AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases DIMACS, 13 June 2005 [email protected]

AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic

reaction catalysed by terpenoid cyclases

DIMACS, 13 June [email protected]

Vladimir Sobolev

Weizmann Institute of Science

1. Approach to molecular docking and definition of surface complementarity



2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases





Where is the binding site located? What is the ligand orientation?Relevant Questions for Docking

Two Major Algorithmic Issues in Molecular Docking:

2. Search procedure

1. Scoring function

CF = Sl - Si - Er

Sl = surface area of legitimate atomic contacts

Si = surface area of illegitimate atomic contacts

Er = a repulsion term

Complementarity Function for molecular docking

Definition of Contact Surface Between Atoms

Ra,Rb ~ 1.5-2.0 Å;

Rw = 1.4 Å

Thus, contact appears

from Rab ~ 6 Å

• contact surface of atom A with B is the surface area of sphere A that penetrates sphere B.

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 HydrophobicCl, 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 III IV V VI VII VIII

I Hydrophilic + + + - + + + +II Acceptor + - + - + + + -III Donor + + - - + + - +IV Hydrophobic - - - + + + + +V Aromatic + + + + + + + +VI Neutral + + + + + + + +VII Neutral-donor + + - + + + - +VIII Neutral-acceptor + - + + + + + -

Hydro

phili

cAcc

ept

orDonor

Hydro

phobic

Arom

atic

Neutra

l

Neutra

l-donor

Neutra

l-acc

epto

r

CF = Sl - Si - Er

Sl = surface area of legitimate atomic contacts

Si = surface area of illegitimate atomic contacts

Er = a repulsion term

Complementarity Function for molecular docking

Input coordinates, size of search cube ,number of initial ligand positions (N), andnumber of best positions kept (M)

Generate random ligand positionand orientation in the search cube

n = 1

n = n+1Maximize complementarity function (CF)

Keep not more than M best maxima

Does n equal N?

Yes

No

.

Optimize H-bond lengths forevery M structure obtained

Cluster maxima

Calculate and list contacts for theposition with highest complementarity

Calculate and list normalized complementarity(CF) following atom substitution

Satisfactory CFposition found?

Yes

No

Neglect steric clashfor a user definednumber of residues

Flow Chart of LIGIN Program

Critical Assessment ofTechniques for ProteinStructure Prediction

http://sgedg.weizmann.ac.il/casp2

Our Results





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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

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Chemical scheme of the substrate (farmecyl diphosphate (FFP)

Flowchart describing semi flexible docking

Free dihedral anglesComplementarityscore (Å2)

