Facilitated proton transfer in enzyme catalysis. It may have a crucial role in determining the efficiency and specificity of enzymes

Ultrafast proton transfer of the aqueous phenol radical cation

Proton transfer (PT) reactions are fundamental to numerous chemical and biological processes. While sub-picosecond PT involving electronically excited states has been extensively studied, little is known about ultrafast PT triggered by photoionization. Here, we employ femtosecond optical pump-probe spectroscopy and quantum dynamics calculations to investigate the ultrafast proton transfer dynamics of the aqueous phenol radical cation (PhOH˙⁺). Analysis of the vibrational wave packet dynamics reveals unusually short dephasing times of 0.18 ± 0.02 ps and 0.16 ± 0.02 ps for the PhOH˙⁺ O-H wag and bend frequencies, respectively, suggestive of ultrafast PT occurring on the ∼0.1 ps timescale. The reduced potential energy surface obtained from ab initio calculations shows that PT is barrierless when it is coupled to the intermolecular hindered translation between PhOH˙⁺ and the proton-acceptor water molecule. Quantum dynamics calculations yield a lifetime of 193 fs for PhOH˙⁺, in good agreement with the experimental results and consistent with the PT reaction being mediated by the intermolecular O⋯O stretch. These results suggest that photoionization can be harnessed to produce photoacids that undergo ultrafast PT. In addition, they also show that PT can serve as an ultrafast deactivation channel for limiting the oxidative damage potential of radical cations.

Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism

Fifty years ago, the group of Tony Mathias and Bob Rabin at University College London deduced the first mechanism for catalysis by an enzyme, ribonuclease [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., and Ross, C. A. (1961) Nature 190, 781-784]. Here, we celebrate this historic accomplishment by surveying knowledge of enzymology and protein science at that time, facts that led to the formulation of the mechanism, criticisms and alternative mechanisms, data that supported the proposed mechanism, and some of the refinements that have since provided a more precise picture of catalysis of RNA cleavage by ribonucleases. The Mathias and Rabin mechanism has appeared in numerous textbooks, monographs, and reviews and continues to have a profound impact on biochemistry.

Influence of Leaving-Group Electronic Effect on alpha-Chymotrypsin: Catalytic Constants of Specific Substrates

Rate constants and binding constants for the alpha-chymotrypsin-catalyzed hydrolysis of N-acetyltyrosine, tryptophan, and phenylalanine anilides are presented. Both k(cat) and K(m) are independent of electronic effects in the substrate over a range of 9.8 orders of magnitude (as measured by pK of the leaving group). Similarly, K(m) is independent of charge and orientation about the alpha-carbon for various substrates and pseudo-substrates. These results are not consistent with the pretransition state protonation hypothesis; instead, they are discussed in terms of a tetrahedral intermediate that is thermodynamically less stable than the Michaelis complex.

Active Site of alpha-Chymotrypsin Activation by Association-Desolvation

High reactivity toward alpha-chymotrypsin is observed for derivatives of beta-arylpropionic acids of varied structure-L-alpha-acylamido compounds, D-cyclized compounds, and, now, L-glycolamide esters. Compensating enthalpy and entropy effects are observed which appear to be caused by changes in water of solvation. High reactivity with varied structure, and physical evidence, appear to rule out induced fit and distortion as important for this enzyme. The high reactivity results from precise fit of the hydrolyzing group at the critical serine-imidazole junction, resulting from binding of the aryl group and restriction of rotation. Part of the energy of binding is used to desolvate the reactant groups of substrate and enzyme, decreasing activation energies by several kilocalories and raising reactivity by 10(3) or more. Solvation by water stabilizes many compounds, allowing them to be present in solution in biological systems. Their reactions may occur as their reactivity is increased when they are desolvated and brought from solution into association with reactive groups in enzymes, membranes, and structured particles.

