Isabelle André

Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.

We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.

Design of α-Transglucosidases of Controlled Specificity for Programmed Chemoenzymatic Synthesis of Antigenic Oligosaccharides

Combined with chemical synthesis, the use of biocatalysts holds great potential to open the way to novel molecular diversity. We report in vitro chemoenzymatic pathways that, for the first time, take advantage of enzyme engineering to produce complex microbial cell-surface oligosaccharides and circumvent the chemical boundaries of glycochemistry. Glycoenzymes were designed to act on nonnatural conveniently protected substrates to produce intermediates compatible with a programmed chemical elongation. The study was focused on the synthesis of oligosaccharides mimicking the O-antigen motif of Shigella flexneri serotypes 1b and 3a, which could be used for the development of multivalent carbohydrate-based vaccines. A semirational engineering approach was successfully applied to amylosucrase, a transglucosidase that uses a low cost sucrose substrate as a glucosyl donor. The main difficulty was to retain the enzyme specificity toward sucrose, while creating a new catalytic function to render the enzyme able to regiospecifically glucosylate protected nonnatural acceptors. A structurally guided library of 133 mutants was generated from which several mutants with either completely new specificity toward methyl alpha-l-rhamnopyranoside or a tremendously enhanced one toward allyl 2-acetamido-2-deoxy-alpha-d-glucopyranoside acceptors were isolated. The best variants were used to synthesize glucosylated building blocks. They were then converted into acceptors and potential donors compatible with chemical elongation toward oligosaccharide fragments of the O-antigens of the two targeted serotypes. This is the first report of a successful engineering of an alpha-transglycosidase acceptor binding site that led to new specificities. It demonstrates the potential of appropriate combinations of a planned chemoenzymatic pathway and enzyme engineering in glycochemistry.

A structure-controlled investigation of lipase enantioselectivity by a path-planning approach.

A novel approach based on efficient path‐planning algorithms was applied to investigate the influence of substrate access on Burkholderia cepacia lipase enantioselectivity. The system studied was the transesterification of 2‐substituted racemic acid derivatives catalysed by B. cepacia lipase. In silico data provided by this approach showed a fair qualitative agreement with experimental results, and hence the potential of this computational method for fast screening of racemates. In addition, a collision detector algorithm used during the pathway searches enabled the rapid identification of amino acid residues hindering the displacement of substrates along the deep, narrow active‐site pocket of B. cepacia lipase and thus provided valuable information to guide the molecular engineering of lipase enantioselectivity.

Role of glycoside phosphorylases in mannose foraging by human gut bacteria.

Background: The relations between the gut microbiota, food, and host play a crucial role in human health. Results: Prevalent bacterial glycoside phosphorylases are able to break down dietary carbohydrates and the N-glycans lining the intestinal epithelium. Conclusion: GH130 enzymes are new targets to study interactions between host and gut microbes. Significance: Glycoside phosphorylases are key enzymes of host glycan catabolism by gut bacteria. To metabolize both dietary fiber constituent carbohydrates and host glycans lining the intestinal epithelium, gut bacteria produce a wide range of carbohydrate-active enzymes, of which glycoside hydrolases are the main components. In this study, we describe the ability of phosphorylases to participate in the breakdown of human N-glycans, from an analysis of the substrate specificity of UhgbMP, a mannoside phosphorylase of the GH130 protein family discovered by functional metagenomics. UhgbMP is found to phosphorolyze β-d-Manp-1,4-β-d-GlcpNAc-1,4-d-GlcpNAc and is also a highly efficient enzyme to catalyze the synthesis of this precious N-glycan core oligosaccharide by reverse phosphorolysis. Analysis of sequence conservation within family GH130, mapped on a three-dimensional model of UhgbMP and supported by site-directed mutagenesis results, revealed two GH130 subfamilies and allowed the identification of key residues responsible for catalysis and substrate specificity. The analysis of the genomic context of 65 known GH130 sequences belonging to human gut bacteria indicates that the enzymes of the GH130_1 subfamily would be involved in mannan catabolism, whereas the enzymes belonging to the GH130_2 subfamily would rather work in synergy with glycoside hydrolases of the GH92 and GH18 families in the breakdown of N-glycans. The use of GH130 inhibitors as therapeutic agents or functional foods could thus be considered as an innovative strategy to inhibit N-glycan degradation, with the ultimate goal of protecting, or restoring, the epithelial barrier.

