Quantum mechanical/molecular mechanical study of three stationary points along the deacylation step of the catalytic mechanism of elastase

A large amount of experimental as well as theoretical information is available about the mechanism of serine proteases, but many questions remain unanswered. Here we study the deacylation step of the reaction mechanism of elastase. The water molecule in the acyl-enzyme active site, the binding mode of the carbonyl oxygen in the oxyanion hole, the characteristics of the tetrahedral intermediate structure, and the mobility of the imidazole ring of His-57 were studied with quantum mechanical/molecular mechanical methods. The models are based on a recent high-resolution crystal structure of the acyl-enzyme intermediate. The nucleophilic water in the active site of the acyl-enzyme has been shown to have two minima that differ by only 2 kcalmol⁻¹ in energy. The carbonyl group of the acyl-enzyme is located in the oxyanion hole and is positioned for attack by the hydrolytic water. The tetrahedral intermediate is a weakly bonded system, which is electrostatically stabilized by short hydrogen bonds to the backbone NH groups of Gly-193 and Ser-195 in the oxyanion hole. The short distance between the N^ɛ2 of His-57 and the O^γ of Ser-195 in the tetrahedral intermediate indicates a small movement of the imidazole ring towards the product in the deacylation step. The carbonyl group of the enzyme-product complex is not held strongly in the oxyanion hole, which shows that the peptide is first released from the oxyanion hole before it leaves the active site to regenerate the native state of the enzyme. Received: 11 September 2000 / Accepted: 15 September 2000 / Published online: 21 March 2001     

Theoretical studies on the deacylation step of serine protease catalysis in the gas phase, in solution, and in elastase

The deacylation step of serine protease catalysis is studied using DFT and ab initio QM/MM calculations combined with MD/umbrella sampling calculations. Free energies of the entire reaction are calculated in the gas phase, in a continuum solvent, and in the enzyme elastase. The calculations show that a concerted mechanism in the gas phase is replaced by a stepwise mechanism when solvent effects or an acetate ion are added to the reference system, with the tetrahedral intermediate being a shallow minimum on the free energy surface. In the enzyme, the tetrahedral intermediate is a relatively stable species ( approximately 7 kcal/mol lower in energy than the transition state), mainly due to the electrostatic effects of the oxyanion hole and Asp102. It is formed in the first step of the reaction, as a result of a proton transfer from the nucleophilic water to His57 and of an attack of the remaining hydroxyl on the ester carbonyl. This is the rate-determining step of the reaction, which requires approximately 22 kcal/mol for activation, approximately 5 kcal/mol less than the reference reaction in water. In the second stage of the reaction, only small energy barriers are detected to facilitate the proton transfer from His57 to Ser195 and the breakdown of the tetrahedral intermediate. Those are attributed mainly to a movement of Ser195 and to a rotation of the His57 side chain. During the rotation, the imidazolium ion is stabilized by a strong H-bond with Asp102, and the C(epsilon)(1)-H...O H-bond with Ser214 is replaced by one with Thr213, suggesting that a "ring-flip mechanism" is not necessary as a driving force for the reaction. The movements of His57 and Ser195 are highly correlated with rearrangements of the binding site, suggesting that product release may be implicated in the deacylation process.     

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     

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study

The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach. The reaction proceeds through the nucleophilic addition of the Ser203 O to the carbonyl C of acetylcholine, and the reaction is facilitated by simultaneous proton transfer from Ser203 to His447. The calculated potential energy barrier at the MP2(6-31+G) QM/MM level is 10.5 kcal/mol, consistent with the experimental reaction rate. The third residue of the catalytic triad, Glu334, is found to be essential in stabilizing the transition state through electrostatic interactions. The oxyanion hole, formed by peptidic NH groups from Gly121, Gly122, and Ala204, is also found to play an important role in catalysis. Our calculations indicate that, in the AChE-ACh Michaelis complex, only two hydrogen bonds are formed between the carbonyl oxygen of ACh and the peptidic NH groups of Gly121 and Gly122. As the reaction proceeds, the distance between the carbonyl oxygen of ACh and NH group of Ala204 becomes smaller, and the third hydrogen bond is formed both in the transition state and in the tetrahedral intermediate.     