The Correlation of RNase A Enzymatic Activity with the Changes in the Distance between Nε2-His12 and Nδ1-His119 Upon Addition of Stabilizing and Destabilizing Salts

The effect of stabilizing and destabilizing salts on the catalytic behavior of ribonuclease A (RNase A) was investigated at pH 7.5 and 25 degrees C, using spectrophotometric, viscometric and molecular dynamic methods. The changes in the distance between N(epsilon2) of His(12) and N(delta1) of His(119) at the catalytic center of RNase A upon the addition of sodium sulfate, sodium hydrogen sulfate and sodium thiocyanate were evaluated by molecular dynamic methods. The compactness and expansion in terms of Stokes radius of RNase A upon the addition of sulfate ions as kosmotropic salts, and thiocyanate ion as a chaotropic salt, were estimated by viscometric measurements. Enzyme activity was measured using cytidine 2', 3'-cyclic monophosphate as a substrate. The results from the measurements of distances between N(epsilon2) of His(12) and N(delta1) of His(119) and Stokes radius suggest (i) that the presence of sulfate ions decreases the distance between the catalytic His residues and increases the globular compactness, and (ii) that there is an expansion of the enzyme surface as well as elongation of the catalytic center in the presence of thiocyanate ion. These findings are in agreement with activity measurements.

The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling

The literature hypothesis that "the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of quantum-mechanical tunneling" is experimentally tested herein for the first time. The system employed is the key to being able to provide this first experimental test of the "enhanced hydrogen tunneling" hypothesis, one that requires a comparison of the three criteria diagnostic of tunneling (vide infra) for the same, or nearly the same, reaction with and without the enzyme. Specifically, studied herein are the adenosylcobalamin (AdoCbl, also known as coenzyme B(12))-dependent diol dehydratase model reactions of (i). H(D)(*) atom abstraction from ethylene glycol-d(0) and ethylene glycol-d(4) solvent by 5'-deoxyadenosyl radical (Ado(*)) and (ii.) the same H(*) abstraction reactions by the 8-methoxy-5'-deoxyadenosyl radical (8-MeOAdo(*)). The Ado(*) and 8-MeOAdo(*) radicals are generated by Co-C thermolysis of their respective precursors, AdoCbl and 8-MeOAdoCbl. Deuterium kinetic isotope effects (KIEs) of the H(*)(D(*)) abstraction reactions from ethylene glycol have been measured over a temperature range of 80-120 degrees C: KIE = 12.4 +/- 1.1 at 80 degrees C for Ado(*) and KIE = 12.5 +/- 0.9 at 80 degrees C for 8-MeOAdo(*) (values ca. 2-fold that of the predicted maximum primary times secondary ground-state zero-point energy (GS-ZPE) KIE of 6.4 at 80 degrees C). From the temperature dependence of the KIEs, zero-point activation energy differences ([E(D) - E(H)]) of 3.0 +/- 0.3 kcal mol(-)(1) for Ado(*) and 2.1 +/- 0.6 kcal mol(-)(1) for 8-MeOAdo(*) have been obtained, both of which are significantly larger than the nontunneling, zero-point energy only maximum of 1.2 kcal mol(-)(1). Pre-exponential factor ratios (A(H)/A(D)) of 0.16 +/- 0.07 for Ado(*) and 0.5 +/- 0.4 for 8-MeOAdo(*) are observed, both of which are significantly less than the 0.7 minimum for nontunneling behavior. The data provide strong evidence for the expected quantum mechanical tunneling in the Ado(*) and 8-MeOAdo(*)-mediated H(*) abstraction reactions from ethylene glycol. More importantly, a comparison of these enzyme-free tunneling data to the same KIE, (E(D) - E(H)) and A(H)/A(D) data for a closely related, Ado(*)-mediated H(*) abstraction reaction from a primary CH(3)- group in AdoCbl-dependent methylmalonyl-CoA mutase shows the enzymic and enzyme-free data sets are identical within experimental error. The Occam's Razor conclusion is that at least this adenosylcobalamin-dependent enzyme has not evolved to enhance quantum mechanical tunneling, at least within the present error bars. Instead, this B(12)-dependent enzyme simply exploits the identical level of quantum mechanical tunneling that is available in the enzyme-free, solution-based H(*) abstraction reaction. The results also require a similar, if not identical, barrier width and height within experimental error for the H(*) abstraction both within, and outside of, the enzyme.

