface complementarity 2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

3. AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 1. Approach to molecular docking and definition of surface complementarity 2.Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

4. Relevant Questions for Docking Where is the binding site located? What is the ligand orientation? Two Major Algorithmic Issues in Molecular Docking: 1. Scoring function 2. Search procedure

5. Complementarity Function for molecular docking CF = Sl - Si - Er Sl= surface area of legitimateatomic contacts Si= surface area of illegitimate atomic contacts Er= a repulsion term

6. Definition of Contact Surface Between Atoms Ra,Rb ~ 1.5-2.0 Å; Rw = 1.4 Å • contact surface of atom A with B is the surface area of sphere A that penetrates sphere B. Thus, contact appears from Rab~ 6 Å

7. Definition of Contact Surface Between Atoms In both cases Rab is the same, while in second case there is no contact between atoms A and B

8. Atomic Classes I Hydrophilic N or O that donate or accept a hydrogen bond (e.g., O of OH group of Ser or Thr) II Acceptor N or O that only accept a hydrogen bond (e.g., O of peptide group) III Donor N that only donates a hydrogen bond (e.g., N of peptide group) IV Hydrophobic Cl, Br, I and C atoms not in aromatic rings and not covalently bonded to N or O V Aromatic C atoms in aromatic rings VI Neutral S, F, P, and metal atoms; C atoms covalently bonded to one or more atoms of class I or two or more atoms of class II or III VII Neutral-donor C atoms that are covalently bonded to only one atom of class III VIII Neut.-acceptor C atoms that are covalently bonded to only one atom of class II

9. Neutral-acceptor Atomic classI II III IV V VI VII VIII I Hydrophilic + + + - + + + + II Acceptor + - + - + + + - III Donor + + - - + + - + IV Hydrophobic - - - + + + + + V Aromatic + + + + + + + + VI Neutral + + + + + + + + VII Neutral-donor + + - + + + - + VIII Neutral-acceptor + - + + + + + - Hydrophilic Hydrophobic Neutral-donor Acceptor Donor Aromatic Neutral Legitimacy (for each pair of contacts)

10. Complementarity Function for molecular docking CF = Sl - Si - Er Sl= surface area of legitimateatomic contacts Si= surface area of illegitimate atomic contacts Er= a repulsion term

11. Flow Chart of LIGIN Program Input coordinates, size of search cube , number of initial ligand positions (N), and number of best positions kept (M) n = 1 Generate random ligand position and orientation in the search cube n = n+1 Maximize complementarity function (CF) . Keep not more than M best maxima No Does n equal N? Yes Optimize H-bond lengths for every M structure obtained Neglect steric clash for a user defined number of residues Cluster maxima No Satisfactory CF position found? Yes Calculate and list contacts for the position with highest complementarity Calculate and list normalized complementarity (CF) following atom substitution

12. Critical Assessment of Techniques for Protein Structure Prediction Our Results http://sgedg.weizmann.ac.il/casp2

13. AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 1.Approach to molecular docking and definition of surface complementarity 2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

14. Chemical scheme of the substrate (farmecyl diphosphate (FFP)

15. Terpenoid cyclases may produce a large number of products from a single substrate. Steele et al., 1998

16. Chemical scheme of the substrate (farmecyl diphosphate (FFP)

17. Flowchart describing semi flexible docking

18. Results of the semi flexible docking for the first stage

19. Residues forming contacts with the leading structure

20. Docking prediction for WT pocket and three mutants. Blue - predicted structure; green - experimental one WT V516G V440G Y520G

21. Contribution for the complementarity function of all groups of 4 adjacent carbons. 8 6 7 9 5 10 13 3 12 4 2 1 11 15 14 O P P

22. Contribution for the complementarity function of all groups of 4 adjacent carbons. 8 6 7 9 5 10 13 3 12 4 2 1 11 15 14 O P P

23. Scheme for the prediction of the second step of the reaction

24. Analysis of the results of the “second stage” reaction model

25. List of super-groups clustered according to the interaction with carbocation C1

26. Two candidates for amino acids involved in stabilising the reaction intermediate

27. Summary 1. Docking algorithm was described 2.First two steps of enzymatic reaction catalysed by terpenoid cyclases were modeled. There is already experimental data confirming correctness of the first step model. While modeling second step in the large extent speculative

28. ACKNOWLEDGMENTS Meir Edelman (WIS) Eran Eyal (WIS) Gert Vriend (EMBL) Rebecca Wade (EMBL)

29. AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases Vladimir Sobolev Weizmann Institute of Science DIMACS Workshop, 12 June 2005 vladimir.sobolev@weizmann.ac.il