A perspective on biological catalysis

Relating Protein Motion to Catalysis

This review examines the linkage between protein conformational motions and enzyme catalysis. The fundamental issues related to this linkage are probed in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase. The extensive experimental and theoretical studies addressing the role of protein conformational changes in these enzyme reactions are summarized. Evidence is presented for a network of coupled motions throughout the protein fold that facilitate the chemical reaction. This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction.

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis

Dynamic processes are implicit in the catalytic function of all enzymes. To obtain insights into the relationship between the dynamics and thermodynamics of protein fluctuations and catalysis, we have measured millisecond time scale motions in the enzyme dihydrofolate reductase using NMR relaxation methods. Studies of a ternary complex formed from the substrate analog folate and oxidized NADP+ cofactor revealed conformational exchange between a ground state, in which the active site loops adopt a closed conformation, and a weakly populated (4.2% at 30 degrees C) excited state with the loops in the occluded conformation. Fluctuations between these states, which involve motions of the nicotinamide ring of the cofactor into and out of the active site, occur on a time scale that is directly relevant to the structural transitions involved in progression through the catalytic cycle.

Hydrogen tunneling in quinoproteins

It is now widely accepted that substrate C-H bond breakage by quinoprotein enzymes occurs by quantum mechanical tunneling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (i.e., including zero-point energy but with no tunneling correction) has been driven over recent years by experimental studies of the temperature dependence of kinetic isotope effects for these reactions in the TTQ-dependent enzymes methylamine dehydrogenase and aromatic amine dehydrogenase, which produced observations also inconsistent with the simple Bell correction model of tunneling. However, these data-specifically, the strong temperature dependence of reaction rates and the variable temperature dependence of kinetic isotope effects-are consistent with other tunneling models (denoted full tunneling models) in which protein and/or substrate fluctuations generate a configuration compatible with tunneling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate quantum states and, when necessary, motion required to increase the probability of tunneling in these states. Furthermore, tunneling mechanisms in quinoproteins are supported by computational studies employing variational transition state theory with multidimensional tunneling corrections; these studies are also discussed in this review. Potential pitfalls in analyzing the temperature dependence of kinetic isotope effects as probes of tunneling are also discussed with reference to PQQ-dependent methanol dehydrogenase.

Structure, dynamics, and catalytic function of dihydrofolate reductase

Molecular motions are widely regarded as contributing factors in many aspects of protein function. The enzyme dihydrofolate reductase (DHFR), and particularly that from Escherichia coli, has become an important system for investigating the linkage between protein dynamics and catalytic function, both because of the location and timescales of the motions observed and because of the availability of a large amount of structural and mechanistic data that provides a detailed context within which the motions can be interpreted. Changes in protein dynamics in response to ligand binding, conformational change, and mutagenesis have been probed using numerous experimental and theoretical approaches, including X-ray crystallography, fluorescence, nuclear magnetic resonance (NMR), molecular dynamics simulations, and hybrid quantum/classical dynamics methods. These studies provide a detailed map of changes in conformation and dynamics throughout the catalytic cycle of DHFR and give new insights into the role of protein motions in the catalytic activity of this enzyme.

Role of conformational flexibility for enzymatic activity in NADH oxidase from Thermus thermophilus

NADH oxidase from Thermus thermophilus is a homodimer with an unknown physiological function. As is typical for an enzyme isolated from a thermophile, the catalytic rate, kcat, is low at low temperatures and increases with temperature, achieving an optimum at the physiological temperature of the organism, i.e. at approximately 70 degrees C for T. thermophilus. At low temperatures, the kcat of several enzymes from thermophilic and mesophilic organisms can be increased by chaotropic agents. The catalytic rate of NADH oxidase increases in the presence of urea. At concentrations of 1.0-1.3 m urea it reaches 250% of the activity in the absence of urea, at 20 degrees C. At higher urea concentrations the enzyme activity is inhibited. The urea-dependent activity changes correlate with changes in the fluorescence intensity of Trp47, which is located in the active site of the enzyme. Both fluorescence and circular dichroism measurements indicate that the activation by chaotropic agents involves local environmental changes accompanied by increased dynamics in the active site of the enzyme. This is not related to the global structure of NADH oxidase. The presence of an aromatic amino acid interacting with the flavin cofactor is common to numerous flavin-dependent oxidases. A comparison of the crystal structure with the activation thermodynamic parameters, deltaH* and TdeltaS*, obtained from the temperature dependence of kcat, suggests that Trp47 interacts with a water molecule and the isoalloxazine flavin ring. The present investigation suggests a model that explains the role of the homodimeric structure of NADH oxidase.