Analysis of catalytic mechanism of serine proteases. Viability of the ring-flip hypothesis

Quantum calculations are applied to the active site of serine proteases, including four specific residues and a water molecule, as well as a substrate and proton donors in the oxyanion hole. Residues are tethered to the protein backbone of an X-ray structure but otherwise allowed to move freely to their lowest energy positions. The viability of the ring-flip hypothesis, which proposes that a 180 degrees rotation of the His-57 imidazole ring facilitates the catalysis, is assessed by comparison of energies of configurations both before and after such a flip. Specifically considered is the contribution to catalysis of the Ser-214 residue and a water molecule that is observed in the active site. The calculations provide detailed information concerning the nature, geometry, and strength of hydrogen bonds that are formed within the active site at each stage of the enzymatic mechanism.     

Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process

The reaction mechanism of serine proteases (trypsin), which catalyze peptide hydrolysis, is studied theoretically by ab initio QM/MM electronic structure calculations combined with Molecular Dynamics-Free Energy Perturbation calculations. We have calculated the entire reaction free energy profiles of the first reaction step of this enzyme (acylation process). The present calculations show that the rate-determining step of the acylation is the formation of the tetrahedral intermediate, and the breakdown of this intermediate has a small energy barrier. The calculated activation free energy for the acylation is approximately 17.8 kcal/mol at QM/MM MP2/(aug)-cc-pVDZ//HF/6-31(+)G/AMBER level, and this reaction is an exothermic process. MD simulations of the enzyme-substrate (ES) complex and the free enzyme in aqueous phase show that the substrate binding induces slight conformational changes around the active site, which favor the alignment of the reactive fragments (His57, Asp102, and Ser195) together in a reactive orientation. It is also shown that the proton transfer from Ser195 to His57 and the nucleophilic attack of Ser195 to the carbonyl carbon of the scissile bond of the substrate occur in a concerted manner. In this reaction, protein environment plays a crucial role to lowering the activation free energy by stabilizing the tetrahedral intermediate compared to the ES complex. The polarization energy calculations show that the enzyme active site is in a very polar environment because of the polar main chain contributions of protein. Also, the ground-state destabilization effect (steric strain) is not a major catalytic factor. The most important catalytic factor of stabilizing the tetrahedral intermediate is the electrostatic interaction between the active site and particular regions of protein: the main chain NH groups in Gly193 and Ser195 (so-called oxyanion hole region) stabilize negative charge generated on the carbonyl oxygen of the scissile bond, and the main chain carbonyl groups in Ile212 approximately Ser214 stabilize a positive charge generated on the imidazole ring of His57.     

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole‐enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen‐bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the α‐carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C? F bond is greatly facilitated by the hydrogen‐bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.     

Quantum chemical calculations on structural models of the catalytic site of chymotrypsin: comparison of calculated results with experimental data from NMR spectroscopy

Hybrid density functional quantum mechanical calculations were used to study the strength of the hydrogen bond between His(57) N(delta)(1) and Asp(102) O(delta)(1) in chymotrypsin and how it changes along the reaction coordinate. Comparison of experimental shifts with the results of chemical shift calculations on a variety of small molecules, including species containing very strong hydrogen bonds, has validated the overall approach and provided the means for calibrating and correcting the calculated values. Models of the active site of chymotrypsin in its resting state and tetrahedral intermediate state were derived from high-resolution X-ray structures. The distance between His(57) N(delta)(1) and Asp(102) O(delta)(1) in each model was varied between 2.77 A (weak hydrogen bond) and 2.50 A (extremely strong hydrogen bond), and the one-dimensional potential energy surface of the hydrogen-bonded proton (or deuteron/triton) was determined. The zero-point energy, probability distribution, and chemical shift were determined for each distance. Calculated values for NMR chemical shifts, NMR chemical shift differences between (1)H and (3)H, and (2)H/(1)H fractionation factors were compared with published experimental values. Energies provided by the calculations indicated that the hydrogen bond between His(57) N(delta)(1) and Asp(102) O(delta)(1) in the chymotrypsin active site increases in strength by 11 kcal mol(-)(1) in going from the resting state of the enzyme to the tetrahedral intermediate state. This result confirms the hypothesis that the strengthened hydrogen bond plays an important role in lowering the energy of the transition state and, hence, in the catalytic efficiency of the enzyme. Models of the transition state that best fit the experimental data are consistent with a "strong" hydrogen bond between His(57) N(delta)(1) and Asp(102) O(delta)(1) but apparently not a "low-barrier" or "very strong" hydrogen bond.     

