Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.     

Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries

The rearrangement of aminoethanol catalyzed by ethanolamine ammonia lyase is investigated by computational means employing DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ). The study aims at providing a detailed account on various crucial aspects, in particular a distinction between a direct intramolecular migration of the partially protonated NH(2) group vs elimination of NH(4)(+). Three mechanistic scenarios were explored: (i) According to the calculations, irrespective of the nature of the protonating species, intramolecular migration of the NH(3) group is energetically less demanding than elimination of NH(4)(+). However, all computed activation enthalpies exceed the experimentally derived activation enthalpy (15 kcal/mol) associated with the rate-determining step, i.e., the hydrogen abstraction from the 5'-deoxyadenosine by the product radical. For example, when imidazole is used as a model system for His interacting with the NH(3) group of the substrate, the activation enthalpy for the migration process amounts to 27.4 kcal/mol. If acetic acid is employed to mimic Asp or Glu, the activation enthalpy is somewhat lower, being equal to 24.2 kcal/mol. (ii) For a partial deprotonation of the substrate 2 at the OH group, the rearrangement mechanism consists of the dissociation of an NH(2) radical from C(2) and its association at C(1) atom. For all investigated proton acceptors (i.e., OH(-), HCOO(-), CH(3)COO(-), CH(2)NH, imidazole), the activation enthalpy for the dissociation step also exceeds 15 kcal/mol. Typical data are 20.2 kcal/mol for Ac(-) and 23.8 kcal/mol for imidazole. (iii) However, in a synergistic action of partial protonation of the NH(2) group and partial deprotonation of the OH group by the two conceivable catalytic auxiliaries Asp/Glu and His, the activation enthalpy computed is compatible with the experimental data. For imidazole and acetate as model systems, the activation enthalpy is equal to 13.7 kcal/mol. This synergistic action of the two catalytic groups is expected to take place in a physiologically realistic pH range of 6-9.5, and the present computational findings may help to further characterize the yet unknown structural details of the ethanolamine ammonia lyase's active site.     

Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxyribose-5-yl radical: a model study of a reaction occurring in the active site of ethanolamine ammonia lyase

Hydrogen abstraction from 2-aminoethanol by the 5'-deoxyadenosyl radical, which is formed upon Co--C bond homolysis in coenzyme B(12), was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5'-deoxyadenosyl moiety the computationally less demanding 1,5-dideoxyribose was employed; two conformers, which differ in ring conformation (C2- and C3-endo), were considered. If hydrogen is abstracted from "free" substrate by the C2-endo conformer of the 1,5-dideoxyribose-5-yl radical, the activation enthalpy is 16.7 kcal mol(-1); with the C3-endo counterpart, the value is 17.3 kcal mol(-1). These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol(-1)) determined experimentally for the rate-determining step of the sequence, that is, hydrogen delivery from 5'-deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol(-1) for the C3-endo conformer and 5.8 kcal mol(-1) for the C2-endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13-15 kcal mol(-1). A synergistic interaction of 2-aminoethanol with two amino acids where His partially protonates the NH(2) group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol(-1) for the C3-endo conformer and 13.2 kcal mol(-1) for the C2-endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol(-1)) than that reported for the rate-determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol(-1).     

Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation

DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.     

Catalytic roles of the metal ion in the substrate-binding site of coenzyme B12-dependent diol dehydratase

Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K(+) ion; however, QM/MM computations indicate that Ca(2+) ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca(2+) ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K(+) ion. Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca(2+) ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca(2+) ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.     

MINDO-SCF-MO-berechnung der cis-trans-isomerisierung von N-methyl- und N-phenylazomethin

MINDO/2-SCF-MO calculations for the ground state properties of N-methyl- and N-phenyl-azomethin have been carried out. The calculated rotation barrier for the methyl group in N-methyl-azomethin was 0·8 kcal/mol, the eclipsed conformation being most stable. The calculated rotation barrier about the CN bond in the protonated methylazomethin was 27·9 kcal/mol. MINDO/1-SCF-MO treatment for the N-inversion barrier of the unprotonated species yielded 13·00 kcal/mol. Similar MINDO/2 calculations for N-phenylazomethin yielded 4·0 kcal/mol for the rotation barrier of the phenyl ring around the CN= bond, the perpendicular conformation of the ring to the CNC plane being most stable. For the corresponding N protonated derivative the value 27·3 kcal/mol was calculated for the rotation barrier around the CN bond. MINDO/1 treatment yielded an inversion barrier of 14·0 kcal/mol for N-phenylazomethin.     