Challenges in enzyme mechanism and energetics

Since the discovery of enzymes as biological catalysts, study of their enormous catalytic power and exquisite specificity has been central to biochemistry. Nevertheless, there is no universally accepted comprehensive description. Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an absolute partitioning of catalytic contributions into independent and energetically additive components. Site-directed mutagenesis has emerged as an enormously powerful approach to probe enzymatic catalysis, illuminating many basic features of enzyme function and behavior. The emphasis of site-directed mutagenesis on the role of individual residues has also, inadvertently, limited experimental and conceptual attention to the fundamentally cooperative nature of enzyme function and energetics. The first part of this review highlights the structural and functional interconnectivity central to enzymatic catalysis. In the second part we ask: What are the features of enzymes that distinguish them from simple chemical catalysts? The answers are presented in conceptual models that, while simplified, help illustrate the vast amount known about how enzymes achieve catalysis. In the last section, we highlight the molecular and energetic questions that remain for future investigation and describe experimental approaches that will be necessary to answer these questions. The promise of advancing and integrating cutting edge conceptual, experimental, and computational tools brings mechanistic enzymology to a new era, one poised for novel fundamental insights into biological catalysis.

H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase

The mechanism of flavin reduction in morphinone reductase (MR) and pentaerythritol tetranitrate (PETN) reductase, and flavin oxidation in MR, has been studied by stopped-flow and steady-state kinetic methods. The temperature dependence of the primary kinetic isotope effect for flavin reduction in MR and PETN reductase by nicotinamide coenzyme indicates that quantum mechanical tunneling plays a major role in hydride transfer. In PETN reductase, the kinetic isotope effect (KIE) is essentially independent of temperature in the experimentally accessible range, contrasting with strongly temperature-dependent reaction rates, consistent with a tunneling mechanism from the vibrational ground state of the reactive C-H/D bond. In MR, both the reaction rates and the KIE are dependent on temperature, and analysis using the Eyring equation suggests that hydride transfer has a major tunneling component, which, unlike PETN reductase, is gated by thermally induced vibrations in the protein. The oxidative half-reaction of MR is fully rate-limiting in steady-state turnover with the substrate 2-cyclohexenone and NADH at saturating concentrations. The KIE for hydride transfer from reduced flavin to the alpha/beta unsaturated bond of 2-cyclohexenone is independent of temperature, contrasting with strongly temperature-dependent reaction rates, again consistent with ground-state tunneling. A large solvent isotope effect (SIE) accompanies the oxidative half-reaction, which is also independent of temperature in the experimentally accessible range. Double isotope effects indicate that hydride transfer from the flavin N5 atom to 2-cyclohexenone, and the protonation of 2-cyclohexenone, are concerted and both the temperature-independent KIE and SIE suggest that this reaction also proceeds by ground-state quantum tunneling. Our results demonstrate the importance of quantum tunneling in the reduction of flavins by nicotinamide coenzymes. This is the first observation of (i) three H-nuclei in an enzymic reaction being transferred by tunneling and (ii) the utilization of both passive and active dynamics within the same native enzyme.

Reversed hydroxamate-bearing thermolysin inhibitors mimic a high-energy intermediate along the enzyme-catalyzed proteolytic reaction pathway

A series of inhibitors that bear a reversed hydroxamate moiety have been evaluated as transition state analogue inhibitors for thermolysin. A linear correlation is observed between the K(i) values of these inhibitors and the kinetic parameters (K(M)/k(cat)) of the parallel series of related substrates, satisfying the criterion stipulated for transition state analogue inhibitors by Bartlett and Marlowe. Furthermore, examination of the binding mode of a related reversed hydroxamate bearing thermolysin inhibitor, in comparison with a transition state postulated for the enzyme-catalyzed proteolytic reaction revealed that the inhibitors under study mimic the electronic as well as the geometric characteristics of the transition state. On the basis of these results it may be concluded that the hydroxamate-bearing zinc protease inhibitors are a new type of transition state analogue inhibitors.

A perspective on enzyme catalysis

The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.

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.

