AN APPROACH TO SEMI FLEXIBLE DOCKING A case

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

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

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

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

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

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

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

Legitimacy (for each pair of contacts) Atomic class I II IV V VI VIII Hydrophilic Acceptor Donor Hydrophobic Aromatic Neutral-donor Neutral-acceptor or t r o cep ic n b c o ic ili do l-ac h h l t l o p op ept or dro ma tra tra r n u d c u u o Hy Ac Do Hy Ar Ne Ne Ne r I II IV V VI VIII + + + - + + + + + + + + + + -

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

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 Maximize complementarity function (CF). n = n+1 Keep not more than M best maxima Does n equal N? No Yes Optimize H-bond lengths for every M structure obtained Cluster maxima Satisfactory CF position found? No Yes Calculate and list contacts for the position with highest complementarity Calculate and list normalized complementarity (CF) following atom substitution Neglect steric clash for a user defined number of residues

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

Chemical scheme of the substrate (farmecyl diphosphate (FFP)

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

Chemical scheme of the substrate (farmecyl diphosphate (FFP)

Flowchart describing semi flexible docking

Results of the semi flexible docking for the first stage

Residues forming contacts with the leading structure Res. Dist. Surf Å Å2 Arg 264 Trp 273 3. 2 3. 6 32 56 Tyr 404 Leu 407 3. 4 3. 9 29 16 Ile 294 Ile 297 Ser 298 Asp 301 Asp 305 Thr 402 Thr 403 3. 7 4. 3 4. 1 3. 0 2. 6 3. 9 4. 1 29 16 23 28 13 21 18 Cys 440 Ile 515 Val 516 Tyr 520 Asp 525 Tyr 527 3. 9 4. 1 4. 8 3. 1 2. 5 3. 9 22 10 10 43 34 48

Docking prediction for WT pocket and three mutants. Blue - predicted structure; green experimental one WT V 516 G V 440 G Y 520 G

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

Contribution for the complementarity function of all groups of 4 adjacent carbons. N Carbon Atoms COMPLEMENTARITY 1 C 10 C 11 C 12 C 15 116 2 C 9 C 10 C 11 C 12 114 3 C 4 C 14 C 5 102 4 C 6 C 7 C 8 C 9 85 5 C 3 C 4 C 5 C 6 81 6 C 4 C 5 C 6 C 7 81 7 C 5 C 6 C 7 C 8 80 8 C 9 C 10 C 11 C 15 78 9 C 2 C 3 C 4 C 14 77 10 C 7 C 8 C 9 C 10 69 11 C 8 C 9 C 10 C 11 69 12 C 5 C 6 C 7 C 13 53 13 C 2 C 3 C 4 C 5 51 14 C 6 C 7 C 8 C 13 50 15 C 7 C 8 C 13 C 9 49 6 7 8 9 5 4 3 2 14 13 1 OPP 10 12 11 15

Scheme for the prediction of the second step of the reaction

Analysis of the results of the “second stage” reaction model K N Compl. Max. Compl. Contacts with (C 1) Cluster 1 107 412 457 Thr 402 a 2 96 459 508 Tyr 520, Asp 444 b 3 16 541 555 Tyr 404, Thr 403, Thr 402 c 3 21 534 555 Tyr 520, Asp 444 d 3 85 519 555 Trp 273 e 4 16 601 615 Trp 273 f 5 10 677 697 Trp 273 e 5 34 661 697 Trp 273 g 5 52 655 697 Tyr 404 h 7 2 819 833 Trp 273 e 9 1 990 Trp 273 e

List of super-groups clustered according to the interaction with carbocation C 1 Super-grope Group number letters 1 e, f, g Contacts with C 1 2 b, d 3 c, h 4 a Tyr 520, Asp 44, Asp 525 Tyr 404, Thr 403, Thr 402 Trp 273

Two candidates for amino acids involved in stabilising the reaction intermediate

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

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

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