Effect of mutation on enzyme motion in dihydrofolate reductase

Hybrid quantum-classical molecular dynamics simulations of a mutant Escherichia coli dihydrofolate reductase enzyme are presented. Although residue 121 is on the exterior of the enzyme, experimental studies have shown that the mutation of Gly-121 to valine reduces the rate of hydride transfer by a factor of 163. The simulations indicate that the decrease in the hydride transfer rate for the G121V mutant is due to an increase in the free energy barrier. The calculated free energy barrier is higher for the mutant than for the wild-type enzyme by an amount that is consistent with the experimentally observed rate reduction. The calculated transmission coefficients are comparable for the wild-type and mutant enzymes. The simulations suggest that this mutation may interrupt a network of coupled promoting motions proposed to play an important role in DHFR catalysis. This phenomenon has broad implications for protein engineering and drug design.     

Preorganization and protein dynamics in enzyme catalysis

Recently, an alternative has been offered to the concept of transition state (TS) stabilization as an explanation for rate enhancements in enzyme-catalyzed reactions. Instead, most of the rate increase has been ascribed to preorganization of the enzyme active site to bind substrates in a geometry close to that of the TS, which then transit the activation barrier impelled by motions along the reaction coordinate. The question as to how an enzyme achieves such preorganization and concomitant TS stabilization as well as potential coupled motions along the reaction coordinate leads directly to the role of protein dynamic motion. Dihydrofolate reductase (DHFR) is a paradigm in which the role of dynamics in catalysis continues to be unraveled by a wealth of kinetic, structural, and computational studies. DHFR has flexible loop regions adjacent to the active site whose motions modulate passage through the kinetically preferred pathway. The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions. The general significance of protein dynamics in understanding other biological processes is briefly discussed.     

Comparison of coupled motions in Escherichia coli and Bacillus subtilis dihydrofolate reductase

Hybrid quantum/classical molecular dynamics simulations are used to compare the role of protein motion in the hydride transfer reaction catalyzed by Escherichia coli and Bacillus subtilis dihydrofolate reductase (DHFR). These two enzymes have 44% sequence identity, and the experimentally determined structures and hydride transfer rates are similar. The simulations indicate that the tertiary structures of both enzymes evolve in a similar manner during the hydride transfer reaction. In both enzymes, the donor-acceptor distance decreases to approximately 2.7 Angstroms at the transition state configurations to enable hydride transfer. Zero point energy and hydrogen tunneling effects are found to be significant for both enzymes. Covariance and rank correlation analyses of motions throughout the protein and ligands illustrate that E. coli and B. subtilis DHFR exhibit both similarities and differences in the equilibrium fluctuations and the conformational changes along the collective reaction coordinate for hydride transfer. A common set of residues that play a significant role in the network of coupled motions leading to configurations conducive to hydride transfer for both E. coli and B. subtilis DHFR was identified. These results suggest a balance between conservation and flexibility in the thermal motions and conformational changes during hydride transfer. Homologous protein structures, in conjunction with conformational sampling, enable enzymes with different sequences to catalyze the same hydride transfer reaction with similar efficiency.     

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically tuned to exchange on the millisecond time scale. The conformational changes of the protein backbone during catalysis were followed by (15)N nuclear spin relaxation dispersion experiments. A conformational transition that is well described by a two-state process with an exchange rate corresponding to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions on the time scale of catalytic turnover were not observed for the enzyme in the resting states, implying that alternative conformers do not accumulate to significant concentrations. These results infer that the turnover rate in glutaredoxin is governed by formation of a productive enzyme-substrate encounter complex, and that catalysis proceeds by an induced fit mechanism rather than by conformer selection driven by intrinsic conformational dynamics.     

Probing single-molecule enzyme active-site conformational state intermittent coherence

The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule fluorescence resonance energy transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single-molecule intensity-time trajectories of enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multistep conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.     

Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.     

Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects

The dynamical behavior and the temperature dependence of the kinetic isotope effects (KIEs) are examined for the proton-coupled electron transfer reaction catalyzed by the enzyme soybean lipoxygenase. The calculations are based on a vibronically nonadiabatic formulation that includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. The rate constant is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling and on time correlation functions of the energy gap and the proton donor-acceptor mode, which can be calculated from classical molecular dynamics simulations of the entire system. The dynamical behavior of the probability flux correlation function is dominated by the equilibrium protein and solvent motions and is not significantly influenced by the proton donor-acceptor motion. The magnitude of the overall rate is strongly influenced by the proton donor-acceptor frequency, the vibronic coupling, and the protein/solvent reorganization energy. The calculations reproduce the experimentally observed magnitude and temperature dependence of the KIE for the soybean lipoxygenase reaction without fitting any parameters directly to the experimental kinetic data. The temperature dependence of the KIE is determined predominantly by the proton donor-acceptor frequency and the distance dependence of the vibronic couplings for hydrogen and deuterium. The ratio of the overlaps of the hydrogen and deuterium vibrational wavefunctions strongly impacts the magnitude of the KIE but does not significantly influence its temperature dependence. For this enzyme reaction, the large magnitude of the KIE arises mainly from the dominance of tunneling between the ground vibronic states and the relatively large ratio of the overlaps between the corresponding hydrogen and deuterium vibrational wavefunctions. The weak temperature dependence of the KIE is due in part to the dominance of the local component of the proton donor-acceptor motion.     

Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

In recent papers, there has been a lively exchange concerning theories for enzyme catalysis, especially the role of protein dynamics/pre-chemistry conformational changes in the catalytic cycle of enzymes. Of particular interest is the notion that substrate-induced conformational changes that assemble the polymerase active site prior to chemistry are required for DNA synthesis and impact fidelity (i.e., substrate specificity). High-resolution crystal structures of DNA polymerase β representing intermediates of substrate complexes prior to the chemical step are available. These structures indicate that conformational adjustments in both the protein and substrates must occur to achieve the requisite geometry of the reactive participants for catalysis. We discuss computational and kinetic methods to examine possible conformational change pathways that lead from the observed crystal structure intermediates to the final structures poised for chemistry. The results, as well as kinetic data from site-directed mutagenesis studies, are consistent with models requiring pre-chemistry conformational adjustments in order to achieve high fidelity DNA synthesis. Thus, substrate-induced conformational changes that assemble the polymerase active site prior to chemistry contribute to DNA synthesis even when they do not represent actual rate-determining steps for chemistry.     

Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle

Many enzymes catalyze reactions with multiple chemical steps, requiring the stabilization of multiple transition states during catalysis. Such enzymes must strike a balance between the conformational reorganization required to stabilize multiple transition states of a reaction and the confines of a preorganized active site in the polypeptide tertiary structure. Here we investigate the compromise between structural reorganization during the catalytic process and preorganization of the active site for a multistep enzyme-catalyzed reaction, the hydrolysis of esters by the Ser-His-Asp/Glu catalytic triad. Quantum mechanical transition states were used to generate ensembles of geometries that can catalyze each individual step in the mechanism. These geometries are compared to each other by superpositions of catalytic atoms to find "consensus" geometries that can catalyze all steps with minimal rearrangement. These consensus geometries are found to be excellent matches for the natural active site. Preorganization is therefore found to be the major defining characteristic of the active site, and reorganizational motions often proposed to promote catalysis have been minimized. The variability of enzyme active sites observed by X-ray crystallography was also investigated empirically. A catalog of geometrical parameters relating active site residues to each other and to bound inhibitors was collected from a set of crystal structures. The crystal-structure-derived values were then compared to the ranges found in quantum mechanically optimized structures along the entire reaction coordinate. The empirical ranges are found to encompass the theoretical ranges when thermal fluctuations are taken into account. Therefore, the active sites are preorganized to a geometry that can be objectively and quantitatively defined as minimizing conformational reorganization while maintaining optimal transition state stabilization for every step during catalysis. The results provide a useful guiding principle for de novo design of enzymes with multistep mechanisms.     

Elastic network normal modes provide a basis for protein structure refinement

It is well recognized that thermal motions of atoms in the protein native state, the fluctuations about the minimum of the global free energy, are well reproduced by the simple elastic network models (ENMs) such as the anisotropic network model (ANM). Elastic network models represent protein dynamics as vibrations of a network of nodes (usually represented by positions of the heavy atoms or by the C(α) atoms only for coarse-grained representations) in which the spatially close nodes are connected by harmonic springs. These models provide a reliable representation of the fluctuational dynamics of proteins and RNA, and explain various conformational changes in protein structures including those important for ligand binding. In the present paper, we study the problem of protein structure refinement by analyzing thermal motions of proteins in non-native states. We represent the conformational space close to the native state by a set of decoys generated by the I-TASSER protein structure prediction server utilizing template-free modeling. The protein substates are selected by hierarchical structure clustering. The main finding is that thermal motions for some substates, overlap significantly with the deformations necessary to reach the native state. Additionally, more mobile residues yield higher overlaps with the required deformations than do the less mobile ones. These findings suggest that structural refinement of poorly resolved protein models can be significantly enhanced by reduction of the conformational space to the motions imposed by the dominant normal modes.     