Multi-subunit acetyl-CoA carboxylases

Acetyl-CoA carboxylase (ACC) catalyses the first committed step of fatty acid synthesis, the carboxylation of acetyl-CoA to malonyl-CoA. Two physically distinct types of enzymes are found in nature. Bacterial and most plant chloroplasts contain a multi-subunit ACC (MS-ACC) enzyme that is readily dissociated into its component proteins. Mammals, fungi, and plant cytosols contain the second type of ACC, a single large multifunctional polypeptide. This review will focus on the structures, regulation, and enzymatic mechanisms of the bacterial and plant MS-ACCs.

Enzymatic conformational fluctuations along the reaction coordinate of cytidine deaminase

Analysis of the crystal structures for cytidine deaminase complexed with substrate analog 3-deazacytidine, transition-state analog zebularine 3,4-hydrate, and product uridine establishes significant changes in the magnitude of atomic-scale fluctuations along the (approximate) reaction coordinate of this enzyme. Differences in fluctuations between the substrate analog complex, transition-state analog complex, and product complex are monitored via changes in corresponding crystallographic temperature factors. Previously, we reported that active-site conformational disorder is substantially reduced in the transition-state complex relative to the two ground-state complexes. Here, this result is statistically corroborated by crystallographic data for fluorinated zebularine 3,4-hydrate, a second transition-state analog, and by multiple regression analysis. Multiple regression explains 70% of the total temperature factor variation through a predictive model for the average B-value of an amino acid as a function of the catalytic state of the enzyme (substrate, transition state, product) and five other physical and structural descriptors. Furthermore, correlations of atomic fluctuation magnitudes throughout the body of each complex are quantified through an auto-correlation function. The transition-state analog complex shows the greatest correlations between temperature factor magnitudes for spatially separated atoms, underscoring the strong ability of this reaction-coordinate species to "organize" enzymatic fluctuations. The catalytic significance for decreased atomic-scale motions in the transition state is discussed. A thermodynamic argument indicates that the significant decreases in local enzymatic conformational entropy at the transition state result in enhanced energetic stabilization there.

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.

Correlative motions and memory effects in molecular dynamics simulations of molecules: principal components and rescaled range analysis suggest that the motions of native BPTI are more correlated than those of its mutants

In this work MD simulations of the native bovine pancreatic trypsin inhibitor (BPTI) and 16 mutants were done in vacuum in order to study memory effects in the mutants using principal component analysis (PCA) and the rescaled range analysis (Hurst exponents). Both PCA and the rescaled range analysis support our previous proposition, based on PCA of lysozyme, that the motions of a native protein are more correlated than those of mutants. The methods are compared, the nature and applications of the rule and the role of the long-range correlations in MD time series (i.e. memory) are discussed in the context of collective motions.

Simulating enzyme reactions: challenges and perspectives

Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.

Correlated conformational fluctuations during enzymatic catalysis: Implications for catalytic rate enhancement

Correlated enzymatic conformational fluctuations are shown to contribute to the rate of enhancement achieved during catalysis. Cytidine deaminase serves as a model system. Crystallographic temperature factor data for this enzyme complexed with substrate analog, transition-state analog, and product are available, thereby establishing a measure of atomic scale conformational fluctuations along the (approximate) reaction coordinate. First, a neural network-based algorithm is used to visualize the decreased conformational fluctuations at the transition state. Second, a dynamic diffusion equation along the reaction coordinate is solved and shows that the flux velocity through the associated enzymatic conformation space is greatest at the transition state. These results suggest (1) that there are both dynamic and energetic restrictions to conformational fluctuations at the transition state, (2) that enzymatic catalysis occurs on a fluctuating potential energy surface, and (3) a form for the potential energy. The Michaelis-Menten equations are modified to describe catalysis on this fluctuating potential energy profile, leading to enhanced catalytic rates when fluctuations along the reaction coordinate are appropriately correlated. This represents a dynamic tuning of the enzyme for maximally effective transformation of the ES complex into EP.

Engineering delta 9-16:0-acyl carrier protein (ACP) desaturase specificity based on combinatorial saturation mutagenesis and logical redesign of the castor delta 9-18:0-ACP desaturase

