31 research outputs found
A Critical Test of the “Tunneling and Coupled Motion” Concept in Enzymatic Alcohol Oxidation
The physical mechanism
of C–H bond activation by enzymes
is the subject of intense study, and we have tested the predictions
of two competing models for C–H activation in the context of
alcohol dehydrogenase. The kinetic isotope effects (KIEs) in this
enzyme have previously suggested a model of quantum mechanical tunneling
and coupled motion of primary (1°) and secondary (2°) hydrogens.
Here we measure the 2° H/T KIEs with both H and D at the 1°
position and find that the 2° KIE is significantly deflated with
D-transfer, consistent with the predictions of recent Marcus-like
models of H-transfer. The results suggest that the fast dynamics of
H-tunneling result in a 1° isotope effect on the structure of
the tunneling ready state: the trajectory of D-transfer goes through
a shorter donor–acceptor distance than that of H-transfer
Noncovalent Intermediate of Thymidylate Synthase: Fact or Fiction?
Thymidylate
synthase is an attractive target for antibiotic and
anticancer drugs due to its essential role in the <i>de novo</i> biosynthesis of the DNA nucleotide thymine. The enzymatic reaction
is initiated by a nucleophilic activation of the substrate via formation
of a covalent bond to an active site cysteine. The traditionally accepted
mechanism is then followed by a series of covalently bound intermediates,
where that bond is only cleaved upon product release. Recent computational
and experimental studies suggest that the covalent bond between the
protein and substrate is actually quite labile. Importantly, these
findings predict the existence of a noncovalently bound bisubstrate
intermediate, not previously anticipated, which could be the target
of a novel class of drugs inhibiting DNA biosynthesis. Here we report
the synthesis of the proposed intermediate and findings supporting
its chemical and kinetic competence. These findings substantiate the
predicted nontraditional mechanism and the potential of this intermediate
as a new drug lead
Network of Remote and Local Protein Dynamics in Dihydrofolate Reductase Catalysis
Molecular
dynamics calculations and bionformatic studies of dihydrofolate
reductase (DHFR) have suggested a network of coupled motions across
the whole protein that is correlated to the reaction coordinate. Experimental
studies demonstrated that distal residues G121, M42, and F125 in E. coli DHFR participate in that network. The missing
link in our understanding of DHFR catalysis is the lack of a mechanism
by which such remote residues can affect the catalyzed chemistry at
the active site. Here, we present a study of the temperature dependence
of intrinsic kinetic isotope effects (KIEs) that indicates synergism
between a remote residue in that dynamic network, G121, and the active
site’s residue I14. The intrinsic KIEs for the I14A–G121V
double mutant showed steeper temperature dependence (Δ<i>E</i><sub>a(T‑H)</sub>) than expected from comparison
of the wild type and two single mutants. That effect was nonadditive
(i.e., Δ<i>E</i><sub>a(T‑H) G121V</sub> + Δ<i>E</i><sub>a(T‑H) I14A</sub> <
Δ<i>E</i><sub>a(T‑H) double mutant</sub>), which indicates a synergism between the two residues. This finding
links the remote residues in the network under investigation to the
enzyme’s active site, providing a mechanism by which these
residues can be coupled to the catalyzed chemistry. This experimental
evidence validates calculations proposing that both remote and active
site residues constitute a network of coupled promoting motions correlated
to the bond activation step (C–H → C hydride transfer
in this case). Additionally, the effect of I14A and G121V mutations
on single turnover rates was additive rather than synergistic. Although
single turnover rate measurements are more readily available and thus
more popular than assessing intrinsic KIEs, the current finding demonstrates
that these rates, which in DHFR reflect several microscopic rate constants,
can fall short of revealing the nature of the C–H bond activation
per se
Hydrogen Donor–Acceptor Fluctuations from Kinetic Isotope Effects: A Phenomenological Model
Kinetic isotope effects (KIEs) and their temperature
dependence
can probe the structural and dynamic nature of enzyme-catalyzed proton
or hydride transfers. The molecular interpretation of their temperature
dependence requires expensive and specialized quantum mechanics/molecular
mechanics (QM/MM) calculations to provide a quantitative molecular
understanding. Currently available phenomenological models use a nonadiabatic
assumption that is not appropriate for most hydride and proton-transfer
reactions, while others require more parameters than the experimental
data justify. Here we propose a phenomenological interpretation of
KIEs based on a simple method to quantitatively link the size and
temperature dependence of KIEs to a conformational distribution of
the catalyzed reaction. This model assumes adiabatic hydrogen tunneling,
and by fitting experimental KIE data, the model yields a population
distribution for fluctuations of the distance between donor and acceptor
atoms. Fits to data from a variety of proton and hydride transfers
catalyzed by enzymes and their mutants, as well as nonenzymatic reactions,
reveal that steeply temperature-dependent KIEs indicate the presence
of at least two distinct conformational populations, each with different
kinetic behaviors. We present the results of these calculations for
several published cases and discuss how the predictions of the calculations
might be experimentally tested. This analysis does not replace molecular
QM/MM investigations, but it provides a fast and accessible way to
quantitatively interpret KIEs in the context of a Marcus-like model
Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase
The optimal description of the reaction coordinate in
chemical
systems is of great importance in simulating condensed phase reactions.
