Communications Chemistry,
Journal Year:
2024,
Volume and Issue:
7(1)
Published: March 27, 2024
Abstract
Norcoclaurine
synthase
from
Thalictrum
flavum
(
Tf
NCS)
demonstrated
high
stereospecificity
and
yield
in
catalyzing
the
Pictet-Spengler
reaction
of
dopamine
with
chiral
aldehydes,
achieving
kinetic
resolution
aldehydes.
However,
mechanism
factors
contributing
to
stereoselectivity
remain
unclear.
Herein,
by
using
quantum
chemical
calculations,
mechanisms
NCS-catalyzed
reactions
both
enantiomers
α-methyl-phenylacetaldehyde
are
studied.
The
calculations
reveal
a
mirroring
natural
substrates,
for
which
deprotonation
C5−H
cyclized
intermediate
is
rate-limiting.
calculated
overall
barriers
20.1
kcal
mol
-1
21.6
R
)-
S
)-α-methyl-phenylacetaldehyde,
respectively.
M97
L72
residues
proposed
be
key
stereospecificity.
obtained
detailed
information
helpful
designing
new
variants
NCS
extended
substrate
scope,
also
advancing
our
understanding
potential
applications.
ChemistryOpen,
Journal Year:
2024,
Volume and Issue:
13(7)
Published: Jan. 15, 2024
Abstract
The
acyltransferase
from
Pseudomonas
protegens
(
Pp
ATase)
catalyzes
in
nature
the
reversible
transformation
of
monoacetylphloroglucinol
to
diacetylphloroglucinol
and
phloroglucinol.
Interestingly,
this
enzyme
has
been
shown
catalyze
promiscuous
3‐hydroxyphenyl
acetate
2′,4′‐dihydroxyacetophenone,
representing
a
biological
version
Fries
rearrangement.
In
present
study,
we
report
mechanistic
investigation
activity
ATase
using
quantum
chemical
calculations.
A
detailed
mechanism
is
proposed,
energy
profile
for
reaction
presented.
calculations
show
that
acylation
highly
exothermic,
while
acetyl
transfer
back
substrate
only
slightly
exothermic.
deprotonation
C6−H
rate‐limiting,
remote
aspartate
residue
(Asp137)
proposed
be
general
base
group
step.
Analysis
binding
energies
various
acceptors
shows
can
promote
both
intramolecular
intermolecular
rearrangement
towards
diverse
compounds.
In
constructing
finite
models
of
enzyme
active
sites
for
use
in
quantum-chemical
calculations,
atoms
at
the
periphery
model
system
are
often
constrained
to
prevent
structural
collapse
during
geometry
relaxation.
A
simple
fixed-atom
or
``coordinate
lock''
approach
is
commonly
employed
but
leads
undesirable
artifacts
including
appearance
small
imaginary
frequencies.
These
preclude
evaluation
finite-temperature
free
energy
corrections,
limiting
thermochemical
calculations
enthalpies
only.
Full-dimensional
vibrational
frequency
possible
by
replacing
constraints
with
harmonic
confining
potentials,
and
here
we
compare
that
an
alternative
strategy
which
contributions
Hessian
simply
omitted.
While
does
eliminate
frequencies,
it
tends
underestimate
both
zero-point
entropy,
addition
artificial
rigidity
already
introduced
constraints.
Harmonic
potentials
frequencies
provide
a
flexible
means
construct
can
be
used
unconstrained
relaxations.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: March 1, 2024
ABSTRACT
The
artificial
metalloenzyme
(referred
to
as
Ir-Q
)
reported
by
Hartwig
and
coworkers
presented
an
important
milestone
in
merging
the
extraordinary
efficiency
of
biocatalyst
with
versatility
small
molecule
chemical
catalyst
catalyzing
a
new-to-nature
carbene
insertion
reaction.
enzyme
results
from
formal
replacement
Fe
Ir(Me)
moiety
along
four
C317G,
T213G,
L69V,
V254L
mutations
natural
Cytochrome
CYP119
directed
evolution
method.
Importantly,
this
is
show-stopper
it
exhibits
catalytic
rate
enhancement
similar
that
enzymes.
Despite
remarkable
discovery,
there
no
mechanistic
understanding
why
displays
efficiency,
so
far
been
intractable
experimental
methods.
In
study,
we
have
deciphered
‘catalytically
active
conformation’
using
large-scale
molecular
dynamics
simulations
rigorous
quantum
calculations.
Our
study
reveals
how
precisely
position
cofactor-substrate
unusual
orientation
within
reshaped
site
emerged
during
fostered
C−H…π
interactions
more
ordered
mutated
L69V
residues.
This
productive
conformation
correctly
reproduces
barrier
height
effect
2.7
kcal/mol,
excellent
agreement
observed
enhancement.
Moreover,
features
unprecedented
bonding
interaction
metal-carbene
species
preferentially
stabilizes
determining
formation
Iridium-Porphyrin
Carbene
intermediate
render
high
acceleration.
While
electrostatic
criteria
are
widely
established,
suggests
new
design
paradigm
towards
realization
fully
programmable
protein
catalysis.
Communications Chemistry,
Journal Year:
2024,
Volume and Issue:
7(1)
Published: March 27, 2024
Abstract
Norcoclaurine
synthase
from
Thalictrum
flavum
(
Tf
NCS)
demonstrated
high
stereospecificity
and
yield
in
catalyzing
the
Pictet-Spengler
reaction
of
dopamine
with
chiral
aldehydes,
achieving
kinetic
resolution
aldehydes.
However,
mechanism
factors
contributing
to
stereoselectivity
remain
unclear.
Herein,
by
using
quantum
chemical
calculations,
mechanisms
NCS-catalyzed
reactions
both
enantiomers
α-methyl-phenylacetaldehyde
are
studied.
The
calculations
reveal
a
mirroring
natural
substrates,
for
which
deprotonation
C5−H
cyclized
intermediate
is
rate-limiting.
calculated
overall
barriers
20.1
kcal
mol
-1
21.6
R
)-
S
)-α-methyl-phenylacetaldehyde,
respectively.
M97
L72
residues
proposed
be
key
stereospecificity.
obtained
detailed
information
helpful
designing
new
variants
NCS
extended
substrate
scope,
also
advancing
our
understanding
potential
applications.