Six amino acid locations in the soluble castor Delta(9)-18:0-acyl carrier protein (ACP) desaturase were identified that can affect substrate specificity. Combinatorial saturation mutagenesis of these six amino acids, in conjunction with selection, using an unsaturated fatty acid auxotroph system, led to the isolation of variants with up to 15-fold increased specific activity toward 16-carbon substrates. The most improved mutant, com2, contained two substitutions (T117R/G188L) common to five of the 19 complementing variants subjected to further analysis. These changes, when engineered into otherwise wild-type 18:0-ACP desaturase to make mutant 5.2, produced a 35-fold increase in specific activity with respect to 16-carbon substrates. Kinetic analysis revealed changes in both k(cat) and K(m) that result in an 82-fold improvement in specificity factor for 16-carbon substrate compared with wild-type enzyme. Improved substrate orientation apparently compensated for loss of binding energy that results from the loss of desolvation energy for 16-carbon substrates. Mutant 5.2 had specific activity for 16-carbon substrates 2 orders of magnitude higher than those of known natural 16-carbon specific desaturases. These data support the hypothesis that it should be possible to reengineer archetypal enzymes to achieve substrate specificities characteristic of recently evolved enzymes while retaining the desired stability and/or turnover characteristics of a parental paralog.

Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase

The wealth of kinetic and structural information makes inorganic pyrophosphatases (PPases) a good model system to study the details of enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps around chemical catalysis and provide strong evidence that a water molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by coordination to two metal ions and D117. They also suggest that a low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part because of steric crowding by W100 and N116. Direct visualization of the double bonds on the phosphates appears possible. The flexible side chains at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a new nucleophile to be generated and creates symmetry in the elementary catalytic steps on the enzyme. We are thus moving closer to understanding phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high resolution structures can thus tease out overlapping complexes and so are as relevant to discussion of enzyme mechanism as structures produced by time-resolved crystallography.

Importance of barrier shape in enzyme-catalyzed reactions. Vibrationally assisted hydrogen tunneling in tryptophan tryptophylquinone-dependent amine dehydrogenases

C-H bond breakage by tryptophan tryptophylquinone (TTQ)-dependent methylamine dehydrogenase (MADH) occurs by vibrationally assisted tunneling (Basran, J., Sutcliffe, M. J., and Scrutton, N. S. (1999) Biochemistry 38, 3218--3222). We show here a similar mechanism in TTQ-dependent aromatic amine dehydrogenase (AADH). The rate of TTQ reduction by dopamine in AADH has a large, temperature independent kinetic isotope effect (KIE = 12.9 +/- 0.2), which is highly suggestive of vibrationally assisted tunneling. H-transfer is compromised with benzylamine as substrate and the KIE is deflated (4.8 +/- 0.2). The KIE is temperature-independent, but reaction rates are strongly dependent on temperature. With tryptamine as substrate reaction rates can be determined only at low temperature as C-H bond cleavage is rapid, and an exceptionally large KIE (54.7 +/- 1.0) is observed. Studies with deuterated tryptamine suggest vibrationally assisted tunneling is the mechanism of deuterium and, by inference, hydrogen transfer. Bond cleavage by MADH using a slow substrate (ethanolamine) occurs with an inflated KIE (14.7 +/- 0.2 at 25 degrees C). The KIE is temperature-dependent, consistent with differential tunneling of protium and deuterium. Our observations illustrate the different modes of H-transfer in MADH and AADH with fast and slow substrates and highlight the importance of barrier shape in determining reaction rate.

Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange

Changes in protein mobility accompany changes in conformation during the trans-activation of enzymes; however, few studies exist that validate or characterize this behavior. In this study, amide hydrogen/deuterium exchange/mass spectrometry was used to probe the conformational flexibility of extracellular signal-regulated protein kinase-2 before and after activation by phosphorylation. The exchange data indicated that extracellular regulated protein kinase-2 activation caused altered backbone flexibility in addition to the conformational changes previously established by x-ray crystallography. The changes in flexibility occurred in regions involved in substrate binding and turnover, suggesting their importance in enzyme regulation.

Use of pH and kinetic isotope effects to dissect the effects of substrate size on binding and catalysis by nitroalkane oxidase

The flavoprotein nitroalkane oxidase catalyzes the oxidation of a broad range of primary and secondary nitroalkanes to the respective aldehydes or ketones, with production of hydrogen peroxide and nitrite. The V/K values for primary nitroalkanes increase with increasing chain length, reaching a maximum with 1-nitrobutane [Gadda, G., and Fitzpatrick, P. F. (1999) Arch. Biochem. Biophys. 363, 309-313]. In the present report, pH and deuterium kinetic isotope effects with a series of primary nitroalkanes and phenylnitromethane as substrates have been used to dissect the effects of chain length on binding and catalysis. The apparent pKa value for a group that must be unprotonated for catalysis decreases from about 7 to 5.3 with increasing size of the substrate. The D(V/K) values for these substrates decrease from 7.5 with nitroethane to 1 with phenylnitromethane. These results show that increasing the size of the substrate results in an increased partitioning forward to catalysis. The D(V/K) and DVmax values at pH 5.5 have been used to calculate the effect of substrate size on the Kd values for primary nitroalkanes. The Kd values decrease with increasing length of the substrate, with a deltadeltaG(binding) of 1.7 kcal mol(-1) for each additional methylene group. Such a value is less than the value of 2.6 kcal mol(-1) previously determined for the effect of a methylene group on the V/K value [Gadda, G., and Fitzpatrick, P. F. (1999) Arch. Biochem. Biophys. 363, 309-313], suggesting that the total energy available per methylene group is used not only to enhance binding but also to increase the rate of catalysis.

Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor"

To obtain a clearer understanding of the forces involved in transition state stabilization by Escherichia coli cytidine deaminase, we investigated the thermodynamic changes that accompany substrate binding in the ground state and transition state for substrate hydrolysis. Viscosity studies indicate that the action of cytidine deaminase is not diffusion-limited. Thus, K(m) appears to be a true dissociation constant, and k(cat) describes the chemical reaction of the ES complex, not product release. Enzyme-substrate association is accompanied by a loss of entropy and a somewhat greater release of enthalpy. As the ES complex proceeds to the transition state (ES), there is little further change in entropy, but heat is taken up that almost matches the heat that was released with ES formation. As a result, k(cat)/K(m) (describing the overall conversion of the free substrate to ES is almost invariant with changing temperature. The free energy barrier for the enzyme-catalyzed reaction (k(cat)/K(m)) is much lower than that for the spontaneous reaction (k(non)) (DeltaDeltaG = -21.8 kcal/mol at 25 degrees C). This difference, which also describes the virtual binding affinity of the enzyme for the activated substrate in the transition state (S), is almost entirely enthalpic in origin (DeltaDeltaH = -20.2 kcal/mol), compatible with the formation of hydrogen bonds that stabilize the ES complex. Thus, the transition state affinity of cytidine deaminase increases rapidly with decreasing temperature. When a hydrogen bond between Glu-91 and the 3'-hydroxyl moiety of cytidine is disrupted by truncation of either group, k(cat)/K(m) and transition state affinity are each reduced by a factor of 10(4). This effect of mutation is entirely enthalpic in origin (DeltaDeltaH approximately 7.9 kcal/mol), somewhat offset by a favorable change in the entropy of transition state binding. This increase in entropy is attributed to a loss of constraints on the relative motions of the activated substrate within the ES complex. In an Appendix, some objections to the conventional scheme for transition state binding are discussed.

Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state

This paper considers how enzymes that catalyze reactions at specific DNA sites have been engineered to overcome the problem of competitive inhibition by excess nonspecific binding sites on DNA. The formation of a specific protein-DNA recognition complex is discussed from both structural and thermodynamic perspectives, and contrasted with formation of nonspecific complexes. Evidence (from EcoRI and BamHI endonucleases) is presented that a wide variety of perturbations of the DNA substrate alter binding free energy but do not affect the free energy of activation for the chemical step; that is, many energetic factors contribute equally to the recognition complex and the transition-state complex. This implies that the specific recognition complex bears a close resemblance to the transition-state complex, such that very tight binding to the recognition site on the DNA substrate does not inhibit catalysis, but instead provides energy that is efficiently utilized along the path to the transition state. It is suggested that this view can be usefully extended to "noncatalytic" site-specific DNA-binding proteins like transcriptional activators and general transcription factors.

Catalytic role of enzymes: short strong H-bond-induced partial proton shuttles and charge redistributions

A two-step reaction mechanism (catalyzed alternatively by acid and base) with partial proton shuttles and charge redistributions promoted by short strong H bonds (SSHBs) (playing a dual role as an amphi-acid/base catalyst) is proposed to explain the enormous rate enhancement observed in enzymatic reactions involving carbanion intermediates. The SSHBs in the two-step reactions are found to be responsible for enhancing enzyme-substrate interactions in favor of the transition state structure over that of reactant. The detailed quantum theoretical studies of ketosteroid isomerase provide evidence of assisting roles of SSHB in enzymatic activity. The understanding of the two-step reaction mechanism would be a useful aid in designing novel functional enzymes and abzymes.

