INFIQC   05475
INSTITUTO DE INVESTIGACIONES EN FISICO- QUIMICA DE CORDOBA
Unidad Ejecutora - UE
artículos
Título:
Protonation state and substrate binding to B2 metallo-b-lactamase CphA from Aeromonas hydrofila.
Autor/es:
F. SIMONA, A. MAGISTRATO, D. M. A. VERA, G. GARAU, A. J. VILA, P. CARLONI.
Revista:
Proteins: Structure, Function, and Bioinformatics
Editorial:
Wiley Interscience
Referencias:
Lugar: New York; Año: 2006
ISSN:
0887-3585
Resumen:
The zinc enzymes metallo b-lactamases counteract
the beneficial action of b-lactam antibiotics
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
the beneficial action of b-lactam antibiotics
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
b-lactamases counteract
the beneficial action of b-lactam antibiotics
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
b-lactam antibiotics
against bacterial infections, by hydrolyzing
their b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
b-lactam rings. To understand
structure/function relationships on a representative
member of this class, the B2 MbL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.
bL
CphA, we have investigated the H-bond pattern
at the Zn enzymatic active site and substrate
binding mode by molecular simulation
methods. Extensive QM calculations at the
DFT-BLYP level on eleven models of the protein
active site, along with MD simulations
of the protein in aqueous solution, allow us
to propose two plausible protonation states
for the unbound enzyme, which are probably
in equilibrium. Docking procedures along
with MD simulations and QM calculations
suggest that in the complex between the
enzyme and its substrate (biapenem), the latter
is stable in only one of the two protonation
states, in addition it exhibits two different
binding modes, of which only one agrees
with previous proposals. In both cases, the
substrate is polarized as in aqueous solution.
We conclude that addressing mechanistic
issues on this class of enzymes requires a
careful procedure to assign protonation states
and substrate docking modes.