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K

Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.     

Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase

Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 ?(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.     

Theoretical analysis of the hydrogen bond of imidazolium C(2)-H with anions

The intermolecular interaction energies of ion pairs of imidazolium-based ionic liquids were studied by MP2/6-311G level ab initio calculations. Although the hydrogen bond between the C(2) hydrogen atom of an imidazolium cation and anion has been regarded as an important interaction in controlling the structures and physical properties of ionic liquids as in the cases of conventional hydrogen bonds, the calculations show that the nature of the C(2)-H...X interaction is considerably different from that of conventional hydrogen bonds. The interaction energies of the imidazolium cation with neighboring anions in the four crystals of ionic liquids were calculated. The size of the interaction is determined mainly by the distance between the imidazolium ring and anion. The calculated interaction energy is nearly inversely proportional to the distance, which shows that the charge-charge interaction is the dominant interaction in the attraction. The orientation of the anion relative to the C(2)-H bond does not greatly affect the size of the interaction energy. Calculated interaction energy potentials of 1,3-dimethylimidazolium tetrafluoroborate ([dmim][BF(4)]) complexes show that the C(2)-H bond does not prefer to point toward a fluorine atom of the BF(4). This shows that the C(2)-H...X hydrogen bond is not essential for the attraction.     

Divergent function in the crotonase superfamily: an anhydride intermediate in the reaction catalyzed by 3-hydroxyisobutyryl-CoA hydrolase

3-Hydroxyisobutyryl-CoA hydrolase (HICH), a member of the enoyl-CoA (crotonase) superfamily, catalyzes the hydrolysis of 3-hydroxyisobutyryl-CoA to 3-hydroxyisobutyrate. Like other members of the superfamily, the sequence of HICH contains conserved sequences for an oxyanion hole that stabilizes anionic intermediates. In contrast to most members of the superfamily, the reaction catalyzed by HICH does not proceed via formation of a thioester enolate anion; instead, evidence based on substrate deuterium isotope effects, the reactivity of substrate analogues that cannot form thioester enolate anions, single-turnover experiments in H218O, and the kinetic phenotypes of site-directed mutants provide evidence for a mechanism involving the formation of an anhydride intermediate involving Glu143 in the active site. In the reactions catalyzed by many members of the superfamily, homologues of Glu143 abstract the alpha proton of the thioester substrate to generate the thioester enolate anion intermediate. Presumably, one or more of the anionic tetrahedral intermediates on the HICH reaction coordinate are stabilized by the oxyanion hole. Thus, we conclude that the conserved oxyanion hole in this superfamily can be used to stabilize a variety of anionic intermediates.     

Regioselectivity of the glycosylation of N-dimethylmaleoyl-protected hexosamine acceptors. An experimental and DFT approach

Both anomers of the methyl glycoside of 6-O-benzyl-N-dimethylmaleoyl-D-allosamine (6 and 7) are glycosylated exclusively on O3 when reacting with the trichloroacetimidate of peracetylated α-D-galactopyranose (5). This regioselectivity is expected for 6, the α-anomer, as a strong hydrogen bond of its H(O)3 with the carbonyl group of the dimethylmaleoyl group occurs, as shown by NMR temperature dependence. However, this hydrogen bond was not encountered experimentally for 7, the β-anomer. A DFT study of the energies implied in an analog of the glycosylation reaction charged intermediate has explained neatly this behavior, in terms of strong hydrogen bonds occurring at these charged intermediates. This approach explains both the experimental regioselectivities found for 6 and 7, but furthermore the calculations have shown a marked agreement with the regioselectivities found for other related compounds in the literature.     

