A R T I C L E S
Zheng et al.
ES complex for wild-type BChE with (-)-cocaine in water by using
Amber8 program package.30 Our previous MD simulations12 on
the prereactive BChE-(-)-cocaine complex (ES) started from the
X-ray crystal structure32 deposited in the Protein Data Bank (pdb
code: 1POP). The present MD simulations on the transition state
for the first step (TS1) were performed in such a way that bond
lengths of the transition bonds in the transition state were all
constrained to be the same as those obtained from our previous ab
initio reaction coordinate calculations on the model reaction system
of wild-type BChE.21 A sufficiently long MD simulation with the
transition bonds constrained should lead to a reasonable protein
environment stabilizing the reaction center in the transition-state
structure simulated. Further, the simulated TS1 structure for wild-
type BChE with (-)-cocaine was used to build the initial structures
of TS1 for the examined BChE mutants with (-)-cocaine; only
the side chains of mutated residues needed to be changed.
environment part, by cutting a covalent σ-bond Y-X. Y and X
refer to boundary atoms of the environment part and the active
part, respectively. Instead of using a hydrogen atom to cap the free
valence of X atom as in the conventional link-atom approach, a
pseudobond Yps-X is formed by replacing the Y atom with a one-
free-valence boundary Y atom (Yps). The Yps atom is parametrized
to make the Yps-X pseudobond mimic the original Y-X bond with
similar bond length and strength and also to have similar effects
on the rest of the active part.34,35 In the pseudobond approach, the
Y
ps atom and all atoms in the active part form a well-defined QM
subsystem which can be treated by a QM method. Excluding the
Y atom, the remaining atoms in the environment part form the MM
subsystem treated by a MM method. The pseudobond ab initio QM/
MM approach has been demonstrated to be powerful in studies of
enzyme reactions.36-38
In order to use exactly the same Amber force field in our QM/
MM calculations as that used in our MD simulations, we developed
and used a revised version of Gaussian03 and Amber8 programs,
instead of the revised Gaussian03 and Tinker programs, to perform
the QM/MM calculations in this study. In all of our QM/MM
calculations, all atoms of (-)-cocaine and the side chains of S198,
H438, and E325 were considered as the QM atoms, whereas the
other atoms were regarded as MM atoms. Our QM/MM calculations
were performed at the B3LYP/6-31*:Amber level, i.e., the QM
calculations were carried out at the B3LYP/6-31G* level, whereas
the MM calculations were carried out by using the Amber force
field implemented in the Amber8 program. The geometry optimiza-
tions were converged to the default criteria of the Gaussian03 (for
the QM part) and Amber8 (for the MM part) programs. The QM/
MM-optimized ES, TS1, and INT geometries were used to perform
vibrational frequency calculations on the QM subsystem at the same
QM/MM level. The vibrational frequency calculations confirmed
that the optimized ES and INT1 geometries are indeed associated
with local minima on the potential energy surface, whereas the
optimized TS1 geometry is indeed associated with a first-order
saddle point on the potential energy surface.
The partial atomic charges for the nonstandard residue atoms,
including cocaine atoms, in the TS1 structures were calculated by
using the RESP protocol implemented in the Antechamber module
of the Amber8 package following electrostatic potential (ESP)
calculations at ab initio HF/6-31G* level using Gaussian03 pro-
gram.33 The geometries used in the ESP calculations came from
those obtained from the previous ab initio reaction coordinate
calculations,21 but the functional groups representing the oxyanion
hole were removed. Thus, residues G116, G117, and A199 were
the standard residues as supplied by Amber8 in the MD simulations.
The general procedure for carrying out the MD simulations in water
is essentially the same as that used in our previously reported other
computational studies.12,21,30,32 Each aforementioned starting TS1
structure was neutralized by adding chloride counterions and was
solvated in a rectangular box of TIP3P water molecules with a
minimum solute-wall distance of 10 Å. The total numbers of atoms
in the solvated protein structures for the MD simulations are nearly
70 000, although the total number of atoms of BChE and (-)-
cocaine is only 8417 (for the wild-type BChE). All of the MD
simulations were performed by using the Sander module of Amber8
package. The solvated systems were carefully equilibrated and fully
energy minimized. These systems were gradually heated from T )
10 K to T ) 298.15 K in 30 ps before running the MD simulation
at T ) 298.15 K for 1 ns or longer, making sure that we obtained
a stable MD trajectory for each of the simulated TS1 structures.
