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.     

Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase

D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.     

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     

醇脱氢酶结构和作用机理研究进展

介绍了醇脱氢酶的种类, 酵母醇脱氢酶和肝醇脱氢酶等两类常用的醇脱氢酶的物理化学性质和活性位点结构. 归纳了对肝醇脱氢酶和酵母醇脱氢酶作用机理的研究, 重点评述了醇脱氢酶催化反应中的两个关键步骤质子转移和氢化物转移过程机理的研究进展.     

Model studies on the active site of carbonic anhydrase: Ligand properties and CO2 binding

In view of building a workable molecular model of tetraliganded zinc at the active site of carbonic anhydrase, an ab initio SCF study using pseudopotentials is performed on Zn²⁺(OH₂)_n from n = 2 to 6, Zn²⁺(NH₃)_n?1 (OH₂) for n = 2 and 4, Zn²⁺(NH₃)₂ (imidazole) (OH₂), and their ionized species involving OH^? or imidazolate, considering in particular the evolution of the properties of the ligands and of the bound cation upon increasing n and upon replacement of one ligand by another. (Comparison of NH₃ and imidazole binding was made in a full SCF calculation.) The results obtained in the tetraliganded complex confirm that zinc binding facilitates water deprotonation more than imidazole deprotonation, so as to reverse the order of their intrinsic ease of ionization. A study of the approach of CO₂ toward the active site is made in an electrostatic approximation using as models the most representative of the computed four-ligand complexes.     

Electronic aspects of LADH catalytic mechanism

Electronic aspects of the catalytic mechanism of liver alcohol dehydrogenase (LADH) are studied with the help of ab initio analytical gradient SCF MO methods. Three points are considered: (i) role of the catalytic zinc; (ii) geometry and electronic structure of the transition state for the hydride transfer reactions; and (iii) factors affecting the energy gap for the hydride transfer step, namely, substrate binding to zinc, reaction field, and serine 48 effects on the potential energy profile. The coordination sphere of the catalytic zinc has been modeled with an ammonia molecule and two SH^? groups; complexes with CH₃O^?, CH₃OH, and CH₂O have been studied; a (6, 2, 2, 2, 1/6, 2, 1/3, 2) basis set has been used for Zn⁺⁺; a (5, 2, 1, 1/3, 2) was used for oxygen, carbon, and sulfur; and a (3, 1) was used for hydrogen atoms. The hydride step was studied with two model systems: pyridinium cation/1,4-dihydropyridine coupled to the CH₃O^?/CH₂O reaction, and cyclopropenyl cation/cyclopropene coupled to the CH₃O^?/CH₂O system. For the latter, the role of Ser48 has been studied at the supermolecule level. The calculation on the hydride transfer step has been done at a 4–31G basis set level. The results obtained shed new light on the sources of catalytic activity of liver alcohol dehydrogenases.     

Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study

The detailed mechanism of metal-cysteine binding is still poorly understood. It is not clear if every metal cation can induce cysteine deprotonation, how the dielectric medium affects this process, and the extent to which other ligands from the metal's first and second coordination shell influence cysteine ionization. It is also not clear if the zinc cation, with its positive charge reduced by charge transfer from the first two bound cysteinates, could still assist deprotonation of the next one or two cysteines in Cys3His and Cys4 zinc-finger cores. Here, we elucidate the factors governing the cysteine protonation state in metal-binding sites, in particular in Zn.Cys4 complexes, using a combined ab initio and continuum dielectric approach. Transition metal dications such as Zn2+ and Cu2+ and trivalent cations such as Al3+ with pronounced ability to accept charge from negatively charged Cys- are predicted to induce cysteine deprotonation, but not "hard" divalent cations such as Mg2+. A high dielectric medium was found to favor cysteine deprotonation, while a low one favored the protonated state. Polarizable ligands in the metal's first shell that can competitively donate charge to the metal cation were found to lower the efficiency of the metal-assisted cysteine deprotonation. The calculations predict that the zinc cation could assist deprotonation of all the cysteines during the folding of Cys4 zinc-finger cores and the [Zn.(Cys-)4]2- state is likely to be preserved in the final folded conformation of the protein provided the binding site is tightly encapsulated by backbone peptide groups or lysine/arginine side chains, which stabilize the ionized cysteine core.     

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.

