The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation

Alginate lyases (ALs) catalyze the depolymerization of brown macroalgae alginates, widely used naturally occurring polysaccharides. Their molecular reaction mechanism remains elusive due to the lack of catalytically competent Michaelis-Menten-like complex structures. Here, we provide structural snapshots and dissect the mechanism of mannuronan-specific ALs from family 7 polysaccharide lyases (PL7), employing time-resolved NMR, X-ray, neutron crystallography, and QM/MM simulations. We reveal the protonation state of critical active site residues, enabling atomic-level analysis of the reaction coordinate. Our approach reveals an endolytic and asynchronous syn β-elimination reaction, with Tyr serving as both Brønsted base and acid, involving a carbanion-type transition state. This study not only reconciles previous structural and kinetic discrepancies, but also establishes a comprehensive PL reaction mechanism which is most likely applicable across all enzymes of the PL7 family as well as other PL families.

Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage

A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.

Ab initio conformational analysis of α/β-D-xylopyranose at pyrolysis conditions

Xylopyranose is the principal monosaccharide unit of hemicellulose, one of the three major biopolymers of lignocellulosic biomass. Understanding its decomposition mechanism is increasingly relevant for thermochemical biorefinery research such as pyrolysis. Significant efforts have been made to study its chemical and structural properties using both computational and experimental methods. However, due to its high structural flexibility and numerous hydroxyl groups, various metastable conformers arise. In this work, we performed a computational exploration of the conformational space of both anomeric forms, α and β, of D-xylopyranose using the semi-empirical GFN2-xTB method in conjunction with metadynamics and density functional theory simulations for structural optimization and vibrational analysis. Xylopyranose conformers free energy and enthalpy variations are analyzed across temperatures typical of fast biomass pyrolysis (298-1068 K), with the Boltzmann population distribution of the most populated conformers determined. This study provides a detailed computational analysis of the conformational space and thermochemistry of xylopyranose. Additionally, 44 and 59 conformers of the α and β anomers were found, for both of which a selection of 10 conformers based on Boltzmann population distribution analysis is performed to reduce the conformational space for ab initio studies of the pyrolysis reaction kinetics.

An Unusual His/Asp Dyad Operates Catalysis in Agar-Degrading Glycosidases

Agarose motifs, found in agars present in the cell walls of red algae, consist of alternating units of d-galactose (G) and α-3,6-anhydro-l-galactose (LA). Glycoside hydrolases from family 117 (GH117) cleave the terminal α-1,3-glycosidic bonds, releasing LA units. Structural studies have suggested that these enzymes use unconventional catalytic machinery, involving a histidine (His302) as a general acid rather than a carboxylic residue as in most glycosidases. By means of quantum mechanics/molecular mechanics metadynamics, we investigated the reaction mechanism of Phocaeicola plebeius GH117, confirming the catalytic role of His302. This residue shares a proton with a neighbor aspartate residue (Asp320), forming a His/Asp dyad. Our study also reveals that, even though the sugar unit at the -1 subsite (LA) can adopt two conformations, 4 C 1 and 1,4 B, only the latter is catalytically competent, defining a 1,4 B → [4 E]‡ → 1,4 B (→ 4 C 1) conformational itinerary. This mechanism may be applicable to similar enzymes with a His/Asp dyad in their active sites, such as GH3 β-N-acetylglucosaminidase and GH156 sialidase. These insights enhance our understanding of glycosidase catalytic strategies and could inform the engineering of enzymes for the more efficient processing of seaweed.