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

Proteins are not rigid structures; they are dynamic entities, with numerous conformational isomers (substates). The dynamic nature of protein structures amplifies the structural variation of the transition state for chemical reactions performed by proteins. This suggests that utilizing a transition state ensemble to describe chemical reactions involving proteins may be a useful representation. Here we re-examine the nature of the transition state of protein chemical reactions (enzyme catalysis), considering both recent developments in chemical reaction theory (Marcus theory for SN2 reactions), and protein dynamics effects. The classical theory of chemical reactions relies on the assumption that a reaction must pass through an obligatory transition-state structure. The widely accepted view of enzymatic catalysis holds that there is tight binding of the substrate to the transition-state structure, lowering the activation energy. This picture, may, however, be oversimplified. The real meaning of a transition state is a surface, not a single saddle point on the potential energy surface. In a reaction with a "loose" transition-state structure, the entire transition-state region, rather than a single saddle point, contributes to reaction kinetics. Consequently, here we explore the validity of such a model, namely, the enzymatic modulation of the transition-state surface. We examine its utility in explaining enzyme catalysis. We analyse the possibility that instead of optimizing binding to a well-defined transition-state structure, enzymes are optimized by evolution to bind efficiently with a transition-state ensemble, with a broad range of activated conformations. For enzyme catalysis, the key issue is still transition state (ensemble) stabilization. The source of the catalytic power is the modulation of the transition state. However, our definition of the transition state is the entire transition-state surface rather just than a single well-defined structure. This view of the transition-state ensemble is consistent with the nature of the protein molecule, as embodied and depicted in the protein energy landscape of folding, and binding, funnels.

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.

Rethinking fundamentals of enzyme action

Despite certain limitations, investigators continue to gainfully employ concepts rooted in steady-state kinetics in efforts to draw mechanistically relevant inferences about enzyme catalysis. By reconsidering steady-state enzyme kinetic behavior, this review develops ideas that allow one to arrive at the following new definitions: (a) V/K, the ratio of the maximal initial velocity divided by the Michaelis-Menten constant, is the apparent rate constant for the capture of substrate into enzyme complexes that are destined to yield product(s) at some later point in time; (b) the maximal velocity V is the apparent rate constant for the release of substrate from captured complexes in the form of free product(s); and (c) the Michaelis-Menten constant K is the ratio of the apparent rate constants for release and capture. The physiologic significance of V/K is also explored to illuminate aspects of antibiotic resistance, the concept of "perfection" in enzyme catalysis, and catalytic proficiency. The conceptual basis of congruent thermodynamic cycles is also considered in an attempt to achieve an unambiguous way for comparing an enzyme-catalyzed reaction with its uncatalyzed reference reaction. Such efforts promise a deeper understanding of the origins of catalytic power, as it relates to stabilization of the reactant ground state, stabilization of the transition state, and reciprocal stabilizations of ground and transition states.

DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis

The roles of divalent metal ions in DNA cleavage by the EcoRV endonuclease were studied by using Co2+ or Mn2+ as substitutes for the natural cofactor Mg2+. In steady-state experiments with a 12 bp oligonucleotide substrate, Co2+ yielded a similar turnover rate to that with Mg2+, but Mn2+ gave a slower rate. Single turnovers of EcoRV on this substrate were analysed by stopped-flow and quench-flow methods, to determine the rates for the formation of the ternary enzyme-DNA-metal complex, the hydrolysis of the phosphodiester bonds and the dissociation of the cleaved DNA. With Co2+, all three steps had similar rates to those with Mg2+. In contrast, Mn2+ gave a faster rate for phosphodiester hydrolysis than either Mg2+ or Co2+, but a slower rate for product dissociation, thus accounting for its low turnover rate. Single turnovers on plasmids also yielded faster rates for substrate hydrolysis with Mn2+ compared to Mg2+ and Co2+. Since Mn2+ gave the most rapid rates for the hydrolytic step, despite being less electronegative than Co2+, the function of the metal ion at the active site of EcoRV cannot be just the polarisation of the scissile phosphate. Moreover, the minimal scheme for the Co2+-catalysed reaction requires two metal ions for DNA cleavage. The metal ions seem to be involved in the precise positioning of both the substrate and the water that acts as the attacking nucleophile and in activating that water molecule. A model is presented to account for how two metal ions might fulfil these functions.

