Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

Computer simulations of the temperature dependence of enzyme reactions using the empirical valence bond (EVB) method have proven to give very accurate results in terms of the thermodynamic activation parameters. Here, we analyze the reasons for why such simulations are able to correctly capture activation enthalpies and entropies and how sensitive these quantities are to parametrization of the reactive potential energy function. We examine first the solution reference reaction for the enzyme ketosteroid isomerase, which corresponds to the acetate catalyzed deprotonation of the steroid in water. The experimentally determined activation parameters for this reaction turn out to be remarkably well reproduced by the calculations. By modifying the EVB potential so that the activation and reaction free energies become significantly shifted, we show that the activation entropy is basically invariant to such changes and that ΔS⧧ is instead determined by the specific mixture of the underlying force fields in the transition state region. The coefficients of this mixture do not change appreciably when the EVB potential is modified within reasonable limits, and hence, the estimate of ΔS⧧ becomes very robust. This is further verified by examining a more complex concerted hydride and proton transfer reaction in the enzyme hydroxybutyrate dehydrogenase.

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

Reusable HNO Sensors Derived from Cu Cyclam: A DFT Study on the Mechanistic Origin of High Reactivity and Favorable Conformation Changes and Potential Improvements

Nitroxyl (HNO) exhibits unique favorable properties in regulating biological and pharmacological activities. However, currently, there is only one Cu-based HNO sensor that can be recycled for reusable detection, which is a Cu cyclam derivative with a mixed thia/aza ligand. To elucidate the missing mechanistic origin of its high HNO reactivity and subsequent favorable conformation change toward a stable CuI product that is critical to be oxidized back by the physiological O2 level for HNO detection again, a density functional theory (DFT) computational study was performed. It not only reproduced experimental structural and reaction properties but also, more importantly, revealed an unknown role of the coordination atom in high reactivity. Its conformation change mechanism was found to not follow the previously proposed one but involve a novel favorable rotation pathway. Several newly designed complexes incorporating beneficial effects of coordination atoms and substituents to further enhance HNO reactivity while maintaining or even improving favorable conformation changes for reusable HNO detection were computationally validated. These novel results will facilitate the future development of reusable HNO sensors for true spatiotemporal resolution and repeated detection.

Pyridinium-Inspired Organocatalysts for Carbon Dioxide Fixation: A Density Functional Theory Inspection

The current project aims to apply the virtues of minimalism to examine the catalytic ability of commercially organic compounds of small chemical structures to catalyze the coupling reaction between carbon dioxide and propylene oxide (PO) under mild conditions. The proposed catalysts are pyridinium iodide (A), 2-hydroxypyridinium iodide (B), and piperidinium iodide (C), where their structure is based on cooperative acidic and nucleophilic motifs. The quantum chemistry model, M062X-D3/def2-TZVP//M062X-D3/def2-SVPP, was used to understand the reaction mechanism and the catalytic performance. Since the coupling reaction was performed under excess PO, we proposed that PO serves as a reactant and solvent. Therefore, calculations were performed in gas and liquid phases for comparison. The findings indicated that the rate-determining step depends on the chemical structure of the catalyst and whether the phase is a gas or liquid phase. In general, modeling in the liquid phase produces potential energy surfaces of lower energy barriers. The noncovalent interactions reflect the role of hydrogen bonding in controlling the kinetic behavior of the coupling reaction. Based on the finding, catalyst A is the best candidate for transforming CO₂ into cyclic carbonates.

Mechanistic Origin of Favorable Substituent Effects in Excellent Cu Cyclam Based HNO Sensors

HNO has broad chemical and biomedical properties. Metal complexes and derivatives are widely used to make excellent HNO sensors. However, their favorable mechanistic origins are largely unknown. Cu cyclam is a useful platform to make excellent HNO sensors including imaging agents. A quantum chemical study of Cu cyclams with various substitutions was performed, which reproduced diverse experimental reactivities. Structural, electronic, and energetic profiles along reaction pathways show the importance of HNO binding and a proton-coupled electron transfer mechanism for HNO reaction. Results reveal that steric effect is primary and electronic factor is secondary (if the redox potential is sufficient), but their interwoven effects can lead to unexpected reactivity, which looks mysterious experimentally but can be explained computationally. This work suggests rational substituent design ideas and recommends a theoretical study of a new design to save time and cost due to its subtle effect.

Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

It has been suggested that heat capacity changes in enzyme catalysis may be the underlying reason for temperature optima that are not related to unfolding of the enzyme. If this were to be a common phenomenon, it would have major implications for our interpretation of enzyme kinetics. In most cases, the support for the possible existence of a nonzero (negative) activation heat capacity, however, only relies on fitting such a kinetic model to experimental data. It is therefore of fundamental interest to try to use computer simulations to address this issue. One way is simply to calculate the temperature dependence of the activation free energy and determine whether the relationship is linear or not. An alternative approach is to calculate the absolute heat capacities of the reactant and transition states from plain molecular dynamics simulations using either the temperature derivative or fluctuation formula for the enthalpy. Here, we examine these different approaches for a designer enzyme with a temperature optimum that is not caused by unfolding. Benchmark calculations for the heat capacity of liquid water are first carried out using different thermostats. It is shown that the derivative formula for the heat capacity is generally the most robust and insensitive to the thermostat used and its parameters. The enzyme calculations using this method give results in agreement with direct calculations of activation free energies and show no sign of a negative activation heat capacity. We also provide a simple scheme for the calculation of binding heat capacity changes, which is of clear interest in ligand design, and demonstrate it for substrate binding to the designer enzyme. Neither in that case do the simulations predict any negative heat capacity change.

A novel PdC monolayer with fully dispersed Pd atoms and a rigid carbon backbone: an intrinsic versatile electrocatalyst for overall water splitting and the corresponding reverse reaction

The electrocatalytic overall water splitting and the corresponding reverse reaction play a vital role in future renewable energy systems and, hence, are frontiers of catalysis research. In this work, we identify a heretofore unknown two-dimensional palladium carbide using the structure swarm intelligence algorithm. The proposed monolayer, named α-PdC, consists of fully dispersed Pd atoms and a rigid carbon backbone, exhibiting high mechanical, dynamical, and thermal stability with desirable electrical conductivity. Further calculations show that the proposed monolayer is an intrinsic multifunctional electrocatalyst. It possesses an excellent catalytic performance toward the hydrogen evolution reaction (HER), the oxygen evolution reaction (OER), and the oxygen reduction reaction (ORR) with low overpotentials. Specifically, the overpotential for the HER is only -0.01 V, and the significantly low activation energy barrier (0.16 eV) on α-PdC elucidates the fast kinetics. Moreover, α-PdC could also be highly active towards the OER and ORR with comparable overpotentials (0.38 and 0.27 V, respectively). This study identifies an intrinsic versatile electrocatalyst with potential applications in the fields of energy conversion and storage.

ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments

The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by characterizing the Bacillus pumilus LipA enzyme. Our results for the lipase show that the enzyme is psychrotolerant, with an activation energy of 15.3 kcal/mol for the chromogenic substrate para-nitrophenyl butyrate. Our results demonstrate that this can produce equivalent curves to the traditional approach while requiring significantly less sample, labour and time. Our method is further validated by characterizing three α-amylases from different species and habitats. The experiments with the α-amylases show that the approach works over a wide range of temperatures and clearly differentiates between psychrophilic, mesophilic and thermophilic enzymes. The methodology is released as an open-source implementation in Python, available online or used locally. This method of determining the activation parameters can make studies of the temperature dependence of enzyme catalysis more widely adapted to understand how enzymes have evolved to function in extreme environments. Moreover, the thermodynamic parameters that are estimated serve as functional validations of the empirical valence bond calculations of enzyme catalysis.

Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis

The existence of temperature optima in enzyme catalysis that occur before protein melting sets in can be described by different types of kinetic models. Such optima cause distinctly curved Arrhenius plots and have, for example, been observed in several cold-adapted enzymes from psychrophilic species. The two main explanations proposed for this behavior either invoke conformational equilibria with inactive substrate-bound states or postulate differences in heat capacity between the reactant and transition states. Herein, we analyze the implications of the different types of kinetic models in terms of apparent activation enthalpies, entropies, and heat capacities, using the catalytic reaction of a cold-adapted α-amylase as a prototypic example. We show that the behavior of these thermodynamic activation parameters is fundamentally different between equilibrium and heat capacity models, and in the α-amylase case, computer simulations have shown the former model to be correct. A few other enzyme-catalyzed reactions are also discussed in this context.

Comparison of Free-Energy Methods to Calculate the Barriers for the Nucleophilic Substitution of Alkyl Halides by Hydroxide

Calculating the free-energy barriers of liquid-phase chemical reactions with explicit solvent is a considerable challenge. Most studies use the energy and entropy of minimized single-point geometries of the reactants and transition state in implicit solvent using normal mode analysis (NMA). Explicit-solvent methods instead make use of the potential of mean force (PMF). Here, we propose a new energy-entropy (EE) method to calculate the Gibbs free energy of reactants and transition states in explicit solvent by combining quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations with multiscale cell correlation (MCC). We apply it to six nucleophilic substitution reactions of the hydroxide transfer to methyl and ethyl halides in water, where the halides are F, Cl, and Br. We compare EE-MCC Gibbs free energy barriers using two Hamiltonians, self-consistent charge density functional based tight-binding (SCC-DFTB) and B3LYP/6-31+G* density functional theory (DFT) with respective PMF values, EE-NMA values using B3LYP/6-31+G* and M06/6-31+G* DFT in implicit solvent and experimental values derived via transition state theory. The barriers using SCC-DFTB are found to agree well with the PMF and experiment and previous computational studies, being slightly higher but improving on the lower values obtained for the implicit solvent. Achieving convergence over many degrees of freedom remains a challenge for EE-MCC in explicit-solvent QM/MM systems, particularly for the more expensive B3LYP/6-31+G* and M06/6-31+G* DFT methods, but the insightful decomposition of entropy over all degrees of freedom should make EE-MCC a valuable tool for deepening the understanding of chemical reactions.

Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening

Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this system particularly challenging to optimize. Yet, experimental screening of a small number of active-site variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (∼2 × 104 M-1 s-1 and ∼102 s-1) for this anthropogenic reaction that compare favorably to those of modern natural enzymes. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, even on scaffolds that were not originally evolved for those functions, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ∼2 kcal mol-1 and indicate that the enhanced activity is linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by computational predictions of catalytic activity, as a generalized approach for computational enzyme design.

A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion

The regio- (and stereo-)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction(s). The accessibility of potential SOMs depends on the relative binding free energy (ΔΔGbind ) of the catalytically active substrate-binding poses, and the probability of the substrate to adopt a transition-state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multistep P450-catalyzed processes that involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multiproduct enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔGbind values, and collision entropies, yielding direct insight into the basis of selectivity in substrate conversion.

Direct oxide transfer from an η2-keto ligand to generate a cobalt PCcarbeneP(O) pincer complex

We report the direct carbonyl cleavage in a κ³-P′,(η²-C,O),P′′ ligand by a monomeric cobalt centre through metal–ligand cooperativity.

Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase fromPseudomonas aeruginosa(PchB)

The substrate preorganization process in the entropically driven PchB-catalyzed chorismate mutase reaction leads to a remarkable apparent entropic effect.

Catalyst free boron carbon bond cleavage and facile formation of five-membered PNBCC heterocycles

The [3 + 2] cycloaddition reaction of phosphanyl aminoborane [N(2,6-iPr₂C₆H₃)(PPh₂)(BCy₂)] (1) with activated alkynes led to boron and phosphorus containing five-membered heterocycles [(2,6-iPr₂C₆H₃)NPPh₂(CO₂R)C-C(Cy)(CO₂R)(BCy)] [R = Me (2), Et (3) and H (4)] with facile cleavage of the B-C bond and concomitant formation of a P-C bond with an ylidic character. DFT calculations indicate that 1 can be considered as a non-conjugated 1,3-dipole having two reaction centers viz., a nucleophilic P-center and an electrophilic B-center. The reaction of 1 with the alkynes proceeds through a stepwise dipolar addition mechanism, followed by the migration of the cyclohexyl group from the B-atom to the adjacent C-atom.

Cold Adaptation of Triosephosphate Isomerase

The main problem for enzymes from psychrophilic species, which need to work near the freezing point of liquid water, is the exponential decay of reaction rates as the temperature is decreased. Cold-adapted enzymes have solved this problem by shifting the activation enthalpy-entropy balance for the catalyzed reaction compared to those of their mesophilic orthologs. To understand the structural basis of this universal feature, it is necessary to examine pairs of such orthologous enzymes, with known three-dimensional structures, at the microscopic level. Here, we use molecular dynamics free energy calculations in combination with the empirical valence bond method to evaluate the temperature dependence of the activation free energy for differently adapted triosephosphate isomerases. The results show that the enzyme from the psychrophilic bacterium Vibrio marinus indeed displays the characteristic shift in enthalpy-entropy balance, compared to that of the yeast ortholog. The origin of this effect is found to be located in a few surface-exposed protein loops that show differential mobilities in the two enzymes. Key mutations render these loops more mobile in the cold-adapted triosephosphate isomerase, which explains both the reduced activation enthalpy contribution from the protein surface and the lower thermostability.

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.

Reaction Mechanism of Covalent Modification of Phosphatidylethanolamine Lipids by Reactive Aldehydes 4-Hydroxy-2-nonenal and 4-Oxo-2-nonenal

4-Hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) are biologically important reactive aldehydes formed during oxidative stress in phospholipid bilayers. They are highly reactive species due to presence of several reaction centers and can react with amino acids in peptides and proteins, as well as phosphoethanolamine (PE) lipids, thus modifying their biological activity. The aim of this work is to study in a molecular detail the reactivity of HNE and ONE toward PE lipids in a simplified system containing only lipids and reactive aldehydes in dichloromethane as an inert solvent. We use a combination of quantum chemical calculations, ¹H NMR measurements, FT-IR spectroscopy, and mass spectrometry experiments and show that for both reactive aldehydes two types of chemical reactions are possible: formation of Michael adducts and Schiff bases. In the case of HNE, an initially formed Michael adduct can also undergo an additional cyclization step to a hemiacetal derivative, whereas no cyclization occurs in the case of ONE and a Michael adduct is identified. A Schiff base product initially formed when HNE is added to PE lipid can also further cyclize to a pyrrole derivative in contrast to ONE, where only a Schiff base product is isolated. The suggested reaction mechanism by quantum-chemical calculations is in a qualitative agreement with experimental yields of isolated products and is also additionally investigated by ¹H NMR measurements, FT-IR spectroscopy, and mass spectrometry experiments.