Cloning, purification and characterization of a thermostable amylosucrase from Deinococcus geothermalis

Amylosucrase is a transglucosidase that catalyses the synthesis of an amylose-type polymer from sucrose, an abundant agro-resource. Here we describe a novel thermostable amylosucrase from the moderate thermophile Deinococcus geothermalis (DGAS). The dgas gene was cloned and expressed in Escherichia coli. The encoded enzyme was purified and characterized. DGAS displays a specific activity of 44 U mg(-1), an optimal temperature of 50 degrees C and a half-life of 26 h at 50 degrees C. Moreover, it produces an alpha-glucan at 50 degrees C, with an average degree of polymerization of 45 and a polymerization yield of 76%. DGAS is thus the most active and thermostable amylosucrase known to date.

On the reaction pathways and determination of transition-state structures for retaining α-galactosyltransferases

The catalytic mechanism of retaining glycosyltransferases is not yet completely understood, but one possible mechanism, by analogy with retaining glycosidases, is a double-displacement mechanism via a covalent glycosyl-enzyme intermediate (CGE). We have investigated various reaction pathways for this mechanism using non-empirical quantum mechanical methods. Because a double-displacement mechanism presumes a reaction happening in two steps, we have used predefined reaction coordinates to calculate the potential energy surface describing each step of the mechanism. By investigating several potential candidates to act as a catalytic base, this study attempts to shed some light on the unclear mechanism of the second step of the reaction. All intermediates and transition states on the reaction pathways were characterized using basis sets up to the DFT/B3LYP/6-311++G**//DFT/B3LYP/6-31G* level. Reaction pathways and structural changes were compared with the results previously obtained for inverting glycosyltransferases. The outcome of this study indicates, that among the reaction models investigated, the energetically favorable one is also the most plausible given the existing experimental data. This model requires the presence of only one catalytic acid in the active site with the UDP functioning as a general base in the second step of the reaction. This mechanism is in agreement with both kinetic data in the literature and the description of X-ray structures of retaining glycosyltransferases solved up to today.

Conformation and dynamics of a cyclic (1 → 2)-β-d-glucan

A molecular modelling and nuclear magnetic resonance spectroscopic study was performed in order to gain insight into the conformational preferences of cyclosophoroheptadecaose. MM3 molecular mechanics calculations predicted a non-symmetric conformer with a small cavity of 3.7 A diameter as the lowest energy form. Molecular dynamics simulations gave insight into the dynamics of the free cyclosophoroheptadecaose and also supported the results of molecular mechanics calculations. A fair agreement was found between experimental data and corresponding average values predicted by molecular modelling.

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

Abstract The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg2+ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.

Chapter 28:Successes in engineering glucansucrases to enhance glycodiversification

Carbohydrates are biomolecules that have an essential role in every form of life. The reservoir of naturally occurring glyco-structures is incredibly large and involves a tremendous number of carbohydrate-active enzymes (more than 280,000 released modules in the Carbohydrate Active enZymes database) for their synthesis and degradation. Nevertheless, natural enzymes do not necessarily present all the requested properties in terms of efficiency, specificity or stability when considering their usage for carbohydrate or glyco-derivative manufacturing. In addition, if existing, the identification of an enzyme perfectly adapted to a specific function from the natural diversity may be critical due to the lack of available biochemical data and may necessitate intensive screening efforts. To circumvent such limitations and provide optimized solutions, protein engineering has been considered. Leloir-type glycosyltransferases, for example, are mainly involved in the biosynthesis of glycoconjugates in Nature and they have been widely studied and engineered for this purpose. However, these enzymes are often found as membrane-bound proteins, what renders difficult their isolation and purification. In addition, their need of low-abundant activated sugars as glycosyl donors also impairs their usage. Alternatively, enzymes that use more abundant glycosyl donor directly issued from agro-ressources have been considered to access to new glyco-derivatives. This has promoted the use of glucansucrases (GS) that catalyze transglycosylation reactions from sucrose substrate. These enzymes are of particular interest for synthetic purpose and have found industrial interest for pharmaceutical and fine chemical applications. To diversify their applications, various approaches of engineering have been exploited to improve expression level, stability, or change substrate or product specificity of these enzymes. In particular, the range of molecules recognized and the osidic linkages formed by GS is broad but yet limited. Therefore, protein engineering methods have been applied to further increase the diversity of glycosylation reactions catalyzed by these enzymes. Sequence analysis and mutagenesis experiments have enabled the identification of key amino acid residues of glucansucrases either involved in catalysis or substrate specificity. Moreover, the determination of three-dimensional structures of glucansucrases from both families 13 and 70 of Glycoside-Hydrolases (GH) have provided powerful information for understanding the sequence-structure-function relationships and guiding structure-based rational and semi-rational engineering of these proteins. To assist these efforts, high-throughput screening and biomolecular methods have been developed for the directed evolution of these enzymes. Here are reported some of the successes in the bioengineering of glucansucrases from precursor work to latest results, as well as the methods developed for screening and developing efficient variant libraries. The major progresses and breakthroughs in the field will be highlighted and further prospects will be considered and discussed.