Herein, we report molecular dynamics simulations of the mononuclear form of the Bacillus cereuszinc-beta-lactamase. We studied two different configurations which differ in the presence of a zinc-bound hydroxide or a zinc-bound water and in the protonation state of the essential His210 residue. Contacts of the catalytically important residues (Asp90, His210, Cys168, etc.) with the zinc center are characterized by the MD analyses. The nature of the Zn-OH(2) --> His210 proton transfer pathway connecting the two configurations was studied by means of QM calculations on cluster models while the relative stability of the two configurations was estimated from QM/MM calculations in the enzyme. From these results, a theoretical model for the kinetically active form of the B. cereus metalloenzyme is proposed. Some mechanistic implications and the influence of mutating the Cys168 residue are also discussed.     

A Potassium Diboryllithate: Synthesis,Bonding Properties,and the Deprotonation of Benzene

A potassium diboryllithate (B₂LiK) was synthesized and structurally characterized. DFT calculations, including NPA and AIM analyses of B₂LiK, revealed ionic interactions between the two bridging boryl anions and Li⁺ and K⁺. Upon standing in benzene, B₂LiK deprotonated the solvent to form a hydroborane and a phenylborane. On the basis of DFT calculations, a detailed reaction mechanism, involving deprotonation and hydride/phenyl exchange processes, is proposed. An NBO analysis of the transition state for the deprotonation of benzene suggests that the deprotonation should be induced by the coordination of benzene to the K⁺.     

A Potassium Diboryllithate: Synthesis,Bonding Properties,and the Deprotonation of Benzene

A potassium diboryllithate (B₂LiK) was synthesized and structurally characterized. DFT calculations, including NPA and AIM analyses of B₂LiK, revealed ionic interactions between the two bridging boryl anions and Li⁺ and K⁺. Upon standing in benzene, B₂LiK deprotonated the solvent to form a hydroborane and a phenylborane. On the basis of DFT calculations, a detailed reaction mechanism, involving deprotonation and hydride/phenyl exchange processes, is proposed. An NBO analysis of the transition state for the deprotonation of benzene suggests that the deprotonation should be induced by the coordination of benzene to the K⁺.     

MO-Studies of enzyme reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase A

Ab initio and semiempiridal (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen-bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn⁺⁺ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zinc-coordinated water to give an active ZnOH⁺ species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol^?1. The next and rate-determining step is the concerted addition of the ZnOH⁺ moiety to the formamide C?O bond. The Zn? O distance in the transition state is more than 3 Å. In four further steps, the amide nitrogen is protonated and the C? N bond cleaved. The net activation energy for the entire process is 15.5 kcal mol^?1 relative to the active site model and 19.6 kcal mol^?1 relative to the most stable point on the calculated reaction profile.     

Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II

We present, for the first time, how transient changes in the coordination number of zinc ion affects the rate determining step in the enzyme human carbonic anhydrase (HCA) II. The latter involves an intramolecular proton transfer between a zinc-bound water and a distant histidine residue (His-64). In the absence of time-resolved experiments, results from classical and QM-MM molecular dynamics and transition path sampling simulations are presented. The catalytic zinc ion is found to be present in two possible coordination states; viz. a stable tetra-coordinated state, T and a less stable penta-coordinated state, P with tetrahedral and trigonal bipyramidal coordination geometries, respectively. A fast dynamical inter-conversion occurs between T and P due to reorganization of active site water molecules making the zinc ion more positively charged in state P. When initiated from different coordination environments, the most probable mechanism of proton transfer is found to be deprotonation of the equatorial water molecule from state P and transfer of the excess proton via a short path formed by hydrogen bonded network of active site water molecules. We estimate the rate constant of proton transfer as from P and from T. A quantitative match of estimated k_P with the experimental value, ( ) suggests that dynamics of Zn coordination triggers the rate determining proton transfer step in HCA II.     

Conformational analysis by bond orbitals with delocalization corrections: Rotation of the ser-195 side chain in α-chymotrypsin

A recently developed procedure for calculation of tails of localized molecular orbitals is applied in order to obtain approximate rotational potential curves. In order to calculate reliable rotational barriers, tails, originating from direct interactions between bonding and antibonding strictly localized orthogonal orbitals, have to be determined. This finding permits us to develop a fast approximate SCF semiempirical procedure offering a reliable tool for studying conformational problems in rather large (bio)molecules. As a first example, a model of the active site of α-chymotrypsin was examined. According to our calculations, a hydrogen bond between Ser-195 and His-57 should exist.     

Dynamic structures of horse liver alcohol dehydrogenase (HLADH): results of molecular dynamics simulations of HLADH-NAD(+)-PhCH(2)OH, HLADH-NAD(+)-PhCH(2)O(-), and HLADH-NADH-PhCHO.