Bimodal substrate binding in the active site of the glycosidase BcX

Bacillus circulans xylanase (BcX) from the glycoside hydrolase family 11 degrades xylan through a retaining, double-displacement mechanism. The enzyme is thought to hydrolyze glycosidic bonds in a processive manner and has a large, active site cleft, with six subsites allowing the binding of six xylose units. Such an active site architecture suggests that oligomeric xylose substrates can bind in multiple ways. In the crystal structure of the catalytically inactive variant BcX E78Q, the substrate xylotriose is observed in the active site, as well as bound to the known secondary binding site and a third site on the protein surface. Nuclear magnetic resonance (NMR) titrations with xylose oligomers of different lengths yield nonlinear chemical shift trajectories for active site nuclei resonances, indicative of multiple binding orientations for these substrates for which binding and dissociation are in fast exchange on the NMR timescale, exchanging on the micro- to millisecond timescale. Active site binding can be modeled with a 2 : 1 model with dissociation constants in the low and high millimolar range. Extensive mutagenesis of active site residues indicates that tight binding occurs in the glycon binding site and is stabilized by Trp9 and the thumb region. Mutations F125A and W71A lead to large structural rearrangements. Binding at the glycon site is sensed throughout the active site, whereas the weak binding mostly affects the aglycon site. The interactions with the two active site locations are largely independent of each other and of binding at the secondary binding site.

Accelerated Lignocellulosic Molecule Adsorption Structure Determination

Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules β-d-xylose and 1,4-β-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.

Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase

Bacterial β-glycosidases are hydrolytic enzymes that depolymerize polysaccharides such as β-cellulose, β-glucans and β-xylans from different sources, offering diverse biomedical and industrial uses. It has been shown that a conformational change of the substrate, from a relaxed 4 C1 conformation to a distorted 1 S3 /1,4 B conformation of the reactive sugar, is necessary for catalysis. However, the molecular determinants that stabilize the substrate's distortion are poorly understood. Here we use quantum mechanics/molecular mechanics (QM/MM)-based molecular dynamics methods to assess the impact of the interaction between the reactive sugar, i. e. the one at subsite -1, and the catalytic nucleophile (a glutamate) on substrate conformation. We show that the hydrogen bond involving the C2 exocyclic group and the nucleophile controls substrate conformation: its presence preserves sugar distortion, whereas its absence (e.g. in an enzyme mutant) knocks it out. We also show that 2-deoxy-2-fluoro derivatives, widely used to trap the reaction intermediates by X-ray crystallography, reproduce the conformation of the hydrolysable substrate at the experimental conditions. These results highlight the importance of the 2-OH⋅⋅⋅nucleophile interaction in substrate recognition and catalysis in endo-glycosidases and can inform mutational campaigns aimed to search for more efficient enzymes.

Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation

Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.

Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes

The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development of sustainable processes to obtain bioproducts and biofuels. In this scenario, the design of efficient inhibitors for glycosidases that can act as drug targets and the engineering of carbohydrate-active enzymes with tailored catalytic properties is of remarkable importance. To guide rational approaches, it is necessary to elucidate enzyme molecular mechanisms, in particular understanding how the microenvironment modulates the conformational space explored by the substrate. Computer simulations, especially those based on ab initio methods, have provided a suitable atomic description of carbohydrate conformations and catalytic reactions in several glycosidase families. In this review, we will focus on how the active-site topology (pocket or cleft) and mode of cleavage (endo or exo) can affect the catalytic mechanisms adopted by glycosidases, in particular the substrate conformations along the reaction coordinate.

Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN 2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the "electrophilic trap" that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C6 H10 Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C-Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMONu -LUMOSubstrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study

Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation (dp6s, dp7s, and dp12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1-4), while IdoA is linked to N-GalNAc through α(1-3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp12s are reduced significantly compared to dp6s or dp7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.

Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases

Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.

Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase

Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.

Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations

Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.

Dynamics of Ligand Binding to a Rigid Glycosidase*

The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.

Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography

XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme's optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pK_a calculations show that D44 has similar position and pK_a value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum.