Investigations of coupling characters in ionic liquids formed between the 1-ethyl-3-methylimidazolium cation and the glycine anion

In this study, novel ionic liquids formed between the 1-ethyl-3-methylimidazolium cation [emim]+ and the glycine anion [Gly]- have been investigated theoretically. The relevant geometrical characteristics, energy properties, the characters of the intermolecular hydrogen bonds (H bonds), and the possibility of proton transfer as well as IR characteristics have been systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses have also been applied to understand the nature of the interactions between ionic pairs in ionic liquids. The most stable geometries have been determined by analyzing the relative energies and interaction energies, where the C-H...O intermolecular H bonds involving the protons attached to the imidazolium ring have been found to possess partial covalent character in nature. Electron transfers from the lone pairs of the carbonyl O atom of [Gly]- to the C-H antibonding orbital of the [emim]+ can explain the elongation and red shift of the C-H stretching frequency. The interaction modes are more favorable when the carbonyl O atoms of [Gly]- interact with the C2-H of the imidazolium ring and the C-H of the methyl group through the formation of double H bonds. The origin of the high stability of the amino acid ionic liquids observed experimentally may be attributed to the nonexistence of the proton-transferred products (neutral pairs) together with the large energy needed for separation of the ionic pairs. Additionally, the characteristics of the IR spectra have been analyzed to demonstrate the variants of the molecular structure of the [emim]+[Gly]- ionic liquids.     

Synthetic utilization of polynitroaromatic compounds. 6. Remarkable regioselectivity in nucleophilic displacement of aromatic nitro groups with amines

5,7-Dinitroquinazoline-4-ones undergo nucleophilic displacement of a nitro group with N-, S-, and O-nucleophiles. In contrast to previously studied dinitro-substituted benzoannulated five- and seven-membered heterocycles (where a high degree of selectivity was observed), these quinazolines mostly yield mixtures of regioisomeric substitution products. At the same time, primary and secondary amines react selectively to afford 5-aminoquinazolones (peri-substitution). A similar effect is observed for some other polynitroaromatic compounds with adjacent nitro and carbonyl groups. This phenomenon is attributed to a stabilization of the intermediate peri-sigma-complex by intramolecular hydrogen bond N(+)-H...O double bond C.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Computational studies of nucleophilic substitution at carbonyl carbon: the S(N)2 mechanism versus the tetrahedral intermediate in organic synthesis

A theoretical study specifically addresses the question of whether nucleophilic addition to the carbonyl groups of acid chlorides, esters, and anhydrides involves an addition-elimination pathway or proceeds by a concerted S(N)2-like mechanism in the absence of the generally assumed tetrahedral intermediate. Density functional calculations [B3LYP/6-31+G(d,p)] establish that chloride ion exchange reactions with both formyl and acetyl chloride proceed by a pi attack on the C=O bond. No discernible tetrahedral intermediate typical of an addition-elimination pathway was found in either case. While a tetrahedral intermediate does exist for the addition of fluoride ion to (Cl)(2)C=O, halide exchange of LiCl with both ClFC=O and (Cl)(2)C=O also proceeds by a concerted S(N)2-like pathway. The formation of a tetrahedral intermediate from the addition of methanol to acetyl chloride is slightly exothermic (4.4 kcal/mol). The ion-dipole complex of methanol weakly bonded to the carbonyl carbon of protonated acetyl chloride is stabilized by 13.8 kcal/mol but does not collapse to a tetrahedral intermediate. When four CH(3)OH molecules are H-bonded to protonated acetyl chloride, a tetrahedral intermediate is not completely formed and this solvated complex more closely resembles the precursor to an S(N)1-type ionization of Cl(-). With six H-bonding methanol molecules, a methanol adds to the carbonyl carbon and a proton relay occurs with formation of a tetrahedral-like structure that immediately loses chloride ion in an S(N)1-like solvolysis. These results corroborate earlier suggestions (Bentley et al. J. Org. Chem. 1996, 61, 7927) that the methanolysis of acetyl chloride does not proceed through the generally assumed addition-elimination pathway with a discrete tetrahedral intermediate but is consistent with ionization of Cl(-). The reaction of methoxide ion with methyl acetate proceeds via a multiple-well energy surface and involves the intermediacy of an asymmetrical species with differing C-OMe bond lengths. Models of synthetic applications of acyl transfer reactions involving anhydrides that form N-acyloxazolidinones also proceed by a concerted S(N)2-type pathway even with the carboxylate leaving group. Concerted transition states were observed for the reactions of each enantiomer of a 1,3-diphenylcycloprop-2-ene carboxylic anhydride by S-3-lithio-4-phenyloxazolidinone. Despite close structural similarities between the diastereomeric transition states, the relative energies correlated closely with the experimental results.     