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Enzyme-mediated catalysis is attributed to enzyme–substrate interactions, with models such as “induced fit” and “conformational selection” emphasizing the role of protein conformational transitions. The dynamic nature of the protein structure, thus, plays a crucial role in molecular recognition and substrate binding. As large-scale protein motions are coupled to water motions, hydration dynamics play a key role in protein dynamics, and hence, in enzyme catalysis. Here, microfluidic techniques and time-dependent fluorescence Stokes shift (TDFSS) measurements are employed to elucidate the role of nanoscopic water dynamics in the interaction of an enzyme, α-Chymotrypsin (CHT), with a substrate, Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) in the cationic reverse micelles of benzylhexadecyldimethylammonium chloride (BHDC/benzene) and anionic reverse micelles of sodium bis(2-ethylhexyl)sulfosuccinate (AOT/benzene). The kinetic pathways unraveled from the microfluidic setup are consistent with the “conformational selection” fit for the interaction of CHT with AMC in the cationic reverse micelles, whereas an “induced fit” mechanism is indicated for the anionic reverse micelles. In the cationic reverse micelles of BHDC, faster hydration dynamics (≈550 ps) aid the pathway of “conformational selection”, whereas in the anionic reverse micelles of AOT, the significantly slower dynamics of hydration (≈1600 ps) facilitate an “induced fit” mechanism for the formation of the final enzyme–substrate complex. The role of water dynamics in dictating the mechanism of enzyme–substrate interaction becomes further manifest in the neutral reverse micelles of Brij-30 and Triton X-100. In the former, the faster water dynamics aid the “conformational selection” pathway, whereas the significantly slower dynamics of water molecules in the latter are conducive to the “induced fit” mechanism in the enzyme–substrate interaction. Thus, nanoscopic water dynamics act as a switch in modulating the pathway of recognition of an enzyme (CHT) by the substrate (AMC) in reverse micelles.     

Single-molecule enzyme kinetics in the presence of inhibitors

Recent studies in single-molecule enzyme kinetics reveal that the turnover statistics of a single enzyme is governed by the waiting time distribution that decays as mono-exponential at low substrate concentration and multi-exponential at high substrate concentration. The multi-exponentiality arises due to protein conformational fluctuations, which act on the time scale longer than or comparable to the catalytic reaction step, thereby inducing temporal fluctuations in the catalytic rate resulting in dynamic disorder. In this work, we study the turnover statistics of a single enzyme in the presence of inhibitors to show that the multi-exponentiality in the waiting time distribution can arise even when protein conformational fluctuations do not influence the catalytic rate. From the Michaelis-Menten mechanism of inhibited enzymes, we derive exact expressions for the waiting time distribution for competitive, uncompetitive, and mixed inhibitions to quantitatively show that the presence of inhibitors can induce dynamic disorder in all three modes of inhibitions resulting in temporal fluctuations in the reaction rate. In the presence of inhibitors, dynamic disorder arises due to transitions between active and inhibited states of enzymes, which occur on time scale longer than or comparable to the catalytic step. In this limit, the randomness parameter (dimensionless variance) is greater than unity indicating the presence of dynamic disorder in all three modes of inhibitions. In the opposite limit, when the time scale of the catalytic step is longer than the time scale of transitions between active and inhibited enzymatic states, the randomness parameter is unity, implying no dynamic disorder in the reaction pathway.     

A theoretical study on the detection of proton transfer pathways in some mutants of human carbonic anhydrase II

Structural and kinetic studies of mutants can give much insight into the function of an enzyme. We report the detection of possible proton transfer pathways into the active site of a number of mutants of the enzyme human carbonic anhydrase II (HCA II). Using a recently developed method of path search in the protein conformational space, we identify hydrogen-bonded networks (or proton paths) that can dynamically connect the protein surface to the active site through fluctuations in protein structure and hydration. The feasibility of establishing such dynamical connectivities is assessed by computing the change in free energy of conformational fluctuations and compared to those identified earlier in the wild type enzyme. It is found that the point mutation facilitates or suppresses one or more of the alternative pathways. Our results allow the use of a generic set of pathways to correlate qualitatively the residual activity in the mutants to the molecular mechanism of proton transfer in the absence of His at position 64. We also demonstrate how the detected pathways may be used to compare the efficiencies of the mutants His-64-Ala/Asn-62-His and His-64-Ala/Asn-67-His using the empirical valence bond theory.     

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Representing and selecting vibrational angular momentum states for quasiclassical trajectory chemical dynamics simulations