Bacillus subtilis chorismate mutase is partially diffusion-controlled

The effect of viscosogens on the enzyme-catalyzed rearrangement of chorismate to prephenate has been studied. The steady-state parameters kcat and kcat/Km for the monofunctional chorismate mutase from Bacillus subtilis (BsCM) decreased significantly with increasing concentrations of glycerol, whereas the 'sluggish' BsCM mutants C75A and C75S were insensitive to changes in microviscosity. The latter results rule out extraneous interactions of the viscosogen as an explanation for the effects observed with the wild-type enzyme. Additional control experiments show that neither viscosogen-induced shifts in the pH-dependence of the enzyme-catalyzed reaction nor small perturbations of the conformational equilibrium of chorismate can account for the observed effects. Instead, BsCM appears to be limited by substrate binding and product release at low and high substrate concentrations, respectively. Analysis of the kinetic data indicates that diffusive transition states are between 30 and 40% rate-determining in these concentration regimes; the chemical step must contribute to the remaining kinetic barrier. The relatively low value of the 'on' rates for chorismate and prephenate (approximately 2 x 106 m-1.s-1) probably reflects the need for a rare conformation of the enzyme, the ligand, or both for successful binding. Interestingly, the chorismate mutase domain of the bifunctional chorismate mutase-prephenate dehydratase from Escherichia coli, which has steady-state kinetic parameters comparable to those of BsCM but has a much less accessible active site, is insensitive to changes in viscosity and the reaction it catalyses is not diffusion-controlled.

RNA catalysis

Our understanding of the relationship between the structure of RNA and its catalytic activity has advanced significantly in the past year. These advances include time-resolved crystallographic studies on the hammerhead ribozyme, as well as new structures of a group I intron, a lead(II)-cleavage ribozyme, a hepatitis delta virus ribozyme, and components of the spliceosome machinery and the peptidyl transferase center of the ribosome and, most significantly, the structure of the ribosome itself.

Kinetic epitope mapping of the chicken lysozyme.HyHEL-10 Fab complex: delineation of docking trajectories

The rate constants, k(on), for the formation of hen (chicken) lysozyme (HEWL). Fab-10 complexes have been determined for wild-type (WT) and epitope-mutated lysozymes by a homogeneous solution method based on the 95% reduced enzymatic activity of the complex. The values fall within a narrow 10-fold range [(0.18 to 1.92) x 10(6) M(-1)s(-l)]. The affinity constants, K(D), cover a broader, 440-fold, range from 0.075 to 33 nM. Values of K(D) as high as 7 microM were obtained for the complexes prepared from some mutations at HEWL positions 96 and 97, but the associated kinetic constants could not be determined. The values of k(on) are negatively correlated with side-chain volume at position 101HEWL, but are essentially independent of this parameter for position 21HEWL substitutions. The multiple mutations made at positions 21HEWL and 101HEWL provide sufficient experimental data on complex formation to evaluate phi values [phi = (deltadeltaGon)/(deltadeltaG(D))] at these two positions to begin to define trajectories for protein-protein association. The data, when interpreted within the concept of a two-step association sequence embracing a metastable encounter complex intermediate, argue that the rate determining step at position 21HEWL (phiavg = 0.2) is encounter complex formation, but the larger phi(avg) value of 0.36 experienced for most position 101HEWL mutations indicates a larger contribution from the post-encounter annealing process at this site for these replacements.

New enzyme lineages by subdomain shuffling

Protein functions have evolved in part via domain recombination events. Such events, for example, recombine structurally independent functional domains and shuffle targeting, regulatory, and/or catalytic functions. Domain recombination, however, can generate new functions, as implied by the observation of catalytic sites at interfaces of distinct folding domains. If useful to an evolving organism, such initially rudimentary functions would likely acquire greater efficiency and diversity, whereas the initially distinct folding domains would likely develop into single functional domains. This represents the probable evolution of the S1 serine protease family, whose two homologous beta-barrel subdomains assemble to form the binding sites and the catalytic machinery. Among S1 family members, the contact interface and catalytic residues are highly conserved whereas surrounding surfaces are highly variable. This observation suggests a new strategy to engineer viable proteins with novel properties, by swapping folding subdomains chosen from among protein family members. Such hybrid proteins would retain properties conserved throughout the family, including folding stability as single domain proteins, while providing new surfaces amenable to directed evolution or engineering of specific new properties. We show here that recombining the N-terminal subdomain from coagulation factor X with the C-terminal subdomain from trypsin creates a potent enzyme (fXYa) with novel properties, in particular a broad substrate specificity. As shown by the 2.15-A crystal structure, plasticity at the hydrophobic subdomain interface maintains activity, while surface loops are displaced compared with the parent subdomains. fXYa thus represents a new serine proteinase lineage with hybrid fX, trypsin, and novel properties.

