Laura Masgrau

Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State

Glycosyltransferases (GTs) catalyze the highly specific biosynthesis of glycosidic bonds and, as such, are important both as drug targets and for biotechnological purposes. Despite their broad interest, fundamental questions about their reaction mechanism remain to be answered, especially for those GTs that transfer the sugar with net retention of the configuration at the anomeric carbon (retaining glycosyltransferases, ret-GTs). In the present work, we focus on the reaction catalyzed by lipopolysaccharyl-α-1,4-galactosyltransferase C (LgtC) from Neisseria meningitides. We study and compare the different proposed mechanisms (S(N)i, S(N)i-like, and double displacement mechanism via a covalent glycosyl-enzyme intermediate, CGE) by using density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations on the full enzyme. We characterize a dissociative single-displacement (S(N)i) mechanism consistent with the experimental data, in which the acceptor substrate attacks on the side of the UDP leaving group that acts as a catalytic base. We identify several key interactions that help this front-side attack by stabilizing the transition state. Among them, Gln189, the putative nucleophile in a double displacement mechanism, is shown to favor the charge development at the anomeric center by about 2 kcal/mol, compatible with experimental mutagenesis data. We predict that using 3-deoxylactose as acceptor would result in a reduction of k(cat) to 0.6-3% of that for the unmodified substrates. The reactions of the Q189A and Q189E mutants have also been investigated. For Q189E, there is a change in mechanism since a CGE can be formed which, however, is not able to evolve to products. The current findings are discussed in the light of the available experimental data and compared with those for other ret-GTs.

Hydrogen tunnelling in enzyme-catalysed H-transfer reactions : flavoprotein and quinoprotein systems

It is now widely accepted that enzyme-catalysed C–H bond breakage occurs by quantum mechanical tunnelling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (TST, i.e. including zero-point energy, but with no tunnelling correction) has been driven over the recent years by experimental studies of the temperature dependence of kinetic isotope effects (KIEs) for these reactions in a range of enzymes, including the tryptophan tryptophylquinone-dependent enzymes such as methylamine dehydrogenase and aromatic amine dehydrogenase, and the flavoenzymes such as morphinone reductase and pentaerythritol tetranitrate reductase, which produced observations that are also inconsistent with the simple Bell-correction model of tunnelling. However, these data—especially, the strong temperature dependence of reaction rates and the variable temperature dependence of KIEs—are consistent with other tunnelling models (termed full tunnelling models), in which protein and/or substrate fluctuations generate a configuration compatible with tunnelling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate nuclear quantum states and, when necessary, motion required to increase the probability of tunnelling in these states. Furthermore, tunnelling mechanisms in enzymes are supported by atomistic computational studies performed within the framework of modern TST, which incorporates quantum nuclear effects.

Insights into the Mechanism of Binding of Arachidonic Acid to Mammalian 15-Lipoxygenases

Mammalian 15-lipoxygenases (15-LOs) are key pharmaceutical targets under strong investigation because of their implication in atherosclerosis and cancer. Here, we present an atomic-level study of the binding modes of arachidonic acid (AA) to rabbit reticulocyte 15-LO, with a particular insight into the 15-LO:AA complexes consistent with known catalytic activity. We take into account both ligand and protein flexibility, by combining protein-ligand docking techniques and molecular dynamics simulations. We have also performed in silico mutagenesis. Our results are in agreement with previous mutagenesis data, in particular with the importance of Arg403 on AA binding. Interestingly, our results also reveal a central role of Arg403 in the conformational change of the alpha2-helix observed upon ligand binding. That induced-fit effect could give a possible framework for the molecular explanation of the known allosteric effect and questions the suitability of the inhibitor-bound crystal structure for accepting AA. Accounting for these dynamical considerations might improve the drug design process.