Entropy and Enzyme Catalysis

The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼10⁷ compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis. Another remarkable instance of entropic effects is found in enzymes that are adapted by evolution to work at low temperatures, near the freezing point of water. These cold-adapted enzymes invariably show a more negative entropy and a lower enthalpy of activation than their mesophilic orthologs, which counteracts the exponential damping of reaction rates at lower temperature. The structural origin of this universal phenomenon has, however, remained elusive. The basic problem with connecting macroscopic thermodynamic quantities, such as activation entropy and enthalpy derived from Arrhenius plots, to the 3D protein structure is that the underlying detailed (microscopic) energetics is essentially inaccessible to experiment. Moreover, attempts to calculate entropy contributions by computer simulations have mostly focused only on substrate entropies, which do not provide the full picture. We have recently devised a new approach for accessing thermodynamic activation parameters of both enzyme and solution reactions from computer simulations, which turns out to be very successful. This method is analogous to the experimental Arrhenius plots and directly evaluates the temperature dependence of calculated reaction free energy profiles. Hence, by extensive molecular dynamics simulations and calculations of up to thousands of independent free energy profiles, we are able to extract activation parameters with sufficient precision for making direct comparisons to experiment. We show here that the agreement with the measured quantities, for both enzyme catalyzed and spontaneous solution reactions, is quite remarkable. Importantly, we can now address some of the most spectacular entropy effects in enzymes and clarify their detailed microscopic origin. Herein, we discuss as examples the conversion of cytidine to uridine catalyzed by cytidine deaminase and reactions taking place on the ribosome, namely, peptide bond formation and GTP hydrolysis by elongation factor Tu. It turns out that the large entropy contributions to catalysis in these cases can now be rationalized by our computational approach. Finally, we address the problem of cold adaptation of enzyme reaction rates and prove by computational experiments that the universal activation enthalpy-entropy phenomenon originates from mechanical properties of the outer protein surface.

General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals

Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to 'monomers' at low temperature before nucleation. We apply (31)P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P-Y and Ph2P(E)-Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals.

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

The structural origin of enzyme adaptation to low temperature, allowing efficient catalysis of chemical reactions even near the freezing point of water, remains a fundamental puzzle in biocatalysis. A remarkable universal fingerprint shared by all cold-active enzymes is a reduction of the activation enthalpy accompanied by a more negative entropy, which alleviates the exponential decrease in chemical reaction rates caused by lowering of the temperature. Herein, we explore the role of protein surface mobility in determining this enthalpy-entropy balance. The effects of modifying surface rigidity in cold- and warm-active trypsins are demonstrated here by calculation of high-precision Arrhenius plots and thermodynamic activation parameters for the peptide hydrolysis reaction, using extensive computer simulations. The protein surface flexibility is systematically varied by applying positional restraints, causing the remarkable effect of turning the cold-active trypsin into a variant with mesophilic characteristics without changing the amino acid sequence. Furthermore, we show that just restraining a key surface loop causes the same effect as a point mutation in that loop between the cold- and warm-active trypsin. Importantly, changes in the activation enthalpy-entropy balance of up to 10 kcal/mol are almost perfectly balanced at room temperature, whereas they yield significantly higher rates at low temperatures for the cold-adapted enzyme.

Enzyme catalysis by entropy without Circe effect

Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.

Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome

Protein synthesis on the ribosome involves hydrolysis of GTP in several key steps of the mRNA translation cycle. These steps are catalyzed by the translational GTPases of which elongation factor Tu (EF-Tu) is the fastest GTPase known. Here, we use extensive computer simulations to explore the origin of its remarkably high catalytic rate on the ribosome and show that it is made possible by a very large positive activation entropy. This entropy term (TΔS(‡)) amounts to more than 7 kcal/mol at 25 °C. It is further found to be characteristic of the reaction mechanism utilized by the translational, but not other, GTPases and it enables these enzymes to attain hydrolysis rates exceeding 500 s(-1). This entropy driven mechanism likely reflects the very high selection pressure on the speed of protein synthesis, which drives the rate of each individual GTPase towards maximal turnover rate of the whole translation cycle.