Peptide Bond Formation Mechanism Catalyzed by Ribosome.

In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule.

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional.

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different conformations of zwitterionic species open the door to different mechanistic paths.

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution.

We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule.

Understanding the different activities of highly promiscuous MbtI by computational methods.

Salicylate synthase from Mycobacterium tuberculosis, MbtI, is a highly promiscuous Mg(2+) dependent enzyme with up to four distinct activities detected in vitro: isochorismate synthase (IS), isochorismate pyruvate lyase (IPL), salicylate synthase (SS) and chorismate mutase (CM). In this paper, Molecular Dynamic (MD) simulations employing hybrid quantum mechanics/molecular mechanics (QM/MM) potentials have been carried out to get a detailed knowledge of the IS and the IPL activities at the molecular level. According to our simulations, the architecture of the MbtI active site allows catalyzing the two reactions: the isochorismate formation, by means of a stepwise mechanism, and the salicylate production from isochorismate, that appears to be pericyclic in nature.

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts.

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism.

Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.

We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism.

Mechanism and plasticity of isochorismate pyruvate lyase: a computational study.

The isochorismate pyruvate lyase (IPL) from Pseudomonas aeruginosa, designated as PchB, catalyzes the transformation of isochorismate into pyruvate and salicylate, but it also catalyzes the rearrangement of chorismate into prephenate, suggesting that both reactions may proceed by a pericyclic mechanism. In this work, molecular dynamics simulations employing hybrid quantum mechanics/molecular mechanics methods have been carried out to get a detailed knowledge of the reaction mechanism of PchB. The results provide a theoretical rate constant enhancement by comparison with the reaction in solution, in agreement with the experimental data, and confirm the pericyclic nature of the reaction mechanism.

Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase.

The reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase is analyzed by means of hybrid QM/MM simulations. A recently developed semiempirical Hamiltonian, AM1/d-PhoT, which takes into account the d orbitals on the phosphorus atom, has been employed. The reaction mechanism obtained is either associative or dissociative, depending on the size of the QM subsystem.

Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of N-formyl-glycine amide and N-formyl-alanine amide radical cations.

Ramachandran maps of neutral and ionized HCO-Gly-NH2 and HCO-Ala-NH2 peptide models have been built at the B3LYP/6-31++G(d,p) level of calculation. Direct optimizations using B3LYP and the recently developed MPWB1K functional have also been carried out, as well as single-point calculations at the CCSD(T) level of theory with the 6-311++G(2df,2p) basis set. Results indicate that for both peptide models ionization can cause drastic changes in the shape of the PES in such a way that highly disallowed regions in neutral PES become low-energy regions in the radical cation surface.

Computational design of biological catalysts.

The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze related reactions. The second possibility is the use of immune systems that recognize stable molecules resembling the transition structure of the target reaction.

Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes.

Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system.

Attractive strain: the disadvantages of rigid multiple H-bond donors and acceptors. A theoretical analysis of the hydrogen-bonding interactions in complexes of tetraazaanthracenedione with pyridylureas.

We report density functional theory calculations at the B3LYP/D95(d,p) level on the hydrogen-bonding complexes of tetraazaanthracenedione, 1, with N-(pyridin-2-yl)urea, 2H, or N-(6-aminopyridin-2-yl)urea, 2N. The interaction energy of the 1-2H complex exceeds that of 1-2N, despite the fact that 1-2N contains a strong N-H..

Influence of the Side Chain in the Structure and Fragmentation of Amino Acids Radical Cations.

The conformational properties of ionized amino acids (Gly, Ala, Ser, Cys, Asp, Gln, Phe, Tyr, and His) have been theoretically analyzed using the hybrid B3LYP and the hybrid-meta MPWB1K functionals as well as with the post-Hartree Fock CCSD(T) level of theory. As a general trend, ionization is mainly localized at the -NH2 group, which becomes more planar and acidic, the intramolecular hydrogen bond in which -NH2 acts as proton donor being strengthened upon ionization. For this reason, the so-called conformer IV(+) becomes the most stable for nonaromatic amino acid radical cations.

Theoretical study of catalytic efficiency of a Diels-Alderase catalytic antibody: an indirect effect produced during the maturation process.

The Diels-Alder reaction is one of the most important and versatile transformations available to organic chemists for the construction of complex natural products, therapeutics agents, and synthetic materials. Given the lack of efficient enzymes capable of catalyzing this kind of reaction, it is of interest to ask whether a biological catalyst could be designed from an antibody-combining site. In the present work, a theoretical study of the different behavior of a germline catalytic antibody (CA) and its matured form, 39 A-11, that catalyze a Diels-Alder reaction has been carried out.

Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement.

Catalytic antibodies are very interesting not only because of the rate enhancement of the reactions that they catalyze but also because of the selectivities they can achieve that are sometimes not present in natural enzyme processes. We have selected the study of the stereoselectivity of the matured AZ28 that catalyzes an oxy-Cope rearrangement. For this particular case, the presence of a chiral center in the substrate provokes the existence of two different enantiomers, R and S.

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations.

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase.

Theoretical insights in enzyme catalysis.

In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a methyl transfer from S-adenosylmethionine to catecholate catalysed by catechol O-methyltransferase.

A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization?

In this work we present a detailed analysis of the activation free energies and averaged interactions for the Claisen and Cope rearrangements of chorismate and carbachorismate catalyzed by Bacillus subtilischorismate mutase (BsCM) using quantum mechanics/molecular mechanics (QM/MM) simulation methods. In gas phase, both reactions are described as concerted processes, with the activation free energy for carbachorismate being about 10-15 kcal mol(-)(1) larger than for chorismate, at the AM1 and B3LYP/6-31G levels. Aqueous solution and BsCM active site environments reduce the free energy barriers for both reactions, due to the fact that in these media the two carboxylate groups can be approached more easily than in the gas phase.

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase.

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates.

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site.