A molecular orbital study on the enzymic reaction mechanism of alpha-chymotrypsin

Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.

Role of Asp102 in the catalytic relay system of serine proteases: a theoretical study

The role of Asp102 in the catalytic relay system of serine proteases is studied theoretically by calculating the free energy profiles of the single proton-transfer reaction by the Asn102 mutant trypsin and the concerted double proton-transfer reaction (so-called the charge-relay mechanism) of the wild-type trypsin. For each reaction, the reaction free energy profile of the rate-determining step (the tetrahedral intermediate formation step) is calculated by using ab initio QM/MM electronic structure calculations combined with molecular dynamics-free energy perturbation method. In the mutant reaction, the free energy monotonically increases along the reaction path. The rate-determining step of the mutant reaction is the formation of tetrahedral intermediate complex, not the base (His57) abstraction of the proton from Ser195. In contrast to the single proton-transfer reaction of the wild-type, MD simulations of the enzyme-substrate complex show that the catalytically favorable alignment of the relay system (the hydrogen bonding network between the mutant triad, His57, Asn102, and Ser195) is rarely observed even in the presence of a substrate at the active site. In the double proton-transfer reaction, the energy barrier is observed at the proton abstraction step, which corresponds to the rate-determining step of the single proton-transfer reaction of the wild-type. Although both reaction profiles show an increase of the activation barrier by several kcals/mol, these increases have different energetic origins: a large energetic loss of the electrostatic stabilization between His57 and Asn102 in the mutant reaction, while the lack of stabilization by the protein environment in the double proton-transfer reaction. Comparing the present results with the single proton transfer of the wild-type, Asp102 is proven to play two important roles in the catalytic process. One is to stabilize the protonated His57, or ionic intermediate, formed during the acylation, and the other is to fix the configuration around the active site, which is favorable to promote the catalytic process. These two factors are closely related to each other and are indispensable for the efficient catalysis. Also the present calculations suggest the importance of the remote site interaction between His57 and Val213-Ser214 at the catalytic transition state.

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.

A new mechanism in serine proteases catalysis exhibited by dipeptidyl peptidase IV (DP IV)--Results of PM3 semiempirical thermodynamic studies supported by experimental results

Herein we present results of semiempirical molecular orbital calculations employing the PM3 molecular model. The compounds studied are related to substrates of the serine protease dipeptidyl peptidase IV (DP IV). Our goal was the thermodynamic characterization of the DP IV-enzyme-catalyzed reaction pathway. A new mechanism of serine proteases catalysis is presented. We found that a tetrahedral intermediate can be stabilized by the formation of an oxazolidine ring with the nonscissile P2-P1 peptide bond. In this way, the negative charge of the tetrahedral intermediate around the scissile bond is transferred to the carbonyl oxygen atom of the preceding peptide bond. This negative charge can be compensated by a proton transfer from the positively charged N-terminus to this oxygen atom. It is shown that the positively charged N-terminus is the driving force in this particular serine protease mechanism of catalysis. The mechanism is supported by observed secondary hydrogen isotope effects on the C alpha proton for an alanine residue in the P2 position. We suggest a trans-cis isomerisation around the P2-P1 peptide bond in the final step of the acylation and cleavage of the substrates. The results obtained by our theoretical calculations are compared with several experimental findings supporting the suggested mechanism.

