Dimas Suárez

Quantum mechanical and molecular dynamics simulations of ureases and Zn β-lactamases

Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo‐β‐lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo‐β‐lactamases and ureases.

Molecular dynamics simulations of the dinuclear zinc-β-lactamase from Bacteroides fragilis complexed with imipenem

Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc β‐lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc‐bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme‐substrate complex combined with Poisson‐Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the β‐lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the β‐lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.

Entropy Calculations of Single Molecules by Combining the Rigid-Rotor and Harmonic-Oscillator Approximations with Conformational Entropy Estimations from Molecular Dynamics Simulations.

As shown by previous theoretical and computational work, absolute entropies of small molecules that populate different conformers can be predicted accurately on the basis of the partitioning of the intramolecular entropy into vibrational and conformational contributions. Herein, we further elaborate on this idea and propose a protocol for entropy calculations of single molecules that combines the rigid rotor harmonic oscillator (RRHO) entropies with the direct sampling of the molecular conformational space by means of classical molecular dynamics simulations. In this approach, the conformational states are characterized by discretizing the time evolution of internal rotations about single bonds, and subsequently, the mutual information expansion (MIE) is used to approach the full conformational entropy from the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. This RRHO&MIE protocol could have broad applicability, as suggested by our test calculations on systems ranging from hydrocarbon molecules in the gas phase to a polypeptide molecule in aqueous solution. For the hydrocarbon molecules, the ability of the RRHO&MIE protocol to predict absolute entropies is assessed by carefully comparing theoretical and experimental values in the gas phase. For the rest of the test systems, we analyze the advantages and limitations of the RRHO&MIE approach in order to capture high order correlation effects and yield converged conformational entropies within a reasonable simulation time. Altogether, our results suggest that the RRHO&MIE strategy could be useful for estimating absolute and/or relative entropies of single molecules either in the gas phase or in solution.

Ketone–Alcohol Hydrogen‐Transfer Equilibria: Is the Biooxidation of Halohydrins Blocked?

To ensure the quasi-irreversibility of the oxidation of alcohols coupled with the reduction of ketones in a hydrogen-transfer (HT) fashion, stoichiometric amounts of α-halo carbonyl compounds have been employed as hydrogen acceptors. The reason that these substrates lead to quasi-quantitative conversions has been tacitly attributed to both thermodynamic and kinetic effects. To provide a clear rationale for this behavior, we investigate herein the redox equilibrium of a selected series of ketones and 2-propanol by undertaking a study that combines experimental and theoretical approaches. First, the activity of the (R)-specific alcohol dehydrogenase from Lactobacillus brevis (LBADH) with these substrates was studied. The docking of acetophenone/(R)-1-phenyethanol and α-chloroacetophenone/(S)-2-chloro-1-phenylethanol in the active site of the enzyme confirms that there seems to be no structural reason for the lack of reactivity of halohydrins. This assumption is confirmed by the fact that the corresponding aluminum-catalyzed Meerwein-Ponndorf-Verley-Oppenauer (MPVO) reactions afford similar conversions to those obtained with LBADH, showing that the observed reactivity is independent of the catalyst employed. While the initial rates of the enzymatic reductions and the IR ν(C=O) values contradict the general belief that electron-withdrawing groups increase the electrophilicity of the carbonyl group, the calculated ΔG values of the isodesmic redox transformations of these series of ketones/alcohols with 2-propanol/acetone support the thermodynamic control of the reaction. As a result, a general method to predict the degree of conversion obtained in the HT-reduction process of a given ketone based on the IR absorption band of the carbonyl group is proposed, and a strategy to achieve the HT oxidation of halohydrins is also shown.

PM3-compatible zinc parameters optimized for metalloenzyme active sites

Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc‐containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6‐311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for “Zinc, Biological.” In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high‐level ab initio results, something existing parameter sets failed to do.

Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide.