How and why plants and human N-glycans are different: Insight from molecular dynamics into the "glycoblocks" architecture of complex carbohydrates

The N-glycosylation is one of the most abundant and diverse post-translational modifications of proteins, implicated in protein folding and structural stability, and mediating interactions with receptors and with the environment. All N-glycans share a common core from which linear or branched arms stem from, with functionalization specific to different species and to the cells’ health and disease state. This diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans’ 3D architecture and dynamics, which remain for the large part unresolved and undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans’ 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We also compare these structural motifs and combine them with mammalian N-glycan motifs to devise strategies for the control of the N-glycan 3D structure through sequence. Our results suggest that the N-glycans’ architecture can be described in terms of the local spatial environment of groups of monosaccharides. We define these “glycoblocks” as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans’ 3D architecture can potentially lead to an easier prediction of sequence-to-structure relationships in complex carbohydrates, with important implications in glycoengineering design.

Describing Polytopal Rearrangements of Fluxional Molecules with Curvilinear Coordinates Derived from Normal Vibrational Modes: A Conceptual Extension of Cremer-Pople Puckering Coordinates

In this work a new curvilinear coordinate system is presented for the comprehensive description of polytopal rearrangements of N-coordinate compounds (N = 4-7) and systems containing an N-coordinate subunit. It is based on normal vibrational modes and a natural extension of the Cremer-Pople puckering coordinates ( J. Am. Chem. Soc. 1975, 97, 1354) together with the Zou-Izotov-Cremer deformation coordinates ( J. Phys. Chem. A 2011, 115, 8731) for ring structures to N-coordinate systems. We demonstrate that the new curvilinear coordinates are ideal reaction coordinates describing fluxional rearrangement pathways by revisiting the Berry pseudorotation and the lever mechanism in sulfur tetrafluoride, the Berry pseudorotation and two Muetterties' mechanisms in pentavalent compounds, the chimeric pseudorotation in iodine pentafluoride, Bailar and Ray-Dutt twists in hexacoordinate tris-chelates as well as the Bartell mechanism in iodine heptafluoride. The results of our study reveal that this dedicated curvilinear coordinate system can be applied to most coordination compounds opening new ways for the systematic modeling of fluxional processes.

Modeling catalytic reaction mechanisms in glycoside hydrolases

Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.

Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes

Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of β-xylosidases and endo-β-1,4-xylanases in the secretomes of Aspergillus niger, by the use of chemical probes inspired by the β-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.

Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase

By means of QM(DFT)/MM metadynamics we have unraveled the hydrolytic reaction mechanism of Neisseria polysaccharea amylosucrase (NpAS), a member of GH13 family. Our results provide an atomistic picture of the active site reorganization along the catalytic double-displacement reaction, clarifying whether the glycosyl-enzyme reaction intermediate features an α-glucosyl unit in an undistorted ⁴C₁ conformation, as inferred from structural studies, or a distorted ¹S₃-like conformation, as expected from mechanistic analysis of glycoside hydrolases (GHs). We show that, even though the first step of the reaction (glycosylation) results in a ⁴C₁ conformation, the α-glucosyl unit undergoes an easy conformational change toward a distorted conformation as the active site preorganizes for the forthcoming reaction step (deglycosylation), in which an acceptor molecule, i.e., a water molecule for the hydrolytic reaction, performs a nucleophilic attack on the anomeric carbon. The two conformations (⁴C₁ ad E₃) can be viewed as two different states of the glycosyl-enzyme intermediate (GEI), but only the E₃ state is preactivated for catalysis. These results are consistent with the general conformational itinerary observed for α-glucosidases.

A novel ring-shaped reaction pathway with interconvertible intermediates in chitinase A as revealed by QM/MM simulation combined with a one-dimensional projection technique

Efficient sampling achieved by the use of a one-dimensional projection technique reveals the catalytic mechanism of chitinase A from Serratia marcescens.