Enzymes work by solvation substitution rather than by desolvation

Considerable attention has recently been drawn to the hypothesis that enzymes catalyze their reactions by displacing solvent and creating an environment similar to the gas phase for the reacting substrates. This "desolvation hypothesis" is reexamined in this paper by defining a common reference energy for reactions in various environments. It is argued that consistent attempts to describe the actual energetics of enzymatic reactions, taking either gas phase or solution as a reference, would contradict the above hypothesis. That is, the enzyme does remove water molecules from its substrate, but substitutes these molecules for another polar environment (namely, its active site). By taking amide hydrolysis as an example, we use experimentally estimated solvation energies and analyze the reaction profile in the gas phase, in solution, and in enzyme active sites. We show that the gas-phase reaction is characterized by an enormous activation barrier (associated with forming the charged nucleophile from neutral fragments), although the nucleophilic attack is essentially barrierless. On the other hand, the enzyme and solution reactions are found to have similar reaction profiles, with a lower activation barrier for the enzymatic reaction. Presumably, the fact that previous analyses of this problem did not involve the construction of the relevant thermodynamic cycles (and quantitative estimates of the corresponding solvation energies) led to the desolvation hypothesis. Our conclusion is that enzyme active sites provide specific polar environments that do not resemble the gas phase but that are designed for electrostatic stabilization of ionic transition states and that "solvate" these states more than water does.

The catalytic mechanism of serine proteases. III. An Indo-ISCRF study of the methylacetate docking in alpha-chymotrypsin

Mechanistic steps of the catalytic hydrolysis of methylacetate by alpha-chymotrypsin have been studied with the inhomogeneous selfconsistent reaction field theory of protein core effects. Protein-substrate interactions were optimized at each step of the reaction path by using the REFINE program. The state of charge of the acid and basic side chains together with the amino terminal group have been used to mimic pH effects. The experimental facts concerning the catalytic activity are fairly well reproduced in our simulations. In particular, the trends in activation barrier as a function of pH are good, although the actual energetic barriers are much too large.

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

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

Stereoelectronic control in peptide bond formation. Ab initio calculations and speculations on the mechanism of action of serine proteases

Ab initio molecular orbital calculations have been performed on the reaction profile for the addition/elimination reaction between ammonia and formic acid, proceeding via a tetrahedral intermediate: NH3 + HCO2H----H2NCH(OH)2----NH2CHO + H2O. Calculated transition state energies for the first addition step of the reaction revealed that a lone pair on the oxygen of the OH group, which is antiperiplanar to the attacking nitrogen, stabilized the transition state by 3.9 kcal/mol, thus supporting the hypothesis of stereoelectronic control for this reaction. In addition, a secondary, counterbalancing stereoelectronic effect stabilizes the second step, water elimination, transition state by 3.1 kcal/mol if the lone pair on the leaving water oxygen is not antiperiplanar to the C-N bond. The best conformation for the transition states was thus one with a lone pair antiperiplanar to the adjacent scissile bond and also one without a lone-pair orbital on the scissile bond oxygen or nitrogen antiperiplanar to the adjacent polar bond. The significance of these stereoelectronic effects for the mechanism of action of serine proteases is discussed.

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

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

Charge state of His-57-Asp-102 couple in a transition state analogue-trypsin complex: a molecular orbital study

Ab initio molecular orbital studies have been made as a model for the deacylation step of trypsin. Ser-195 is modeled by H2O in which one H is replaced either by--PO2(OH)- (monoisopropyl phosphoryl, MIP) or by--CHO(OH)- (a transition state analogue, TSD). The quantum mechanical region includes imidazole+ and acetate- as models for His-57+ and Asp-102-, two hydrogen bonds from two formamide molecules to the oxyanion MIP or TSD, and three hydrogen bonds to Asp-102. The remainder of the enzyme is treated classically as a fractional charge model. The effect of proton transfer from His-57+ to Asp-102- is very similar for the MIP and TSD models, and the proton transfer is energetically unfavorable for all models that include at least the hydrogen bond from an H2O that models Ser-214. Thus, the several hydrogen bonds to the models of the catalytic unit (substrate, Ser-195, His-57, and Asp-102) stabilize the His-57+/Asp-102- salt link, and this indicates that proton transfer does not occur from His-57+ to Asp-102-. (Also, the similarities of energy of transfer of this proton transfer for the various models show that the model substrate analogue behaves very similarly to the MIP inhibitor.)