Investigation of a general base mechanism for ester hydrolysis in C-C hydrolase enzymes of the alpha/beta-hydrolase superfamily: a novel mechanism for the serine catalytic triad

Previous mechanistic and crystallographic studies on two C-C hydrolase enzymes, Escherichia coli MhpC and Burkholderia xenovorans BphD, support a general base mechanism for C-C hydrolytic cleavage, rather than the nucleophilic mechanism expected for a serine hydrolase. The role of the active site serine residue could be to form a hydrogen bond with a gem-diolate intermediate, or to protonate such an intermediate. Hydrolase BphD is able to catalyse the hydrolysis of p-nitrophenyl benzoate ester substrates, which has enabled an investigation of these mechanisms using a Hammett analysis, and comparative studies upon five serine esterases and lipases from the alpha/beta-hydrolase family. A reaction parameter (rho) value of +0.98 was measured for BphD-catalysed ester hydrolysis, implying a build-up of negative charge in the transition state, consistent with a general base mechanism. Values of +0.31-0.61 were measured for other serine esterases and lipases, for the same series of esterase substrates. Pre-steady state kinetic studies of ester hydrolysis, using p-nitrophenyl acetate as the substrate, revealed a single step kinetic mechanism for BphD-catalysed ester hydrolysis, with no burst kinetics. A general base mechanism for BphD-catalysed ester hydrolysis is proposed, in which Ser-112 stabilises an oxyanion intermediate through hydrogen bonding, and assists the rotation of this oxyanion intermediate via proton transfer, a novel reaction mechanism for the serine catalytic triad.     

Crystal engineering through face interactions between tetrahedral and octahedral building blocks: crystal structure of [epsilon-Al13O4(OH)24(H2O)12]2[V2W4O19]3(OH)2).27H2O

A new intercluster salt crystal [epsilon-Al13O4(OH)24(H2O)12]2[V2W4O19]3(OH)2).27H2O (1) was synthesized from the reaction of octahedral Lindqvist-type polyoxometalate [V2W4O19](4-) and truncated tetrahedral Keggin-type [epsilon-Al13O4(OH)24-H2O)(12)](7+) cluster ions. The crystal structure shows that the oppositely charged cluster ions are arranged alternately and have their contacting faces parallel to each other for maximal interactions, both electrostatic and hydrogen bonding. The face-to-face interaction mode of the clusters allows analysis of the crystal structure in an analogy to the bond directionality of conventional inorganic crystals. Therefore, the packing of clusters in 1 is that of As2O3 (Claudetite-II). With the bond directionality, the crystal has large one-dimensional channels with a cross-sectional area of 14.17 x 13.88 A(2) that are filled by lattice water and charge-balancing OH-.     

pKa,MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step

The acylation step of the catalytic mechanism of beta-lactamases and penicillin-binding proteins (PBPs) has been studied with various approaches. The methods applied range from molecular dynamics (MD) simulations to multiple titration calculations using the Poisson-Boltzmann approach to quantum mechanical (QM) methods. The mechanism of class A beta-lactamases was investigated in the greatest detail. Most approaches support the critical role of Glu-166 and hydrolytic water in the acylation step of the enzymatic catalysis in class A beta-lactamases. The details of the catalytic mechanism have been revealed by the QM approach, which clearly pointed out the critical role of Glu-166 acting as a general base in the acylation step with preferred substrates. Lys-73 shuffles a proton abstracted by Glu-166 O(epsilon ) to the beta-lactam nitrogen through Ser-130 hydroxyl. This proton is transferred from O(gamma) of the catalytic Ser-70 through the bridging hydrolytic water to Glu-166 O(epsilon ). Then the hydrogen is simultaneously passed through S(N)2 inversion mechanism at Lys-73 N(zeta) to Ser-130 O(gamma), which loses its proton to the beta-lactam nitrogen. The protonation of beta-lactam nitrogen proceeds with an immediate ring opening and collapse of the first tetrahedral species into an acyl-enzyme intermediate. However, the studies that considered the effect of solvation lower the barrier for the pathway, which utilizes Lys-73 as a general base, thus creating a possibility of multiple mechanisms for the acylation step in the class A beta-lactamases. These findings help explain the exceptional efficiency of these enzymes. They emphasize an important role of Glu-166, Lys-73, and Ser-130 for enzymatic catalysis and shed light on details of the acylation step of class A beta-lactamase mechanism. The acylation step for class C beta-lactamases and six classes of PBPs were also considered with continuum solvent models and MD simulations.