Molecular dynamics simulations of the oxidation of benzyl alcohol by horse liver alcohol dehydrogenase (HLADH) have been carried out. The following three states have been studied: HLADH.PhCH(2)OH.NAD(+) (MD1), HLADH.PhCH(2)O(-).NAD(+) (MD2), and HLADH.PhCHO.NADH (MD3). MD1, MD2, and MD3 simulations were carried out on one of the subunits of the dimeric enzyme covered in a 32-A-radius sphere of TIP3P water centered on the active site. The proton produced on ionization of the alcohol when HLADH.PhCH(2)OH.NAD(+) --> HLADH.PhCH(2)O(-).NAD(+) is transferred from the active site to solvent water via a hydrogen bonding network consisting of serine48 hydroxyl, ribose 2'- and 3'-hydroxyl groups, and Hist51. Hydrogen bonding of the 3'OH of ribose to Ile269 carbonyl maintains this proton in position to be transferred to water. Molecular dynamic simulations have been employed to track water1287 from the TIP3 water pool to the active site, thus exhibiting the mode of entrance of water to the active site. With time the water1287 accumulates in two different positions in order to accept the proton from the ribose 3'-OH and from His51. There can be identified two structural substates for proton passage. In the first substate the imidazole Ne2 of His51 is adjacent to the nicotinamide ribose C2'-OH and hydrogen bonding distances for proton transfer through the hydrogen bonded relay series PhCH(2)OH...Ser48-OH...Ribose2'-OH...His51...OH(2) (path 1) average 2.0, 2.0, and 2.1 A and (for His51...OH(2)) minimal distances less or equal to 2.5 A. The structure for path 1 is present 20% of the time span. And in the second substate, there are two possible proton passages: path 1 as before and path 2. Path 2 involves the hydrogen-bonded relay series PhCH(2)OH...Ser48-OH...Ribose2'-OH...Ribose3'-OH...His51.OH(2) with the average bonding distances being 2.0, 2.0, 2.1, and 2.0 A and (for His51...OH(2)) minimal distances less or equal to 2.5 A (20% probability of the time span), respectively. During the molecular dynamics simulation the NAD(+) ribose conformations have stabilized at the C2'-endo-C3'-exo or the C2'-endo conformations. With the C2'-endo conformation the first and second substates are able to persist for different time spans, while with the C2'-endo-C3'-exo conformation the only possible pathway involves the first substate. For both first and second substates the fluctuation of the distances between the ribose-OH protons and N epsilon 2 of His51 imidazole ring is partially contributed by the "windshield wiper" motion of the His51 imidazole ring. Since the imidazole of His-51 contributes only about 10-fold to activity, as estimated from the decrease in activity upon substitution with a Gln, there must be an alternate route for the proton to pass to solvent without going through this histidine. A third pathway involves ribose C3'-OH and Ile-269. In MD2, near attack conformers (NACs) for hydride transfer from PhCH(2)O(-) to NAD(+) represent approximately 60% of E.S conformers. The molecular dynamic study of MD3 at mildly basic pH reveals that reactive ground state conformers (NACs) for hydride transfer from NADH to PhCHO amount to 12 mol % of conformers. In MD3, anisotropic bending of the dihydronicotinamide ring of NADH (average value of alpha(c) = 4.0 degrees and alpha(n) = 0.5 degrees, respectively) is observed.     

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.     

Application of experimental (FT-ICR) and theoretical (AM1) methods to the study of proton-transfer reactions for tautomerizing amidines in the gas phase

Semiempirical calculations (AM1) together with experimental mass spectrometric (FT-ICR) data indicate the imino nitrogen atom as the favoured site of protonation and the amino nitrogen atom as the site of deprotonation of the amidine group in the gas phase. For tautomerizing N-methyl-N'-phenylbenzamidine the tautomer with the phenyl group at the imino nitrogen atom weakly predominates in tautomeric mixture.     

Ytterbium (II) Hydride as a Powerful Multielectron Reductant

A dimeric β-diketiminato ytterbium(II) hydride affects both the two-electron aromatization of 1,3,5,7-cyclooctatetraene (COT) and the more challenging two-electron reduction of polyaromatic hydrocarbons, including naphthalene (E⁰=−2.60 V). Confirmed by Density Functional Theory calculations, these reactions proceed via consecutive polarized Yb−H/C=C insertion and deprotonation steps to provide the respective ytterbium (II) inverse sandwich complexes and hydrogen gas. These observations highlight the ability of a simple ytterbium(II) hydride to act as a powerful two-electron reductant at room temperature without the necessity of an external electron to initiate the reaction and avoiding radicaloid intermediates.     