PA-O5A O5A-C1 C1-C2 C3-C4 C4-C5 C5-C6 C7-C8 C8-C9 C9-C10

1 84.6 -121.7 173.7 -107.7 111.4 -35.9 -124.3 -103.9 32.6 541.3

2 14.9 183.3 -123.1 2.5 61.7 59.6 41.5 -126 36.9 532.6

3 90 -118.2 191.2 -122.8 114 -43.9 117.4 109.1 29 524.2

4 84.4 -119.2 178.1 -117.4 105.3 -29.9 -102.2 -107.1 33.4 522.6

5 39.6 180.6 -124 116.8 -116.5 20.9 123 80.6 32.5 521.7

6 102.6 -142.3 133.4 -23.4 115.5 -115.9 -118.1 -62.4 -24.3 518.5

7 89.9 171.6 130.5 152.5 -64.6 -24.5 245.6 -126.8 37.9 516.3

8 46.5 178.1 -130.3 30.3 -30.9 129.6 182.6 121.4 -10.5 516.0

9 43.3 182.5 -126.5 116.2 -107 22.7 186 -53.2 195.7 516.0

10 92.3 -125.5 156.1 -60.2 102.4 -102.7 -77 -137.2 26.9 515.9

11 99.9 -130.7 131.3 -29.6 105.1 187.1 -163.9 68.5 40.2 515.5

12 86.2 -121.4 175.1 -124.5 117.9 -26.7 -107.5 -61.1 -30.3 515.4

13 88.7 -122.1 172.1 -110.9 108.2 -58.9 191.2 70.9 35 514.9

14 94.1 -129.3 133.7 -40.3 110.7 185.5 -12.2 -77 -21 514.4

15 87.5 -117.5 159.9 -97.4 105.3 -117.7 -5.8 -102.2 39.9 514.1

16 88.7 -124.3 168.8 -123 118.8 -43.9 -104.8 -40.8 -98.2 513.9

17 102 -145.8 133.7 -30.5 115.3 -104.2 126.2 123.1 -23.7 513.9

18 100.9 -147.6 140.8 -31 108 -40.4 163.4 -95.4 48.1 511.8

Results of the semi flexible docking for the first stage

Residues forming contacts with the leading structure

Res. Dist.

Å

Surf

Å2

Res. Dist.

Å

Surf

Å2

Arg264 3.2 32 Tyr404 3.4 29

Trp273 3.6 56 Leu407 3.9 16

Ile294 3.7 29 Cys440 3.9 22

Ile297 4.3 16 Ile515 4.1 10

Ser298 4.1 23 Val516 4.8 10

Asp301 3.0 28 Tyr520 3.1 43

Asp305 2.6 13 Asp525 2.5 34

Thr402 3.9 21 Tyr527 3.9 48

Thr403 4.1 18

Crystal structure

Predicted structure

Crystal structure

Predicted structure

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

WT V516G

Y520GV440G

Order

Carbon atoms(see Fig. 3)

Complementarity sum

1 C10C11C12C15 116.002 C9

C10C11C12114.00

3 C3 C4 C14C5 102.004 C6 C7 C8 C9 85.005 C3 C4 C5 C6 81.006 C4 C5 C6 C7 81.007 C5 C6 C7 C8 80.008 C9 C10C11C15 78.009 C2 C3 C4 C14 77.0010 C1 C2 C3 C14 72.0011 C7 C8 C9 C10 69.0012 C8 C9 C10C11 69.0013 C5 C6 C7 C13 53.0014 C2 C3 C4 C5 51.0015 C6 C7 C8 C13 50.0016 C7 C8 C13C9 49.0017 C1 C2 C3 C4 44.00

OPP

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Contribution for the complementarity function of all groups of 4 adjacent carbons.

OPP

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Contribution for the complementarity function of all groups of 4 adjacent carbons.

N Carbon Atoms COMPLEMENTARITY

1 C10 C11 C12 C15 116

2 C9 C10 C11 C12 114

3 C3 C4 C14 C5 102

4 C6 C7 C8 C9 85

5 C3 C4 C5 C6 81

6 C4 C5 C6 C7 81

7 C5 C6 C7 C8 80

8 C9 C10 C11 C15 78

9 C2 C3 C4 C14 77

10 C7 C8 C9 C10 69

11 C8 C9 C10 C11 69

12 C5 C6 C7 C13 53

13 C2 C3 C4 C5 51

14 C6 C7 C8 C13 50

15 C7 C8 C13 C9 49

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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 (C1) Cluster

1 107 412 457 Thr402 a

2 96 459 508 Tyr520, Asp444 b

3 16 541 555 Tyr404, Thr403, Thr402 c

3 21 534 555 Tyr520, Asp444 d

3 85 519 555 Trp273 e

4 16 601 615 Trp273 f

5 10 677 697 Trp273 e

5 34 661 697 Trp273 g

5 52 655 697 Tyr404 h

7 2 819 833 Trp273 e

9 1 990 990 Trp273 e

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

Super-grope number

Group letters

Contacts with C1

1 e, f, g Trp273

2 b, d Tyr520, Asp44, Asp525

3 c, h Tyr404, Thr403, Thr402

4 a Thr402

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)



DIMACS Workshop, 12 June [email protected]

Vladimir Sobolev

Weizmann Institute of Science

Documents

AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases DIMACS, 13 June 2005 [email protected]