Natural Mutations of the anti-Müllerian Hormone type II Receptor Found in Persistent Müllerian Duct Syndrome affect Ligand Binding, Signal Transduction and Cellular Transport

The anti-Müllerian hormone type II (AMHRII) receptor is the primary receptor for anti-Müllerian hormone (AMH), a protein produced by Sertoli cells and responsible for the regression of the Müllerian duct in males. AMHRII is a membrane protein containing an N-terminal extracellular domain (ECD) that binds AMH, a transmembrane domain, and an intracellular domain with serine/threonine kinase activity. Mutations in the AMHRII gene lead to persistent Müllerian duct syndrome in human males. In this paper, we have investigated the effects of 10 AMHRII mutations, namely 4 mutations in the ECD and 6 in the intracellular domain. Molecular models of the extra- and intracellular domains are presented and provide insight into how the structure and function of eight of the mutant receptors, which are still expressed at the cell surface, are affected by their mutations. Interestingly, two soluble receptors truncated upstream of the transmembrane domain are not secreted, unless the transforming growth factor beta type II receptor signal sequence is substituted for the endogenous one. This shows that the AMHRII signal sequence is defective and suggests that AMHRII uses its transmembrane domain instead of its signal sequence to translocate to the endoplasmic reticulum, a characteristic of type III membrane proteins.

The reactions CHnD4−n+OH→P and CH4+OD→CH3+HOD as a test of current direct dynamics computational methods to determine variational transition-state rate constants. I.

In the present work, we have theoretically calculated the rate constants and their temperature dependence for the reactions CHnD4−n+OH→P, and for the reaction of methane with OD, by means of variational transition-state theory plus multidimensional tunneling corrections, at the MP-SAC2//MP2/cc-pVTZ/// and CCSD(T)//MP2/cc-pVTZ/// electronic levels. Also, the newly developed single-point energy interpolation algorithm has been used at the CCSD(T)/aug-cc-pVTZ//MP2/cc-pVTZ and CCSD(T)-SAC//MP2/cc-pVTZ levels. For reactions with n=1, 2 or 3, the competitive canonical unified statistical theory has been applied as they involve more than one nonequivalent reaction channel. Variational effects and tunneling have been found to be very important. The proton shift classical energy barrier turns out to be 5.83 and 4.97 kcal/mol at the CCSD(T)/aug-cc-pVTZ//MP2/cc-pVTZ and CCSD(T)-SAC//MP2/cc-pVTZ levels, respectively. Even though we have used the highest ab initio electronic level reported up to now for dynamics calcu...

The Importance of Ensemble Averaging in Enzyme Kinetics

Conspectus The active site of an enzyme is surrounded by a fluctuating environment of protein and solvent conformational states, and a realistic calculation of chemical reaction rates and kinetic isotope effects of enzyme-catalyzed reactions must take account of this environmental diversity. Ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) was developed as a way to carry out such calculations. This theory incorporates ensemble averaging, quantized vibrational energies, energy, tunneling, and recrossing of transition state dividing surfaces in a systematic way. It has been applied successfully to a number of hydrogen-, proton-, and hydride-transfer reactions. The theory also exposes the set of effects that should be considered in reliable rate constants calculations. We first review the basic theory and the steps in the calculation. A key role is played by the generalized free energy of activation profile, which is obtained by quantizing the classical potential of mean force as a function of a reaction coordinate because the one-way flux through the transition state dividing surface can be written in terms of the generalized free energy of activation. A recrossing transmission coefficient accounts for the difference between the one-way flux through the chosen transition state dividing surface and the net flux, and a tunneling transmission coefficient converts classical motion along the reaction coordinate to quantum mechanical motion. The tunneling calculation is multidimensional, accounting for the change in vibrational frequencies along the tunneling path and shortening of the tunneling path with respect to the minimum energy path (MEP), as promoted by reaction-path curvature. The generalized free energy of activation and the transmission coefficients both involve averaging over an ensemble of reaction paths and conformations, and this includes the coupling of protein motions to the rearrangement of chemical bonds in a statistical mechanically correct way. The standard deviations of the transmissions coefficients provide information on the diversity of the distribution of reaction paths, barriers, and protein conformations along the members of an ensemble of reaction paths passing through the transition state. We first illustrate the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR is of special interest because the protein conformational changes have been widely studied. Then we present shorter discussions of several other applications of EA-VTST/MT to transfer of protons, hydrogen atoms, and hydride ions and their deuterated analogs. Systems discussed include hydride transfer in alcohol dehydrogenase, xylose isomerase, and thymidylate synthase, proton transfer in methylamine dehydrogenase, hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic substitution in haloalkane dehalogenase and two-dimensional potentials of mean force for potentially coupled proton and hydride transfer in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain acyl-CoA dehydrogenase and in the pyruvate to lactate transformation catalyzed by lactate dehydrogenase.