Transition-state theoretical interpretation of the catalytic power of pyruvate decarboxylases: the roles of static and dynamical considerations

The catalytic power of two thiamin diphosphate (ThDP)-dependent enzymes, yeast pyruvate decarboxylase (the hysteretically regulated enzyme from Saccharomyces cerevisiae, SCPDC) and bacterial pyruvate decarboxylase (the unregulated enzyme from Zymomonas mobilis, ZMPDC), are analyzed by thorough-going application of transition-state theory, i.e. by a static approach that emphasizes the state-function character of the free energy of activation and takes no explicit account of dynamical considerations. The overall catalytic reaction is resolved into manifolds for addition (conversion of free enzyme and substrate to the complex of enzyme with the pyruvate:ThDP adduct), decarboxylation, and elimination (conversion of the complex of enzyme with the acetaldehyde:ThDP adduct formed by decarboxylation into free product and free enzyme). For SCPDC, the addition manifold is most strongly catalyzed (3x1012-fold, corresponding to net transition-state stabilization of 72 kJ/mol, transition-state stabilization of 83 kJ/mol diminished by reactant-state stabilization of 11 kJ/mol), the decarboxylation manifold is least strongly catalyzed (5x107-fold, corresponding to net transition-state stabilization of 41 kJ/mol, transition-state stabilization of 68 kJ/mol diminished by reactant-state stabilization of 27 kJ/mol), and the elimination manifold is catalyzed to an intermediate degree (2x1010-fold, corresponding to net transition-state stabilization of 59 kJ/mol, transition-state stabilization of 76 kJ/mol diminished by reactant-state stabilization of 17 kJ/mol). A similar situation holds for ZMPDC. There is no need to make an explicit analysis of dynamical factors in order to describe the catalytic mechanism and catalytic power of these complex enzymes.

Conformational dynamics and enzyme activity

Conformational flexibility and structural fluctuations play an important role in enzyme activity. A great variety of internal motions ranging over different time scales and of different amplitudes are involved in the catalytic cycle. These different types of motions and their functional consequences are considered in the light of experimental data and theoretical analyses. The conformational changes upon substrate binding, and particularly the hinge-bending motion which occurs in enzymes made of two domains, are analyzed from several well documented examples. The conformational events accompanying the different steps of the catalytic cycle are discussed. The last section concerns the motions involved in the allosteric transition which regulates the enzyme activity.

Synthesis of novel proteins

De novo and rational protein design are progressing towards the chemical synthesis of proteins with pre-selected structure and function. The data illustrate diverse experimental and computational approaches which test our comprehension of protein structure, hydrophobic core packing and global stability, especially of coiled-coil proteins. The incorporation of biological cofactors, including hemes, as well as active sites, such as that of iron superoxide dismutase, into designed proteins provides an exciting next step towards the synthesis of proteins with enzymatic function.

Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate

Poisson-Boltzmann calculations were used to determine the pKa of protein functional groups in the unliganded dihydrofolate reductase enzyme, and the pKa of protein and ligand groups in methotrexate-enzyme complexes. The results reported here are in conflict with two fundamental tenets of dihydrofolate reductase inhibition by methotrexate: (1) Asp27 is not expected to be protonated near pH 6.5 in the apoenzyme as previously proposed based on fitting of empirical equations to binding data, and (2) the calculated pKa for the pteridine N1 of the inhibitor while bound to the protein is significantly lower than that estimated for this group from interpretation of NMR data (>10). In fact, the electrostatic calculations and complementary quantum chemical calculations indicate that Asp27 is likely protonated when methotrexate is bound, resulting in a neutral dipole-dipole interaction rather than a salt-bridge between the enzyme and the inhibitor. Reasons for this discrepancy with the experimental data are discussed. Furthermore, His45 and Glu17 in the Escherichia coli enzyme are proposed to be in part responsible for the pH dependence of the conformational degeneracy in the inhibitor-enzyme complex.

The state of antibody catalysis

One of the fascinations of catalytic antibodies is the possibility of harnessing the mechanisms available to enzymes for chemical transformation and applying them to the broad realm of chemistry encountered in organic synthesis. Recently, the catalytic repertoire of antibodies has been extended to include mechanistically more complex bimolecular reactions and the immunological response to the hapten can be more thoroughly examined as a result of the advent of new screening technology using bacterial phages or auxotrophic cell lines.