A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase

The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two‐layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn‐bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate‐determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn‐bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate‐determining step is the proton transfer from Zn‐OH to 6‐NH₂ of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin

The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.     

Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70

Beta-lactamase acquisition is the most prevalent basis for Gram-negative bacteria resistance to the beta-lactam antibiotics. The mechanism used by the most common class A Gram-negative beta-lactamases is serine acylation followed by hydrolytic deacylation, destroying the beta-lactam. The ab initio quantum mechanical/molecular mechanical (QM/MM) calculations, augmented by extensive molecular dynamics simulations reported herein, describe the serine acylation mechanism for the class A TEM-1 beta-lactamase with penicillanic acid as substrate. Potential energy surfaces (based on approximately 350 MP2/6-31+G calculations) reveal the proton movements that govern Ser70 tetrahedral formation and then collapse to the acyl-enzyme. A remarkable duality of mechanism for tetrahedral formation is implicated. Following substrate binding, the pathway initiates by a low energy barrier (5 kcal mol(-1)) and an energetically favorable transfer of a proton from Lys73 to Glu166, through the catalytic water molecule and Ser70. This gives unprotonated Lys73 and protonated Glu166. Tetrahedral formation ensues in a concerted general base process, with Lys73 promoting Ser70 addition to the beta-lactam carbonyl. Moreover, the three-dimensional potential energy surface also shows that the previously proposed pathway, involving Glu166 as the general base promoting Ser70 through a conserved water molecule, exists in competition with the Lys73 process. The existence of two routes to the tetrahedral species is fully consistent with experimental data for mutant variants of the TEM beta-lactamase.     

Catalytic mechanism of class A beta-lactamase. I. The role of Glu166 and Serl30 in the deacylation reaction

The tetrahedral intermediate formation process, which is the first step in the deacylation reaction by class A beta-lactamase, was investigated by the ab initio molecular orbital method. In this study, benzyl penicillin was used as the substrate. From the results of our molecular dynamics study of the structure of beta-lactam antibiotics-beta-lactamase complex, the substrate, Ser70, Lys73, Ser130, Glu166 and a water molecule for the deacylation reaction were considered for construction of a model for calculation. The calculation results indicated that Glu166 plays a role in holding a water molecule, which is necessary for the deacylation reaction, and that the hydrogen bond network among Lys73Nzeta, Ser130Ogamma, and the carboxyl group of the beta-lactam antibiotics was formed by the uptake of beta-lactam antibiotics by beta-lactamase. The activation energy for this reaction was 33.3 kcal/mol, and it is very likely that the reaction occurred at body temperature. Subsequent calculation results obtained by using the model excluding Ser130 and the carboxyl group of the substrate indicated that the activation energy for this reaction was 40.8 kcal/mol, which is 7.5 kcal/mol higher than that of the previous reaction. It was found that the hydrogen bond network plays an important role in decreasing the activation energy for the tetrahedral intermediate formation reaction. Lys73Nzeta, which is located at the edge of the hydrogen bond network, played a role in forming a hydrogen bond with Glu166Oepsilon in order to help the deacylation reaction. The role of amino acid residues around the active site of class A beta-lactamase was also discussed.     