Towards a quantum-chemical representation of enzyme activity. A scrf pce cndo/2 study of the ladh proton relay system

The proton translocation process via the proton relay system of LADH has been studied within the self-consistent reaction field protein core effect (SCRF PCE) theory. The inhomogeneous electric field of the protein atoms, other than those belonging to the cage system, the Zn atom and the NAD⁺ coenzyme, have been let in step by step; the polarization reaction field is being allowed for at the last stage. The spatial charge-separation process appearing in the LADH action mechanism is substantiated by the present calculations. These results strongly suggest that the proposed scheme would be a faithful representation of some of the enzyme activity factors.     

Carbonic anhydrase activators. Activation of isozymes I, II, IV, VA, VII, and XIV with l- and d-histidine and crystallographic analysis of their adducts with isoform II: engineering proton-transfer processes within the active site of an enzyme

Activation of six human carbonic anhydrases (CA, EC 4.2.1.1), that is, hCA I, II, IV, VA, VII, and XIV, with l- and d-histidine was investigated through kinetics and by X-ray crystallography. l-His was a potent activator of isozymes I, VA, VII, and XIV, and a weaker activator of hCA II and IV. d-His showed good hCA I, VA, and VII activation properties, being a moderate activator of hCA XIV and a weak activator of hCA II and IV. The structures as determined by X-ray crystallography of the hCA II-l-His/d-His adducts showed the activators to be anchored at the entrance of the active site, contributing to extended networks of hydrogen bonds with amino acid residues/water molecules present in the cavity, explaining their different potency and interaction patterns with various isozymes. The residues involved in l-His recognition were His64, Asn67, Gln92, whereas three water molecules connected the activator to the zinc-bound hydroxide. Only the imidazole moiety of l-His interacted with these amino acids. For the d-His adduct, the residues involved in recognition of the activator were Trp5, His64, and Pro201, whereas two water molecules connected the zinc-bound water to the activator. Only the COOH and NH(2) moieties of d-His participated in hydrogen bonds with these residues. This is the first study showing different binding modes of stereoisomeric activators within the hCA II active site, with consequences for overall proton-transfer processes (rate-determining for the catalytic cycle). The study also points out differences of activation efficiency between various isozymes with structurally related activators, convenient for designing alternative proton-transfer pathways, useful both for a better understanding of the catalytic mechanism and for obtaining pharmacologically useful derivatives, for example, for the management of Alzheimer's disease.     

Theoretical study of carbonic anhydrase-catalyzed hydration of co2: A brief review

Quantum mechanical calculations have been used to study the reaction mechanism of human carbonic anhydrase-catalyzed hydration of CO₂. This reaction is responsible for fast metabolism of CO₂ in the human body. For each of the reaction steps, possible catalytic effects of active site residues are examined. The pertinent results are as follows. (1) For CO₂ binding, the experimentally observed 2.5 cm^?1 frequency shift of the asymmetic stretching frequency between measurements taken in the aqueous solution and in the enzyme is reproduced in our theoretical calculations. Our results suggest that CO₂ binds to the zinc ion within the hydrophobic pocket. (2) No energy barrier is found for the nucleophilic attack from Zn²⁺?bound OH^? to C of CO₂ to form Zn²⁺?bound HCO₃^?. (3) For the internal proton transfer within zinc-bound HCO₃^?, the barrier of 35.6 kcal/mol for the direct internal proton transfer is reduced to 3.5 and 1.4 kcal/mol, respectively, when one or two water molecules are included for proton relay. (4) Displacement of Zn²⁺?bound HCO₃^? by H₂O is facilitated by the presence of the negatively charged Glu 106-Thr 199 chain and by the association and the subsequent ionization of a fifth water ligand. (5) For the intramolecular proton transfer between Zn²⁺-bound H₂O and His 64, the Zn²⁺ ion lowers the pK_a of Zn²⁺?bound water and repels the proton. His 64, or a similar proton receptor with a larger proton affinity than H₂O, functions as proton receiver; and the active site water molecules visualized by x-ray crystallography are important for the proton relay function. In summary, it is demonstrated that in order to achieve effective catalysis, a sequence of precisely coordinated catalytic events among all participating catalytic elements in the enzyme's active site is essential.