Pentavalent Organo-Vanadates as Transition State Analogues for Phosphoryl Transfer Reactions

Pentavalent organo-vanadates have been put forth as transition state analogues for a variety of phosphoryl transfer reactions. In particular, uridine 2',3'-cyclic vanadate (U>v) has been proposed to resemble the transition state during catalysis by ribonuclease A (RNase A). Here, this hypothesis is tested. Lys41 of RNase A is known to donate a hydrogen bond to a nonbridging phosphoryl oxygen in the transition state during catalysis. Site-directed mutagenesis and semisynthesis were used to create enzymes with natural and nonnatural amino acid residues at position 41. These variants differ by 10(5)-fold in their k(cat)/K(m) values for catalysis, but <40-fold in their K(i) values for inhibition of catalysis by U>v. Plots of logK(i) vs log(K(m)/k(cat)) for three distinct substrates [poly(cytidylic acid), uridine 3'-(p-nitrophenyl phosphate), and cytidine 2',3'-cyclic phosphate] have slopes that range from 0.25 and 0.36. These plots would have a slope of unity if U>v were a perfect transition state analogue. Values of K(i) for U>v correlate weakly with the equilibrium dissociation constant for the enzymic complexes with substrate or product, indicating that U>v bears some resemblance to the substrate and product as well as the transition state. Thus, U>v is a transition state analogue for RNase A, but only a marginal one. This finding indicates that a pentavalent organo-vanadate cannot necessarily be the basis for a rigorous analysis of the transition state for a phosphoryl transfer reaction.

Ribonuclease a: revealing structure-function relationships with semisynthesis

Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of P–O5′ bonds in RNA. Structural analyses had suggested that the active-site lysine residue (K41) may interact preferentially with the transition state for covalent bond cleavage, thus facilitating catalysis. Here, site-directed mutagenesis and semisynthesis were combined to probe the role of K41 in the catalysis of RNA cleavage. Recombinant DNA techniques were used to replace K41 with an arginine residue (K41R) and with a cysteine residue (K41C), which had the only sulfhydryl group in the native protein. The value of k cat/K m for cleavage of poly(C) by K41C RNase was 105-fold lower than that by the wild-type enzyme. The sulfhydryl group of K41C RNase A was alkylated with 5 different haloalkylamines. The value of k cat/K m for the resulting semisynthetic enzymes and K41R RNase A were correlated inversely with the values of pK a for the side chain of residue 41. Further, no significant catalytic advantage was gained by side chains that could donate a second hydrogen bond. These results indicate that residue 41 donates a single hydrogen bond to the rate-limiting transition state during catalysis.

A model for the mechanism of chloride activation of oxygen evolution in photosystem II