In the current work, we present a collective reaction coordinate which
is composed of several geometric coordinates which represent structural
progress during the course of a hydride transfer reaction: the antisymmetric
reactive stretch coordinate, the donor–acceptor distance (DAD)
coordinate, and an orbital rehybridization coordinate. In this approach,
the former coordinate serves as a distinguished reaction coordinate,
while the latter two serve as environmental, Marcus-type inner-sphere
reorganization coordinates. The classical free energy surface is obtained
from multidimensional quantum mechanics–molecular mechanics
(QM/MM) potential of mean force (PMF) simulations in conjunction with
a general and efficient multidimensional weighted histogram method
implementation. The minimum free energy path, or the collective reaction
coordinate, connecting the dividing hypersurface to reactants and
products, is obtained using an iterative scheme. In this approach,
the string method is used to find the minimum free energy path. This
path guides the multidimensional sampling, while the path is adaptively
refined until convergence is achieved. As a model system, we choose
the hydride transfer reaction in Escherichia coli dihydrofolate reductase (<i>ec</i>DHFR) using a recently
developed accurate semiempirical potential energy surface. To estimate
the advantages of the collective reaction coordinate, we perform activated
dynamics simulations to obtain the reaction transmission coefficient.
The results show that the combination of a distinguished reaction
coordinate and an inner-sphere reorganization coordinate considerably
reduces the dividing surface recrossing
Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase
The optimal description of the reaction coordinate in
chemical
systems is of great importance in simulating condensed phase reactions.
In the current work, we present a collective reaction coordinate which
is composed of several geometric coordinates which represent structural
progress during the course of a hydride transfer reaction: the antisymmetric
reactive stretch coordinate, the donor–acceptor distance (DAD)
coordinate, and an orbital rehybridization coordinate. In this approach,
the former coordinate serves as a distinguished reaction coordinate,
while the latter two serve as environmental, Marcus-type inner-sphere
reorganization coordinates. The classical free energy surface is obtained
from multidimensional quantum mechanics–molecular mechanics
(QM/MM) potential of mean force (PMF) simulations in conjunction with
a general and efficient multidimensional weighted histogram method
implementation. The minimum free energy path, or the collective reaction
coordinate, connecting the dividing hypersurface to reactants and
products, is obtained using an iterative scheme. In this approach,
the string method is used to find the minimum free energy path. This
path guides the multidimensional sampling, while the path is adaptively
refined until convergence is achieved. As a model system, we choose
the hydride transfer reaction in Escherichia coli dihydrofolate reductase (<i>ec</i>DHFR) using a recently
developed accurate semiempirical potential energy surface. To estimate
the advantages of the collective reaction coordinate, we perform activated
dynamics simulations to obtain the reaction transmission coefficient.
The results show that the combination of a distinguished reaction
coordinate and an inner-sphere reorganization coordinate considerably
reduces the dividing surface recrossing
Substrate Activation in Flavin-Dependent Thymidylate Synthase
Thymidylate is a critical DNA nucleotide
that has to be synthesized
in cells <i>de novo</i> by all organisms. Flavin-dependent
thymidylate synthase (FDTS) catalyzes the final step in this <i>de novo</i> production of thymidylate in many human pathogens,
but it is absent from humans. The FDTS reaction proceeds via a chemical
route that is different from its human enzyme analogue, making FDTS
a potential antimicrobial target. The chemical mechanism of FDTS is
still not understood, and the two most recently proposed mechanisms
involve reaction intermediates that are unusual in pyrimidine biosynthesis
and biology in general. These mechanisms differ in the relative timing
of the reaction of the flavin with the substrate. The consequence
of this difference is significant: the intermediates are cationic
in one case and neutral in the other, an important consideration in
the construction of mechanism-based enzyme inhibitors. Here we test
these mechanisms via chemical trapping of reaction intermediates,
stopped-flow, and substrate hydrogen isotope exchange techniques.