Calculations of electrostatic interactions in biological systems and in solutions

Correlating the structure and action of biological molecules requires knowledge of the corresponding relation between structure and energy. Probably the most important factors in such a structure– energy correlation are associated with electrostatic interactions. Thus the key requirement for quantative understanding of the action of biological molecules is the ability to correlate electrostatic interactions with structural information. To appreciate this point it is useful to compare the electrostatic energy of a charged amino acid in a polar solvent to the corresponding van der Waals energy. The electrostatic free energy, ΔGel, can be approximated (as will be shown in Section II) by the Born formula (ΔGel= –(166Q2/ā) (I – I/E)). Where ΔGelis given in kcal/mol,Qis the charge of the given group, in units of electron charge,āis the effective radius of the group, andEis the dielectric constant of the solvent. With an effective radius of charged amino acids of approximately 2 Å, Born's formula gives about – 80 kcal/mol for their energy in polar solvents whereEis larger than 10. This energy is two orders of magnitude larger than the van der Waals interaction of such groups and their surroundings.

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

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

Interactions between Asp, His, Ser residues within models of the active site of serine proteases. A theoretical empirical study

Empirical theoretical calculations have been performed on a simplified model of the active site of two serine proteases: alpha-chymotrypsin and subtilisin Novo. The stability of the catalytic triad and the hydrogen bond formation between the Asp-His and His-Ser pairs have been examined for different protonation states. The results show that the Asp-His interactions prevail upon the His-Ser ones. Agreement between calculated configurations and the crystal structure of the site suggests that the presence of other residues near the functional residues is not determinant for the stability of the triad in alpha-chymotrypsin. In subtilisin Novo, on the contrary, the presence of the neighbouring residues seems to contribute more largely to the stability. Strong hydrogen bond interactions between the His and Ser residues do not exist in the resting enzymes. Any improvement of the His-Ser interactions requires large destabilization of the Asp-His diad. Our results suggest that the mechanism of the proton transfer can occur only from perturbations of the active site structure induced by the presence of the substrate.

Model of serine proteases charge relay system -- PCILO study

The PCILO (Perturbative Configuration Interaction Using Localized Orbitals) method had been used to determine the electronic structure of the active center of serine proteases. The results show that the carboxyl group of the aspartic acid residue is the ultimate proton acceptor of the catalytic triad (Asp, His, Ser)-. In the absence of a substrate the negative charge of the active centre is delocalized, causing polarization of the Ser O gamma-H bond and an increase of the nucleophilicity of imidazole His. The hydration of the model charge relay system is also investigated.

Dynamics of proton transfer and enzymatic activity

The rate-determining elementary reaction step, i.e. proton transfer from the chymotrypsin active centre to the scissile substrate bond had been studied in the present work. On the basis of our theoretical results a hypothesis was formulated to explain chymotrypsin enzymatic efficiency. After ES complex formation excited vibrational states are populated in the enzyme molecule. In the rate-determining elementary reaction step, the proton transfer takes place from the first excited vibrational state of the N-H bond in the imidazole group of His57. This proton transfer is realised by quantum mechanical tunneling mechanism.

Molecular orbital studies of enzyme activity: I: Charge relay system and tetrahedral intermediate in acylation of serine proteinases

The charge relay ststem and its role in the acylation of serine proteinases is studied using the partial retention of diatomic differential overlap (PRDDO) technique to perform approximate ab initio molecular orbital calculations on a model of the enzyme-substrate complex. The aspartate in the charge relay system is seen to act as the ultimate proton acceptor during the charging of the serine nucleophile. A projection of the potential energy surface is obtained in a subspace corresponding to this charge transfer and to the coupled motions of active site residues and the substrate. These results together with extended basis set results for cruder models suggest that a concerted transfer of protons from Ser-195 to His-57 and from His-57 to Asp-102 occurs with an energy barrier of 20-25 kcal/mole (84-105 kJ/mole). The subsequent nucleophilic attack on the scissile peptide linkage by the charged serine is then seen to proceed energetically downhill to the tetrahedral intermediate. The formation of the tetrahedral intermediate from the Michaelis complex is calculated to be nearly thermoneutral.