The time step used for the MD simulations was 2 fs. Periodic
boundary conditions in the NPT ensemble at T ) 298.15 K with
Berendsen temperature coupling and P ) 1 atm with isotropic
molecule-based scaling were applied. The SHAKE algorithm was
used to fix all covalent bonds containing hydrogen atoms. The
nonbonded pair list was updated every 10 steps. The particle mesh
Ewald (PME) method was used to treat long-range electrostatic
interactions. A residue-based cutoff of 10 Å was utilized to the
noncovalent interactions. The coordinates of the simulated systems
were collected every 1 ps during the production MD stages.
2. QM/MM Calculations. All of the QM/MM calculations were
performed by a pseudobond QM/MM method.34,35 The pseudobond
QM/MM method was initially implemented in revised Gaussian03
and Tinker programs.34,35 The revised Gaussian03 and Tinker
programs can be used to carry out the QM and MM parts of the
QM/MM calculation iteratively until the full self-consistency is
achieved. The pseudobond QM/MM method uses a seven-valence-
electron atom with an effective core potential constructed to replace
the boundary atom of the environment part and to form a
pseudobond with the boundary atom of the active part. The main
idea of the pseudobond approach is as follows: one considers that
a large molecule is partitioned into two parts, an active part and an
Most of the MD simulations and QM/MM calculations were
performed in parallel on an HP Superdome (with 256 processors)
and an IBM X-series cluster (with 1360 processors) at the Center
for Computational Sciences, University of Kentucky. Some com-
putations were carried out on a 34-processors IBM x335 Linux
cluster and SGI Fuel workstations in our own laboratory.
3. Materials for in Vitro Studies. Cloned pfu DNA polymerase
and Dpn I endonuclease were obtained from Stratagene (La Jolla,
CA). [3H](-)-cocaine (50 Ci/mmol) was purchased from Perkin-
Elmer Life Sciences (Boston, MA). The expression plasmid pRc/
CMV was a gift from Dr. O. Lockridge, University of Nebraska
Medical Center (Omaha, NE). All oligonucleotides were synthesized
by the Integrated DNA Technologies, Inc. (Coralville, IA). The
QIAprep spin plasmid miniprep kit and Qiagen plasmid purification
kit and QIAquick PCR purification kit were obtained from Qiagen
(Santa Clarita, CA). Human embryonic kidney 293T/17 cells were
from ATCC (Manassas, VA). Dulbecco’s modified Eagle’s medium
(DMEM) was purchased from Fisher Scientific (Fairlawn, NJ).
3,3′,5,5′-Tetramethylbenzidine (TMB) was obtained from Sigma
(Saint Louis, MO). Antibutyrylcholinesterase (mouse monoclonal
antibody, product no. HAH00201) was purchased from Antibody-
Shop (Gentofte, Denmark), and goat antimouse IgG HRP conjugate
was from Zymed (San Francisco, CA).
4. Site-Directed Mutagenesis, Protein Expression, and in
Vitro Activity Assay. Site-directed mutagenesis of human BChE
cDNA was performed by using the QuikChange method.39 Muta-
tions were generated from wild-type human BChE in a pRc/CMV
(32) Nicolet, Y.; Lockridge, O.; Masson, P.; Fontecilla-Camps, J. C.;
Nachon, F. J. Biol. Chem. 2003, 278, 41141–41147.
(33) Frisch, M. J.; et al. Gaussian 03, revision A.1; Gaussian: Pittsburgh,
PA, 2003.
(34) Zhang, Y.; Lee, T.; Yang, W. J. Chem. Phys. 1999, 110, 46–54.
(35) Zhang, Y. J. Chem. Phys. 2005, 122, 024114.
(36) Corminboeuf, C.; Hu, P.; Tuckerman, M. E.; Zhang, Y. J. Am. Chem.
Soc. 2006, 128, 4530–4531.
(37) Zhang, Y.; Liu, H.; Yang, W. J. Chem. Phys. 2000, 112, 3483–3492.
(38) Hu, P.; Zhang, Y. J. Am. Chem. Soc. 2006, 128, 1272–1278.
(39) Braman, J.; Papworth, C.; Greener, A. Methods Mol. Biol. 1996, 57,
31–44.
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12154 J. AM. CHEM. SOC. VOL. 130, NO. 36, 2008