Ligand induced formation of transient dimers of mammalian 12/15-lipoxygenase: A key to allosteric behavior of this class of enzymes?

Mammalian lipoxygenases (LOXs) have been implicated in cellular defense response and are important for physiological homeostasis. Since their discovery, LOXs have been believed to function as monomeric enzymes that exhibit allosteric properties. In aqueous solutions, the rabbit 12/15‐LOX is mainly present as hydrated monomer but changes in the local physiochemical environment suggested a monomer–dimer equilibrium. Because the allosteric character of the enzyme can hardly be explained using a single ligand binding‐site model, we proposed that the binding of allosteric effectors may shift the monomer–dimer equilibrium toward dimer formation. To test this hypothesis, we explored the impact of an allosteric effector [13(S)‐hydroxyoctadeca‐9(Z),11(E)‐dienoic acid] on the structural properties of rabbit 12/15‐LOX by small‐angle X‐ray scattering. Our data indicate that the enzyme undergoes ligand‐induced dimerization in aqueous solution, and molecular dynamics simulations suggested that LOX dimers may be stable in the presence of substrate fatty acids. These data provide direct structural evidence for the existence of LOX dimers, where two noncovalently linked enzyme molecules might work in unison and, therefore, such mode of association might be related to the allosteric character of 12/15‐LOX. Introduction of negatively charged residues (W181E + H585E and L183E + L192E) at the intermonomer interface disturbs the hydrophobic dimer interaction of the wild‐type LOX, and this structural alteration may lead to functional distortion of mutant enzymes. Proteins 2011.

Atomistic insight into the origin of the temperature-dependence of kinetic isotope effects and H-tunnelling in enzyme systems is revealed through combined experimental studies and biomolecular simulation

The physical basis of the catalytic power of enzymes remains contentious despite sustained and intensive research efforts. Knowledge of enzyme catalysis is predominantly descriptive, gained from traditional protein crystallography and solution studies. Our goal is to understand catalysis by developing a complete and quantitative picture of catalytic processes, incorporating dynamic aspects and the role of quantum tunnelling. Embracing ideas that we have spearheaded from our work on quantum mechanical tunnelling effects linked to protein dynamics for H-transfer reactions, we review our recent progress in mapping macroscopic kinetic descriptors to an atomistic understanding of dynamics linked to biological H-tunnelling reactions.

A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase

Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host-pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl-3-phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP-Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum-mechanics/molecular-mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front-side substrate-assisted SN i-type reaction.

An insight into the regiospecificity of linoleic acid peroxidation catalyzed by mammalian 15-lipoxygenases.

15-Lipoxygenases (15-LOs) catalyze the peroxidation reaction of linoleic acid (LA) in mammals producing almost exclusively 13-(S)-hydroperoxyoctadecadienoic acid (13-(S)-HPODE). Although several hypotheses have been formulated, the molecular basis of such enzymatic regiospecificity is unclear. We have here combined quantum mechanics/molecular mechanics (QM/MM) calculations with molecular dynamics simulations to analyze the peroxidation mechanism using a complete rabbit 15-LO-1/LA solvated model. C9 and C13 being equivalent for planarity and spin density, the QM/MM potential energy profiles of the O2 addition to those two atoms were calculated. The difference in the potential energy barrier heights is clear enough to justify that O2 selectively attacks C13 giving 13-(S)-HPODE. Oxygenation at C9 is hindered by two steric-shielding residues (Leu597 and Gln548). The calculated free energy profile at 300 K for the O2 addition to C13 confirms that the peroxidation on C13 is a reversible viable process in agreement with experiments. Thus, the subsequent reduction of the peroxyl radical to give the final hydroperoxidated product is expected to give the irreversibility character to the overall process.