A hypothesis is proposed to explain the function of Cl(-) in activating the oxygenevolving complex (OEC) of photosystem II (PS II), based on the results of recent (35)Cl-NMR studies. The putative mechanism involves Cl(-) binding to two types of sites. An intrinsic site is suggested to be composed of three histidyl residues (His 332 and His 337 from D1 and His 337 D2). It is proposed that Cl(-) binding to this site accelerates the abstraction of H(+) from water by raising the pKa's of the histidine imidazole groups. Cl(-) binding also stimulates the transfer of H(+) from this intrinsic site to a set of extrinsic sites on the 33 kD extrinsic polypeptide. The extrinsic Cl(-) binding sites are suggested to involve four protein domains that are linked together by salt-bridge contacts. Chloride and H(+) donated from the intrinsic site attack these intramolecular salt-bridges in a defined sequence, thereby exposing previously inaccessible Cl(-) and H(+) binding sites and stimulating the oxidation of water. This hypothesis also proposes a possible structure for the Mn active site within the D1/D2 complex. Specific amino-acid residues that are likely to participate as Mn lignads are identified on the lumenal portions of the D1 and D2 proteins that are different from those in the L and M subunits of photosynthetic bacteria; the choice of these residues is based on the metal coordination chemistry of these residues, their location within the polypeptide chain, the regularity of their spacing, and their conservation through evolution. The catalytic Mn-binding residues are suggested to be D-61, E-65, E-92, E-98, D-103; D-308, E-329, E-342 and E-333 in D1, and H-62, E-70, H-88, E-97, D-101; E-313, D-334, E-338 and E-345 in D2. Finally, this hypothesis identifies sites on both D2 and the 33 kD extrinsic polypeptide that might be involved in high- and low-affinity Ca(2+) binding.

The catalytic mechanism of serine proteases II: The effect of the protein environment in the alpha-chymotrypsin proton relay system

The proton relay system of alpha-chymotrypsin is analyzed by the INDOISCRF method. The effects of the protein electric and polarization fields are explicitly introduced in the calculations. It is shown that the multicharged structure Ser-His+Asp- is the most sensitive, from an energetic view-point, towards the protein surrounding effects. Variations in the permanent and polarization fields are discussed, as well as the influence of the substrate and one water molecule localized in the active site of the enzyme. The catalytic role of such changes is conjectured.

Role of catalytic residues in the formation of a tetrahedral adduct in the acylation reaction of bovine beta-trypsin. A molecular orbital study

In the acylation reaction of serine proteases the effect of amino acid residues on the geometrical change of the catalytic site from Michaelis to tetrahedral state was studied by using ab initio molecular orbital calculations. Amino acid residues in the catalytic site and the peptide substrate were calculated as a quantum mechanical region, and all the other amino acid residues and the calcium ion were included in the calculation as the electrostatic effects. The effects of Asp102, Asp194, N-terminus and the oxyanion binding site are large. The oxyanion binding site directly stabilizes the tetrahedral substrate. Asp102 stabilizes the enzyme intermediate, interacting with the protonated His57 residue. In order to elucidate the roles of Asp102 and the oxyanion binding site, energy decomposition analyses were done for the intermolecular interactions. The contribution of Asp102 and the oxyanion binding site to the decrease of energy in the geometrical change is due to the electrostatic effect. The energies of the proton shuttle from Ser195 O gamma to the leaving group of the substrate were calculated for amide and ester substrate models.

The dynamic basis of energy transduction in enzymes

The most important idea underlying our treatment herein is the unity of the enzyme molecule and the medium. Appreciation of this relationship is vital, if enzymology is to graduate from its present reductionistic status to a more holistic posture. Enzymes are biological entities firstly, and isolated objects of physicochemical analysis secondly. Perhaps the most crucial 'biological lesson', particularly apropos of enzymes in intermediary metabolism, concerns the 'cytosociology' of enzyme action in vivo [94,128]. The natural habitat of many enzymes in the living cell is far different from that in bulk aqueous solution in vitro. In order to obtain a real grasp of the nature of enzyme function, one must ultimately couch enzymology in concepts emerging from contemporary cell biology [95]. Notwithstanding, analysis precedes synthesis; and one must needs begin with the individual enzyme molecule. The trenchant efforts of the physical chemist and the organic chemist have produced a wealth of information on the nature of the binding and catalytic events at the enzyme active site. While it is not yet possible to explain precisely the complete sequence of events in the catalytic process, nevertheless, the basic mechanisms by which enzymes effect catalysis (i.e., reduce activation energy) now seem apparent [81,129]. The new frontier is to be found, in exploring the dynamic role of the protein matrix [17]. Not only does the protein provide the 3-D scaffolding for active-site processes, but, more importantly, it serves as the local solvent for the bound chemical subsystem. Thus, the dynamical aspects of enzyme catalysis (for thermally based systems) must arise from the fluctuational properties of the protein molecule. This notion is the common denominator in all of the models in subsection IIC. It is the anisotropic nature of this fluctuational behavior, which would characterize the energy-transduction phenomenon leading to localized catalytic events at the active-site. In Section III we attempted to show that all of the various enzyme models contribute pieces to a single, all-embracing jig-saw puzzle. Some models focus on the dynamical properties of the protein per se, whereas others deal with the stochastic aspects of protein-solvent interaction. The two approaches are complementary, as are mutually interlocking pieces of a puzzle. The ultimate picture depicted by this 'jig-saw puzzle' is still somewhat vague--owing to the present paucity of empirical information on protein motions.(ABSTRACT TRUNCATED AT 400 WORDS)