Our findings suggest that an initial activation of the pyrimidine
substrate by reduced flavin is required for catalysis, and a revised
mechanism is proposed on the basis of previous and new data. These
findings and the newly proposed mechanism add an important piece to
the puzzle of the mechanism of FDTS and suggest a new class of intermediates
that, in the future, may serve as targets for mechanism-based design
of FDTS-specific inhibitors
QM/MM Calculations Suggest a Novel Intermediate Following the Proton Abstraction Catalyzed by Thymidylate Synthase
The
cleavage of covalent C–H bonds is one of the most energetically
demanding, yet biologically essential, chemical transformations. Two
C–H bond cleavages are involved in the reaction catalyzed by
thymidylate synthase (TSase), which provides the sole <i>de novo</i> source of thymidylate (i.e., the DNA base T) for most organisms.
Our QM/MM free energy calculations show that the C–H →
O proton transfer has three transition states that are energetically
similar but structurally diverse. These characteristics are different
from our previous calculation results on the C–H → C
hydride transfer, providing an explanation for differences in temperature
dependences of KIEs on these two C–H bond activation steps.
The calculations also suggest that the traditionally proposed covalent
bond between the protein and substrate (the C6–S bond) is very
labile during the multistep catalytic reaction. Collective protein
motions not only assist cleavage of the C6–S bond to stabilize
the transition state of the proton transfer step but also rearrange
the H-bond network at the end of this step to prepare the active site
for subsequent chemical steps. These computational results illustrate
functionalities of specific protein residues that reconcile many previous
experimental observations and provide guidance for future experiments
to examine the proposed mechanisms. The synchronized conformational
changes in the protein and ligands observed in our simulations demonstrate
participation of protein motions in the reaction coordinate of enzymatic
reactions. Our computational findings suggest the existence of new
reaction intermediates not covalently bound to TSase, which may lead
to a new class of drugs targeting DNA biosynthesis
Extension and Limits of the Network of Coupled Motions Correlated to Hydride Transfer in Dihydrofolate Reductase
Enzyme catalysis
has been studied extensively, but the role of
enzyme dynamics in the catalyzed chemical conversion is still an enigma.
The enzyme dihydrofolate reductase (DHFR) is often used as a model
system to assess a network of coupled motions across the protein that
may affect the catalyzed chemical transformation. Molecular dynamics
simulations, quantum mechanical/molecular mechanical studies, and
bioinformatics studies have suggested the presence of a “global
dynamic network” of residues in DHFR. Earlier studies of two
DHFR distal mutants, G121V and M42W, indicated that these residues
affect the chemical step synergistically. While this finding was in
accordance with the concept of a network of functional motions across
the protein, two residues do not constitute a network. To better define
the extent and limits of the proposed network, the current work studied
two remote residues predicted to be part of the same network: W133
and F125. The effect of mutations in these residues on the nature
of the chemical step was examined via measurements of the temperature-dependence
of the intrinsic kinetic isotope effects (KIEs) and other kinetic
parameters, and double mutants were used to tie the findings to G121
and M42. The findings indicate that residue F125, which was implicated
by both calculations and bioinformatic methods, is a part of the same
global dynamic network as G121 and M42, while W133, implicated only
by bioinformatics, is not. These findings extend our understanding
of the proposed network and the relations between functional and genomic
couplings. Delineating that network illuminates the need to consider
remote residues and protein structural dynamics in the rational design
of drugs and of biomimetic catalysts
How Accurate Are Transition States from Simulations of Enzymatic Reactions?
The rate expression of traditional
transition state theory (TST)
assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium
between the ground state and the TS. Currently, it is not well understood
to what extent these assumptions influence the nature of the activated
complex obtained in traditional TST-based simulations of processes
in the condensed phase in general and in enzymes in particular. Here
we scrutinize these assumptions by characterizing the TSs for hydride
transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches.
Specifically, we compare the TSs obtained with common TST-based methods
and a dynamics-based method. Using a recently developed accurate hybrid
quantum mechanics/molecular mechanics potential, we find that the
TST-based and dynamics-based methods give considerably different TS
ensembles. This discrepancy, which could be due equilibrium solvation
effects and the nature of the reaction coordinate employed and its
motion, raises major questions about how to interpret the TSs determined
by common simulation methods. We conclude that further investigation
is needed to characterize the impact of various TST assumptions on
the TS phase-space ensemble and on the reaction kinetics