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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 [email protected]. - PowerPoint PPT Presentation
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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
AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic
reaction catalysed by terpenoid cyclases
2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases
1. Approach to molecular docking and definition of surface complementarity
AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic
reaction catalysed by terpenoid cyclases
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 ClassesI 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 OV Aromatic C atoms in aromatic ringsVI 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 IIIVII Neutral-donor C atoms that are covalently bonded to only one atom of class IIIVIII 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 + - + + + + + -
Hydrophili
cAcce
pt
or Donor
Hydrophobic
Aromatic
NeutralNeu
tral-d
onor
Neutral-a
cceptor
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
1. Approach to molecular docking and definition of surface complementarity
AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic
reaction catalysed by terpenoid cyclases
2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases
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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 angles Complementarityscore (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
SurfÅ2
Res. Dist.
Å
SurfÅ2
Arg264 3.2 32 Tyr404 3.4 29Trp273 3.6 56 Leu407 3.9 16Ile294 3.7 29 Cys440 3.9 22Ile297 4.3 16 Ile515 4.1 10Ser298 4.1 23 Val516 4.8 10Asp301 3.0 28 Tyr520 3.1 43Asp305 2.6 13 Asp525 2.5 34Thr402 3.9 21 Tyr527 3.9 48Thr403 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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1+
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 a2 96 459 508 Tyr520, Asp444 b3 16 541 555 Tyr404, Thr403, Thr402 c3 21 534 555 Tyr520, Asp444 d3 85 519 555 Trp273 e4 16 601 615 Trp273 f5 10 677 697 Trp273 e5 34 661 697 Trp273 g5 52 655 697 Tyr404 h7 2 819 833 Trp273 e9 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)
AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic
reaction catalysed by terpenoid cyclases
DIMACS Workshop, 12 June [email protected]
Vladimir Sobolev
Weizmann Institute of Science