Structural Considerations on the Use of Endo-Xylanases for the Production of prebiotic Xylooligosaccharides from Biomass

Xylooligosaccharides (XOS) have gained increased interest as prebiotics during the last years. XOS and arabinoxylooligosaccharides (AXOS) can be produced from major fractions of biomass including agricultural by-products and other low cost raw materials. Endo-xylanases are key enzymes for the production of (A)XOS from xylan. As the xylan structure is broadly diverse due to different substitutions, diverse endo-xylanases have evolved for its degradation. In this review structural and functional aspects are discussed, focusing on the potential applications of endo-xylanases in the production of differently substituted (A)XOS as emerging prebiotics, as well as their implication in the processing of the raw materials. Endo-xylanases are found in at least eight different glycoside hydrolase families (GH), and can either have a retaining or an inverting catalytic mechanism. To date, it is mainly retaining endo-xylanases that are used in applications to produce (A)XOS. Enzymes from these GH-families (mainly GH10 and GH11, and the more recently investigated GH30) are taken as prototypes to discuss substrate preferences and main products obtained. Finally, the need of new and accessory enzymes (new specificities from new families or sources) to increase the yield of different types of (A)XOS is discussed, along with in vitro tests of produced oligosaccharides and production of enzymes in GRAS organisms to facilitate use in functional food manufacturing.

Structure-guided engineering of the substrate specificity of a fungal β-glucuronidase toward triterpenoid saponins

Glycoside hydrolases (GHs) have attracted special attention in research aimed at modifying natural products by partial removal of sugar moieties to manipulate their solubility and efficacy. However, these modifications are challenging to control because the low substrate specificity of most GHs often generates undesired by-products. We previously identified a GH2-type fungal β-glucuronidase from Aspergillus oryzae (PGUS) exhibiting promiscuous substrate specificity in hydrolysis of triterpenoid saponins. Here, we present the PGUS structure, representing the first structure of a fungal β-glucuronidase, and that of an inactive PGUS mutant in complex with the native substrate glycyrrhetic acid 3-O-mono-β-glucuronide (GAMG). PGUS displayed a homotetramer structure with each monomer comprising three distinct domains: a sugar-binding, an immunoglobulin-like β-sandwich, and a TIM barrel domain. Two catalytic residues, Glu⁴¹⁴ and Glu⁵⁰⁵, acted as acid/base and nucleophile, respectively. Structural and mutational analyses indicated that the GAMG glycan moiety is recognized by polar interactions with nine residues (Asp¹⁶², His³³², Asp⁴¹⁴, Tyr⁴⁶⁹, Tyr⁴⁷³, Asp⁵⁰⁵, Arg⁵⁶³, Asn⁵⁶⁷, and Lys⁵⁶⁹) and that the aglycone moiety is recognized by aromatic stacking and by a π interaction with the four aromatic residues Tyr⁴⁶⁹, Phe⁴⁷⁰, Trp⁴⁷², and Tyr⁴⁷³ Finally, structure-guided mutagenesis to precisely manipulate PGUS substrate specificity in the biotransformation of glycyrrhizin into GAMG revealed that two amino acids, Ala³⁶⁵ and Arg⁵⁶³, are critical for substrate specificity. Moreover, we obtained several mutants with dramatically improved GAMG yield (>95%). Structural analysis suggested that modulating the interaction of β-glucuronidase simultaneously toward glycan and aglycone moieties is critical for tuning its substrate specificity toward triterpenoid saponins.

Molecular dynamics simulations of hexopyranose ring distortion in different force fields

The four classical, biomolecular force fields designed to study hexopyranose-based carbohydrates (GROMOS 56a6CARBO/56a6CARBO_R, GROMOS 53a6GLYC, CHARMM and GLYCAM06) have been tested in the context of ring-inversion properties. These properties were evaluated for both unfunctionalized monomers of all hexopyranoses of the d series and for residues in a chain composed of uniform units connected by α(1→4) and β(1→4) glycosidic linkages. The results indicate that the tested force fields differ in their predictions of the ring-inversion properties of both monomers and residues in a chain. The comparison with the available experimental data and with the semi-empirical Angyal scheme reveals that, at the level of monomers, GROMOS 56a6CARBO, GROMOS 53a6GLYC and CHARMM correctly reproduce the ring-inversion free energies. However, due to the lack of analogous reference data we cannot state which force field is more or less accurate in the context of ring distortion of residues in a chain. Therefore, the use of ab initio potentials is recommended in the prospective, quantitative studies on the related subject.