Linear molecules with degenerate bending modes have states, which may be represented by the quantum numbers N and L. The former gives the total energy for these modes and the latter identifies their vibrational angular momentum jz. In this work, the classical mechanical analog of the N,L-quantum states is reviewed, and an algorithm is presented for selecting initial conditions for these states in quasiclassical trajectory chemical dynamics simulations. The algorithm is illustrated by choosing initial conditions for the N = 3 and L = 3 and 1 states of CO2. Applications of this algorithm are considered for initial conditions without and with zero-point energy (zpe) included in the vibrational angular momentum states and the C-O stretching modes. The O-atom motions in the x,y-plane are determined for these states from classical trajectories in Cartesian coordinates and are compared with the motion predicted by the normal-mode model. They are only in agreement for the N = L = 3 state without vibrational angular momentum zpe. For the remaining states, the Cartesian O-atom motions are considerably different from the elliptical motion predicted by the normal-mode model. This arises from bend-stretch coupling, including centrifugal distortion, in the Cartesian trajectories, which results in tubular instead of elliptical motion. Including zpe in the C-O stretch modes introduces considerable complexity into the O-atom motions for the vibrational angular momentum states. The short-time O-atom motions for these trajectories are highly irregular and do not appear to have any identifiable characteristics. However, the O-atom motions for trajectories integrated for substantially longer period of times acquire unique properties. With C-O stretch zpe included, the long-time O-atom motion becomes tubular for trajectories integrated to approximately 14 ps for the L = 3 states and to approximately 44 ps for the L = 1 states.     

Protein motions promote catalysis

A relationship between molecular dynamics motions of noncatalytic residues and enzyme activity has recently been proposed. We present examples where mutations either near or distal from the active site residues modify internal enzyme motion with resulting modification of catalysis. A better understanding of internal protein motions correlated to catalysis will lead to a greater insight into enzyme function.     

Influences of Quantum Mechanically Mixed Electronic and Vibrational Pigment States in 2D Electronic Spectra of Photosynthetic Systems: Strong Electronic Coupling Cases

In 2D electronic spectroscopy studies, long‐lived quantum beats have recently been observed in photosynthetic systems, and several theoretical studies have suggested that the beats are produced by quantum mechanically mixed electronic and vibrational states. Concerning the electronic‐vibrational quantum mixtures, the impact of protein‐induced fluctuations was examined by calculating the 2D electronic spectra of a weakly coupled dimer with the Franck‐Condon active vibrational modes in the resonant condition [Fujihashi et al., J. Chem. Phys.­ 2015 , 142, 212403.]. This analysis demonstrated that quantum mixtures of the vibronic resonance are rather robust under the influence of the fluctuations at cryogenic temperatures, whereas the mixtures are eradicated by the fluctuations at physiological temperatures. However, this conclusion cannot be generalized because the magnitude of the coupling inducing the quantum mixtures is proportional to the inter‐pigment electronic coupling. In this study, we explore the impact of the fluctuations on electronic‐vibrational quantum mixtures in a strongly coupled dimer with an off‐resonant vibrational mode. Toward this end, we calculate energy transfer dynamics and 2D electronic spectra of a model dimer that corresponds to the most strongly coupled bacteriochlorophyll molecules in the Fenna‐Matthews‐Olson complex in a numerically accurate manner. The quantum mixtures are found to be robust under the exposure of protein‐induced fluctuations at cryogenic temperatures, irrespective of the resonance. At 300 K, however, the quantum mixing is disturbed more strongly by the fluctuations, and therefore, the beats in the 2D spectra become obscure even in a strongly coupled dimer with a resonant vibrational mode. Further, the overall behaviors of the energy transfer dynamics are demonstrated to be dominated by the environment and coupling between the 0 0 vibronic transitions as long as the Huang‐Rhys factor of the vibrational mode is small. The electronic‐vibrational quantum mixtures do not necessarily play a significant role in electronic energy transfer dynamics despite contributing to the enhancement of long‐lived quantum beating in the 2D spectra.     

Revealing time bunching effect in single-molecule enzyme conformational dynamics

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a cross correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis.     

Freezing a single distal motion in dihydrofolate reductase

Constraining a single motion between distal residues separated by approximately 28 A in hybrid quantum/classical molecular dynamics simulations is found to increase the free energy barrier for hydride transfer in dihydrofolate reductase by approximately 3 kcal/mol. Our analysis indicates that a single distal constraint alters equilibrium motions throughout the enzyme on a wide range of time scales. This alteration of the conformational sampling of the entire system is sufficient to significantly increase the free energy barrier and decrease the rate of hydride transfer. Despite the changes in conformational sampling introduced by the constraint, the system assumes a similar transition state conformation with a donor-acceptor distance of approximately 2.72 A to enable the hydride transfer reaction. The modified thermal sampling leads to a substantial increase in the average donor-acceptor distance for the reactant state, however, thereby decreasing the probability of sampling the transition state conformations with the shorter distances required for hydride transfer. These simulations indicate that fast thermal fluctuations of the enzyme, substrate, and cofactor lead to conformational sampling of configurations that facilitate hydride transfer. The fast thermal motions are in equilibrium as the reaction progresses along the collective reaction coordinate, and the overall average equilibrium conformational changes occur on the slower time scale measured experimentally. Recent single molecule experiments suggest that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time scale of the hydride transfer reaction. Thus, introducing a constraint that modifies the conformational sampling of an enzyme could significantly impact its catalytic activity.