The catalytic mechanism of serine proteases: single proton versus double proton transfer

The two possible mechanisms of proton transfer on the catalytic process of serine proteases (single or double proton transfer) have been analysed. Intermediate neglect of differential overlap calculations have been performed in the absence and in the presence of the substrate molecule and one water molecule localized in the active site. It is shown that, in the absence of the substrate and water, double proton transfer seems to be the most feasible mechanism. However, when these molecules are introduced in the calculation, the role played by them is to facilitate the formation of the zwitterionic structure (single proton transfer) and to destabilize the intermediate structure which leads to double proton transfer. All calculations were made in vacuo.

Properties of horse liver alcohol dehydrogenase modified by the affinity label 3-chloroacetylpyridine-adenine dinucleotide

The reactive analogue of NAD+, CPAD+, was incorporated in the horse liver alcohol dehydrogenase (EC 1.1.1.1) linearly with its inactivation, to stoichiometry, with no apparent subunit interaction. No hydride transfer could take place in the modified enzyme, nor the interaction of trans-4-N,N-dimethylaminocinnamaldehyde with its reduced form, indicating an impairment of the accessibility to the catalytic zinc atom. The labeling in the enzyme, alkylated by [carbonyl-14C]CPAD+ was not stable, with a half-life of 32 h.

Enzyme specificity: base recognition and hydrolysis of RNA by ribonuclease A

The substrate specificity of pancreatic ribonuclease A is discussed in light of observations based on accurate X-ray structure analysis of several enzyme-nucleotide complexes. A hypothesis for protein-nucleic acid recognition is presented which proposes that: (a) pyrimidine bases in RNA are recognised by ribonuclease due to the charge complementarity of two groups (the amide nitrogen and the side chain oxygen (OG) of threonine 45) of the protein and relevant atoms in the heterocyclic base (O2 and N3 in pyrimidine nucleotides); (b) interaction of the protein with the ribose moiety of the nucleotides is non-specific; and (c) conformational flexibility in the region of the scissile P-O bond is provided by different locations of the phosphoryl oxygens, rather than by an overall translation of the phosphate moiety.

The pentaammineruthenium(III)-histidine complex in ribonuclease A as an optical probe of conformational change

The formation of stable transition metal complexes between pentaammineruthenium(III) and the imidazole moiety of histidine residues in ribonuclease A is described. Studies of the kinetics of incorporation suggest that three of the four histidines are reactive and ion-exchange chromatography affords the isolation of three derivatives containing a single ruthenium-histidine complex. Equilibrium studies of the thermal- and urea-induced unfolding of one of these derivatives show that the ligand-to-metal change-transfer absorptions above 300 nm can be used to follow the conformational changes in the vicinity of the complex. For the urea-induced unfolding of this derivative, the coincidence of the transition curves obtained from the change-transfer absorptions and from difference ultraviolet spectroscopy at 286 nm, which measures the exposure of buried tyrosine residues to solvent, suggest that only two conformations, native and unfolded, are present at equilibrium in significant concentrations.

