in silico tethering

In the publication Erlanson et al., PNAS 2000, 97, 9367 the cysteine C146 of the active site of E.coli were used for tethering experiments. Five crystal structures were solved (no electron density maps available):

PDB	Name	SG	Res	monomers /AU
1f4b	native	I213	1.75	1	without ligand
1f4c	C146 tethered N-tosyl-D-proline	P63	2.0	2	covalent bound to active site cysteine C146
1f4d	L143C tethered N-tosyl-D-proline	P63	2.15	2	covalent bound to new cysteine L143C, C146S
1f4e	Noncovalent N-tosyl-D-proline	I213	1.90	1
1f4f	Glu-TP	P63	2.0	2
1f4g	Glu-TP-beta-Ala	P63	1.75	2

For in silico tethering, structure 1f4c (monomer A) was used together with the ligand N-tosyl-D-proline. The ligand was covalently bound to Cys143 (active site cysteine) via flexible linker. The docking program GOLD 3.1.1 can not handle a flexible side chain covalently connected to a ligand. To make the side chain of Cys143 flexible during the docking process it was removed from the receptor structure and were put to the ligand as an extension. The ligand can be treated as flexible.
Afterwards the same flexible docking was performed with human TS structure 1hvy.

/home/henricsn/LIGHTS/results/docking2_C195/

E.coli TS

receptor preparation:

1f4c.pdb superimposed to mono1hvy - mono1f4c_sup21hvy.pdb
removing monomer B
adding hydrogens by pymol
removing of side chain C146,
removing of alternative conformations (Phe150)
removing residue 1 (CXM)

input files:
gold_1f4cC146G.conf (without flexible residues)
CID_445503-cys3D.sdf
mono1f4c_4tethering_C146G.pdb

output file:
docking_1f4c-C146G_445503.sdf

Docking results

Most of the docking solutions have totally different conformations like found in the X-ray structure 1f4c, but occupying similar region like dUMP in TS structures (eg., 1hvy). Using the receptor as a monomer or dimer showed just slightly different docking results.

receptor: monomer A of 1f4c, ligand: N-tosyl-D-proline
all docking solutions (purple)
X-ray conformation of ligand of 1f4c (gray)

receptor: monomer A of 1f4c, ligand: N-tosyl-D-proline
best docking solution (purple) (manual selection)
X-ray conformation of ligand of 1f4c (gray)

Dimer

/home/henricsn/LIGHTS/results/docking2_C195/

input:
di1f4c_4tethering_C146G.pdb (Phe149: altconf B)
gold_di1f4cC146G.conf

output:
docking_di1f4c-C146G_445503.sdf

receptor: dimer A and B of 1f4c, ligand: N-tosyl-D-proline
all docking solutions (orange)
X-ray conformation of ligand of 1f4c (gray)

receptor: dimer A and B of 1f4c, ligand: N-tosyl-D-proline
best docking solution (orange) (manual selection)
X-ray conformation of ligand of 1f4c (gray)

human TS

input:
gold_1hvyC195G.conf (without flexible residues)
CID_445503-cys3D.sdf
mono1hvy_4tethering_C195G.pdb

output:
docking_1hvy-C195G_445503.sdf

receptor: monomer A of 1hvy, ligand: N-tosyl-D-proline
all docking solutions (orange)
X-ray conformation of ligand of 1hvy (gray)

receptor: monomer A of 1hvy, ligand: N-tosyl-D-proline
best docking solution (orange) (manual selection)
X-ray conformation of ligand of 1hvy (gray)

may be useful as flexible residues:
Trp109
Met311
Ala312
Val313

(under construction)
rotamer_lib
name 1hvy-cys195Trp109
chi1 1355 1354 1356 1355
chi2 1354 1355 1358 1359
rotamer 0 (30)

SH 22.03.2007

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