Herein, we first review different methodologies that have been proposed for computing the quantum mechanical (QM) energy and other molecular properties of large systems through a linear combination of subsystem (fragment) energies, which can be computed using conventional QM packages. Particularly, we emphasize the similarities among the different methods that can be considered as variants of the multibody expansion technique. Nevertheless, on the basis of thermochemical arguments, we propose yet another variant of the fragment energy methods, which could be useful for, and readily applicable to, biomolecules using either QM or hybrid quantum mechanical/molecular mechanics methods. The proposed computational scheme is applied to investigate the stability of a triple-helical collagen model peptide. To better address the actual applicability of the fragment QM method and to properly compare with experimental data, we compute average energies by carrying out single-point fragment QM calculations on structures generated by a classical molecular dynamics simulation. The QM calculations are done using a density functional level of theory combined with an implicit solvent model. Other free-energy terms such as attractive dispersion interactions or thermal contributions are included using molecular mechanics. The importance of correcting both the intermolecular and intramolecular basis set superposition error (BSSE) in the QM calculations is also discussed in detail. On the basis of the favorable comparison of our fragment-based energies with experimental data and former theoretical results, we conclude that the fragment QM energy strategy could be an interesting addition to the multimethod toolbox for biomolecular simulations in order to investigate those situations (e.g., interactions with metal clusters) that are beyond the range of applicability of common molecular mechanics methods.

ANACAL: a program to carry out a configurational analysis of the wave function of reactive systems

Abstract A method to analyze the wave function of a closed-shell composed system in terms of the electronic configuration of its closed-shell components is presented. The molecular orbitals of a supersystem A-B (or A-B-C) are presented as linear combinations of the molecular orbitals of the fragments A, B (or A, B, and C), thus allowing the wave function of a two-fragment (A-B) or a three-fragment (A-B-C) composed system to be interpreted in terms of the electronic configurations of the reactants ( ABC, A + B - C,…,A ∗ BC,… ).

Theoretical Study of the Oxidation of Histidine by Singlet Oxygen

Herein we present a theoretical study of the reaction of singlet oxygen with histidine performed both in the gas phase and in aqueous solution. The potential energy surface of the reactive system was explored at the B3LYP/cc-pVTZ level of theory and the electronic energies were refined by means of single-point CCSD(T)/cc-pVTZ(-f) calculations. Solvent effects were taken into account by using a solvent continuum model (COSMO) and by adding explicit water molecules. The results show that the first step in the reaction mechanism corresponds to a nearly symmetric Diels-Alder addition of the singlet oxygen molecule to the imidazole ring to yield an endoperoxide, in agreement with experimental evidence. The intermediate formed can evolve along two different reaction paths leading to two isomeric hydroperoxides and, eventually, to open-chain or internally cyclised oxidised products. Water plays a significant role in stabilising the reaction structures by solvation and by acting as a bifunctional catalyst in the elimination/addition reaction steps. Our results explain why substituents at the N1-imidazole ring can hamper the evolution of the initial endoperoxide and result in Gibbs energy barriers in solution similar to those experimentally measured and suggest a likely route to the formation of peptide aggregates during the oxidation of histidine by singlet molecular oxygen.

Molecular dynamics simulations of human butyrylcholinesterase.

Herein, we present results from molecular dynamics (MD) simulations of the human butyrylcholinesterase (BuChE) enzyme in aqueous solution. Two configurations of the unbound form of BuChE differing in the presence or absence of a sodium ion inside the protein gorge were simulated for 10 and 5 ns, respectively. Besides complementing the structural information provided by X‐ray data, the MD simulations give insight into the structure of the native BuChE enzyme. For example, it is shown that: the nucleophilic Ser198 residue and the various binding subsites in the BuChE catalytic cavity are readily accessible from the exterior of the protein; the presence of the sodium ion dynamically explores two different binding sites in the gorge leading to the active site and stabilizes the productive conformation of the Glu325/His438/Ser198 catalytic triad; several long‐lived water bridges are fully integrated into the architecture of the active site; the positions of the residues at the rim of the gorge region display large deviations with respect to the crystal structure; and two side doors, constituted by residues situated at the tip of the acyl‐ and Ω‐loops, respectively, open wide enough to allow the passage of water molecules. In conclusion, we compare our theoretical results with those from previous work on mouse acetylcholinesterase and discuss their implications for substrate binding and catalysis in BuChE. Proteins 2005.

CENCALC: a computational tool for conformational entropy calculations from molecular simulations.

We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas‐phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation‐corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/.