The molecular mechanism of the ligand exchange reaction of an antibody against a glutathione-coated gold cluster

The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double S_N2-like reaction mechanism, involving a proton transfer, with low activation barriers only if one of the two distinct peptide/peptidic ligands (the one that occupies the side position) is substituted. Positively charged residues in the vicinity of the incoming thiol result in strong interactions between the antibody and the AuMPC, favoring the ligand exchange reaction for suitable protein mutants. These results pave the way for future investigations aimed at engineering biomolecules to increase their reactivity towards a desired gold atom cluster.

Strategies for carbohydrate model building, refinement and validation

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

Carbohydrate structure: the rocky road to automation

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.

In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass

Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation.

Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation

Carbohydrates play crucial roles in many biological processes, from cell-cell adhesion to chemical signaling. Their complexity and diversity, related to α/β anomeric configuration, ring substituents, and conformational variations, require a diverse set of enzymes for their processing. Among them, glycoside hydrolases (GHs) are responsible for the hydrolysis of one of the strongest bonds in nature: the glycosidic bond. These highly specialized biological catalysts select particular conformations their carbohydrate substrates to enhance catalysis. The evolution of this conformation during the reaction of glycosidic bond cleavage, known as the conformational catalytic itinerary, is of fundamental interest in glycobiology, with impact on inhibitor and drug design. Here we review some of the aspects and the main strategies one needs to take into account when simulating a reaction in a GH enzyme using QM/MM metadynamics. Several specific aspects are highlighted, from the importance of the distortion of the substrate at the Michaelis complex to the variable control during the metadynamics simulation or the analysis of the reaction mechanism and conformational itinerary. The increasing speed of computer power and methodological advances have added a vital tool to the study of GH mechanisms, as shown here and recent reviews. It is hoped that this chapter will serve as a first guide for those attempting to perform a metadynamics simulation of these relevant and fascinating enzymes.

Dipole moments of trans- and cis-(4-methylcyclohexyl)methanol (4-MCHM): obtaining the right conformer for the right reason

Accurate computational estimates of fundamental physical properties can be used as inputs in the myriad of extant models employed to predict toxicity, transport, and fate of contaminants. However, as molecular complexity of contaminants increases, it becomes increasingly difficult to determine the magnitude of the errors introduced by ignoring the 3D conformational space averaging within group-additivity and semi-empirical approaches. The importance of considering 3D molecular structure is exemplified for the dipole moments of cis and trans isomers of (4-methylcyclohexyl)methanol (4-MCHM). When 10 000 gallons of 4-MCHM was spilled into the Elk River in January 2014, a lack of toxicological data and environmental partitioning coefficients hindered the immediate protection of human health and the local water supply in West Virginia, USA. Post-spill analysis of the contaminants suggested that the cis and trans isomers had observably different partitioning coefficients and solubility, and thus differing environmental fates. Obtaining high-quality dipole moments using ab initio quantum chemical methods for the isomeric pair was crucial in validating their experimental differences in solubility [Environ. Sci. Technol. Lett., 2015, 2, 127]. The use of first principles electronic structure theory is further explored here to obtain accurate conformer relative energies and dipole moments of cis- and trans-4-MCHM. Overall, the MP2 aug-cc-pVDZ level of theory affords the best balance between accuracy and computational cost.

The Raman optical activity of β-D-xylose: where experiment and computation meet

Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.