Catalytic mechanism of matrix metalloproteinases: two-layered ONIOM study

The two-layered ONIOM(B3LYP:MNDO) method has been used to investigate the hydrolytical mechanism of matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases capable of degrading a wide range of macromolecules of the extracellular matrix. Human stromelysin-1 (MMP-3) was chosen as a physiologically important member of the MMP family. As a structural reference, X-ray data on the stromelysin-1 catalytic domain (SCD) complexed to the transition state analogue diphenyl piperidine sulfonamide inhibitor was used. The backbone spacer of 11 residues (201-211) was included in the final model, spanning the catalytic Glu202 residue and the three structural His201,205,211 zinc ligands. The polypeptide framework incorporated, partly accounting for the protein rigidity, reduces the activation free energy slightly by 1.6 kcal/mol. Essentially a single-step catalytic mechanism was obtained, generally following a classical proposal for MMPs. Glu202 here acts as a base, abstracting a proton from the metal-bound reactant water and delivering this proton to the peptide nitrogen. An auxiliary water molecule is suggested to be of crucial importance acting as an electrophilic agent to the carbonyl oxygen of the substrate. The direct inclusion of the auxiliary water molecule decreases the activation free energy by about 5 kcal/mol via donation of a strong hydrogen bond. The calculated activation barrier of 13.1 kcal/mol agrees well with experimental rates.     

New model for a theoretical density functional theory investigation of the mechanism of the carbonic anhydrase: how does the internal bicarbonate rearrangement occur?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle of the carbonic anhydrase. A model system including the Glu106 and Thr199 residues and the "deep" water molecule has been used. It has been found that the nucleophilic attack of the zinc-bound OH on the CO(2) molecule has a negligible barrier (only 1.2 kcal mol(-1)). This small value is due to a hydrogen-bond network involving Glu106, Thr199, and the deep water molecule. The two usually proposed mechanisms for the internal bicarbonate rearrangement have been carefully examined. In the presence of the two Glu106 and Thr199 residues, the direct proton transfer (Lipscomb mechanism) is a two-step process, which proceeds via a proton relay network characterized by two activation barriers of 4.4 and 9.0 kcal mol(-1). This pathway can effectively compete with a rotational mechanism (Lindskog mechanism), which has a barrier of 13.2 kcal mol(-1). The fast proton transfer found here is basically due to the effect of the Glu106 residue, which stabilizes an intermediate situation where the Glu106 fragment is protonated. In the absence of Glu106, the barrier for the proton transfer is much larger (32.3 kcal mol(-1)) and the Lindskog mechanism becomes favored.     

The "somersault" mechanism for the p-450 hydroxylation of hydrocarbons. The intervention of transient inverted metastable hydroperoxides

A series of model theoretical calculations are described that suggest a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. A new class of metastable metal hydroperoxides is described that involves the rearrangement of the ground-state metal hydroperoxide to its inverted isomeric form with a hydroxyl radical hydrogen bonded to the metal oxide (MO-OH --> MO....HO). The activation energy for this somersault motion of the FeO-OH group is 20.3 kcal/mol for the P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] to produce the isomeric ferryl oxygen hydrogen bonded to an *OH radical [Por(SH)Fe(III)-O....HO(-)]. This isomeric metastable hydroperoxide, the proposed primary oxidant in the P450 hydroxylation reaction, is calculated to be 17.8 kcal/mol higher in energy than the ground-state iron(III) hydroperoxide Cpd 0. The first step of the proposed mechanism for isobutane oxidation is abstraction of a hydrogen atom from the C-H bond of isobutane by the hydrogen-bonded hydroxyl radical to produce a water molecule strongly hydrogen bonded to anionic Cpd II. The hydroxylation step involves a concerted but nonsynchronous transfer of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concomitant rebound of the incipient *OH radical to the carbon radical of isobutane to produce the C-O bond of the final product, tert-butyl alcohol. The TS for the oxygen rebound step is 2 kcal/mol lower in energy than the hydrogen abstraction TS (DeltaE() = 19.5 kcal/mol). The overall proposed new mechanism is consistent with a lot of the ancillary experimental data for this enzymatic hydroxylation reaction.     