Mechanism-controlled stereospecificity. Acylation of subtilisin with enantiomeric alkyl and nitrophenyl ester substrates

The activation parameters of acylation of subtilisin with alkyl and p-nitrophenyl esters of N-acylamino acid enantiomers were determined. It was found that (1) the activation entropy is much higher with the nitrophenyl esters than with the corresponding methyl esters, (2) the difference in rate constants between enantiomers is 10(4)--10(5) with methyl esters whereas it is only of the order of 10 with nitrophenyl esters. The results indicate that the catalytic mechanism is simpler for nitrophenyl esters than for alkyl esters. The simple mechanism requires only general base catalysis, and thus permits more freedom of motion in the transition state, whereas the complex mechanism involves both general base and general acid catalysis. Furthermore, the strikingly low enantiomeric specificity with nitrophenyl esters indicates that not only binding but also the catalytic mechanism is an important factor in determining the stereospecificity of an enzyme. The activation parameters for enantiomeric nitrophenyl ester reactions suggest that structurally related substrates can be transformed by the enzyme in different conformations which may be energetically similar or not. The energetically different conformations may account for the activation enthalpy-entropy compensation.

Proton conduction in phosphatidylethanolamine

The dc conductivity of polycrystalline phosphatidylethanolamine (PE) was measured in the temperature range 60-120 degrees C. Since no conclusive evidence had so far been obtained for the presence of proteon conduction in this phospholipid, hydrogen gas was shown in the present experiment to evolve during the electrolysis in its premelted state between 91 and 124 degrees C. In this temperature range molecules assume rotation around the molecular axes and proton conduction of the Grotthus type takes place possibly along two chains of intermolecular hydrogen bonds running in parallel. Zwitter-ions behave cooperatively as proton donors and acceptors in transferring proton from molecule and molecule via the hydrogen bond networks. This efficient push-pull way of proton transferring seems to account for the fact that no polarization was observed in the dc conduction experiments. The amount of devolved gas appears to be not exactly in accordance with Faraday's law and discussions are made on possible causes for this slight deviation.

Inactivation of horse liver alcohol dehydrogenase by modification of cysteine residue 174 with diazonium-1H-tetrazole

Diazonium-1H-tetrazole was tested as a potential active-site-directed reagent for amino acid residues involved in catalysis by alcohol dehydrogenase. In a novel reaction with a protein, diazonium-1H-tetrazole inactivated the enzyme selectively, and almost stoichiometrically, but reacting with the sulfur of a cysteine residue, Cys-174. As a model compound, the tetrazole adduct of free cysteine was prepared. Elementary and spectral analyses of the adduct were consistent with the structure 5-tetrazoleazo-S-cysteine. The adduct absorbs light with a maximun at 316 nm, and is destroyed by irradiation at this wavelength. The inactivated enzyme still bound NADH as determined by difference spectroscopy, but did not enhance the fluorescence of the bound NADH as did native enzyme. X-ray crystallographic studies of free enzyme have shown that Cys-174 coordinates the zinc at the active site (Eklund, H., Nordström, B., Zeppezauer, E., Söderlund, G., Ohlsson, I., Boiwe, T., and Brändén, C-I. (1974), FEBS Lett. 44, 200-204). The modified enzyme is probably inactive because the large, negatively charged tetrazole ring interferes sterically or electrostatically with the binding of substrates or with hydride transfer.

Chiral recognition of prochiral centres and general acid-base catalysis. Necessarily interrelated manifestations of active-site structure

On the basis of Ogston's [(1948) Nature (London) 162, 963] argument, the following conclusions are indicated by the stereochemistry of the reversible oxidation of glycollate by lactate dehydrogenase: (1) general acid-base catalysis is involved in the reaction; (2) the transformation of enzyme-bound (tetrahedral) substrate into enzyme-bound (trigonal) product involves a conformational transition of the enzyme-coenzyme complex.