New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study

The reaction pathway of Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase (DHQD) from S. enterica has been studied by performing molecular dynamics (MD) simulations and density functional theory (DFT) calculations and the corresponding potential energy profile has also been identified. On the basis of the results, the catalytic hydrolysis process for the wild-type enzyme consists of three major reaction steps, including nucleophilic attack on the carbon atom involved in the carbon-nitrogen double bond of the Schiff base intermediate by a water molecule, deprotonation of the His143 residue, and dissociation between the product and the Lys170 residue of the enzyme. The remarkable difference between this and the previously proposed reaction mechanism is that the second step here, absent in the previously proposed reaction mechanism, plays an important role in facilitating the reaction through a key proton transfer by the His143 residue, resulting in a lower energy barrier. Comparison with our recently reported results on the Schiff base formation and dehydration processes clearly shows that the Schiff base hydrolysis is rate-determining in the overall reaction catalyzed by type I DHQD, consistent with the experimental prediction, and the calculated energy barrier of ～16.0 kcal mol(-1) is in good agreement with the experimentally derived activation free energy of ～14.3 kcal mol(-1). When the imidazole group of His143 residue is missing, the Schiff base hydrolysis is initiated by a hydroxide ion in the solution, rather than a water molecule, and both the reaction mechanism and the kinetics of Schiff base hydrolysis have been remarkably changed, clearly elucidating the catalytic role of the His143 residue in the reaction. The new mechanistic insights obtained here will be valuable for the rational design of high-activity inhibitors of type I DHQD as non-toxic antimicrobials, anti-fungals, and herbicides.     

Catalytic mechanism of dopamine beta-monooxygenase mediated by Cu(III)-oxo

Mechanisms of dopamine hydroxylation by the Cu(II)-superoxo species and the Cu(III)-oxo species of dopamine beta-monooxygenase (DBM) are discussed using QM/MM calculations for a whole-enzyme model of 4700 atoms. A calculated activation barrier for the hydrogen-atom abstraction by the Cu(II)-superoxo species is 23.1 kcal/mol, while that of the Cu(III)-oxo, which can be viewed as Cu(II)-O*, is 5.4 kcal/mol. Energies of the optimized radical intermediate in the superoxo- and oxo-mediated pathways are 18.4 and -14.2 kcal/mol, relative to the corresponding reactant complexes, respectively. These results demonstrate that the Cu(III)-oxo species can better mediate dopamine hydroxylation in the protein environment of DBM. The side chains of three amino acid residues (His415, His417, and Met490) coordinate to the Cu(B) atom, one of the copper sites in the catalytic core that plays a role for the catalytic function. The hydrogen-bonding network between dopamine and the three amino acid residues (Glu268, Glu369, and Tyr494) plays an essential role in substrate binding and the stereospecific hydroxylation of dopamine to norepinephrine. The dopamine hydroxylation by the Cu(III)-oxo species is a downhill and lower-barrier process toward the product direction with the aid of the protein environment of DBM. This enzyme is likely to use the high reactivity of the Cu(III)-oxo species to activate the benzylic C-H bond of dopamine; the enzymatic reaction can be explained by the so-called oxygen rebound mechanism.     

New insights into the mechanism of the Schiff base formation catalyzed by type I dehydroquinate dehydratase from <Emphasis Type="Italic">S. enterica</Emphasis>

The Schiff base formation catalyzed by type I dehydroquinate dehydratase (DHQD) from Salmonella enterica has been studied by molecular docking, molecular dynamics simulation, and quantum chemical calculations. The substrate locates stably a similar position as the Schiff base intermediate observed in the crystal structure and forms strong hydrogen bonds with several active site residues. This binding mode is different from that of several other Schiff base enzymes. Then, the quantum chemical model has been constructed and the fundamental reaction pathways have been explored by performing quantum chemical calculation. The energy barrier of the previously proposed reaction pathway is calculated to be 30.7 kcal/mol, which is much higher than the experimental value of 14.3 kcal/mol of the whole dehydration reaction by type I DHQD from S. enterica. It means that this pathway is not favorable in energy. Therefore, a new and unexpected reaction pathway has been investigated with the favorable and reasonable energy barrier of 12.1 kcal/mol. The complicated role of catalytic His143 residue has also been elucidated that it mediates two proton transfers to facilitate the reaction. Moreover, the similarity and the difference between these two reaction pathways have been analyzed in detail. The new structural and mechanistic insights may direct the design of the inhibitors of type I dehydroquinate dehydratase as non-toxic antimicrobials, antifungals, and herbicides.     

Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor

The hydrogen abstraction reaction of camphor in cytochrome P450(cam) has been investigated in the native enzyme environment by combined quantum mechanical/molecular mechanical (QM/MM) calculations and in the gas phase by density functional calculations. This work has been motivated by contradictory published QM/MM results. In an attempt to pinpoint the origin of these discrepancies, we have systematically studied the factors that may affect the computed barriers, including the QM/MM setup, the optimization procedures, and the choice of QM region, basis set, and protonation states. It is found that the ChemShell and QSite programs used in the published QM/MM calculations yield similar results at given geometries, and that the discrepancies mainly arise from two technical issues (optimization protocols and initial system preparation) that need to be well controlled in QM/MM work. In the course of these systematic investigations, new mechanistic insights have been gained. The crystallographic water 903 placed near the oxo atom of Compound I lowers the hydrogen abstraction barrier by ca. 4 kcal/mol, and thus acts as a catalyst for this reaction. Spin density may appear at the A-propionate side chain of the heme if the carboxylate group is not properly screened, which might be expected to happen during protein dynamics, but not in static equilibrium situations. There is no clear correlation between the computed A-propionate spin density and the hydrogen abstraction barrier, and hence, no support for a previously proposed side-chain mediated transition state stabilization mechanism. Standard QM/MM optimizations yield an A-propionate environment close to the X-ray structure only for protonated Asp297, and not for deprotonated Asp297, but the computed barriers are similar in both cases. An X-ray like A-propionate environment can also be obtained when deprotonated Asp297 is included in the QM region and His355 is singly protonated, but this Compound II-type species with a closed-shell porphyrin ring has a higher hydrogen abstraction barrier and should thus not be mechanistically relevant.     

Ab initio and density functional theory studies of the catalytic mechanism for ester hydrolysis in serine hydrolases

We present results from ab initio and density functional theory studies of the mechanism for serine hydrolase catalyzed ester hydrolysis. A model system containing both the catalytic triad and the oxyanion hole was studied. The catalytic triad was represented by formate anion, imidazole, and methanol. The oxyanion hole was represented by two water molecules. Methyl formate was used as the substrate. In the acylation step, our computations show that the cooperation of the Asp group and oxyanion hydrogen bonds is capable of lowering the activation barrier by about 15 kcal/mol. The transition state leading to the first tetrahedral intermediate in the acylation step is rate limiting with an activation barrier (ΔE₀) of 13.4 kcal/mol. The activation barrier in the deacylation step is smaller. The double-proton-transfer mechanism is energetically unfavorable by about 2 kcal/mol. The bonds between the Asp group and the His group, and the hydrogen bonds in the oxyanion hole, increase in strength going from the Michaelis complex toward the transition state and the tetrahedral intermediate. In the acylation step, the tetrahedral intermediate is a very shallow minimum on the energy surface and is not viable when molecular vibrations are included. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 89–103, 1998     

Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O <--> H2O + OH

This article describes an ab initio investigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O <--> H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen-bonding complexes [HOH--OH] and [H2O--HO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOH--OH] complex, while the OH radical acts as a hydrogen donor in the [H2O--HO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS-APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as -2.1 approximately -2.3 and -4.1 approximately -4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2O--HO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS-APNO energy evaluations. After fitting the CBS-APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values.     

Class I ribonucleotide reductase revisited: the effect of removing a proton on Glu441

The substrate mechanism of class I ribonucleotide reductase has been revisited using the hybrid density functional B3LYP method. The molecular model used is based on the X-ray structure and includes all the residues of the R1 subunit commonly considered in the RNR substrate conversion scheme: Cys439 initiating the reaction as a thiyl radical, the redox-active cysteines Cys225 and Cys462, and the catalytically important Glu441 and Asn437. In contrast to previous theoretical studies of the overall mechanism, Glu441 is added as an anion. All relevant transition states have been optimized, including one where an electron is transferred 8 A from the disulfide to the substrate simultaneously with a proton transfer from Glu441. The calculated barrier for this step is 19.1 kcal/mol, which can be compared to the rate-limiting barrier indicated by experiments of about 17 kcal/mol. Even though the calculated barrier is somewhat higher than the experimental limit, the discrepancy is within the normal error bounds of B3LYP. The suggestion from the present modeling study is thus that a protonated Glu441 does not need to be present at the active site from the beginning of the catalytic cycle. However, the previously suggested mechanism with an initial protonation of Glu441 cannot be ruled out, because even with the cost added for protonation of Glu441 with a typical pK(a) of 4, the barrier for that mechanism is lower than the one obtained for the present mechanism. The results are compared to experimental results and suggestions.