Current Status of Carbohydrates Information in the Protein Data Bank

Unravelling carbohydrate binding module 21 (CBM21) dynamics of interaction with amylose

The carbohydrate binding module 21 (CBM21) from Rhizopus oryzae is a dual-site CBM proposed to disrupt polysaccharide structures. Additionally, it serves as a purification tag in industry. CBM21 crystal structure features a Glc residue in an unusual 1S3 conformation, whose relevance for the CBM mechanism of action is unclear. In this context, we seek to contribute for the understanding of CBM21 mechanism of action by: i) investigating the role of the 1S3 conformation on carbohydrate recognition, and ii) characterize the protein-carbohydrate binding dynamics using molecular dynamics and metadynamics simulations at MM and QM/MM levels. Results indicate the 1S3 Glc conformation is unlikely to occur under biological conditions, being originated from the crystallographic environment. CBM21 binding to small ligands appears transient and unstable, while protein dimerization and polysaccharide chain size influence complex stability. In interactions with amylose, CBM21 exhibits a repeated unbinding followed by re-binding, while simultaneously alternating between binding sites I and II. These results suggest that CBM21 acts through transient interactions, directing carbohydrates to the catalytic center rather than forming strong and long-lasting bonds with carbohydrates. Accordingly, we expect such atomistic depiction of CBM21 mechanism could aid in CBM design targeting biotechnological applications.

SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation

Glycans constitute one of the most complex families of biological molecules. Despite their crucial role in a plethora of biological processes, they remain largely uncharacterized because of their high complexity. Their intrinsic flexibility and the vast variability associated with the many combination possibilities have hampered their experimental determination. Although theoretical methods have proven to be a valid alternative to the study of glycans, the large size associated with polysaccharides, proteoglycans, and glycolipids poses significant challenges to a fully atomistic description of biologically relevant glycoconjugates. On the other hand, the exquisite dependence on hydrogen bonds to determine glycans' structure makes the development of simplified or coarse-grained (CG) representations extremely challenging. This is particularly the case when glycan representations are expected to be compatible with CG force fields that include several molecular types. We introduce a CG representation able to simulate a wide variety of polysaccharides and common glycosylation motifs in proteins, which is fully compatible with the CG SIRAH force field. Examples of application to N-glycosylated proteins, including antibody recognition and calcium-mediated glycan-protein interactions, highlight the versatility of the enlarged set of CG molecules provided by SIRAH.

Exploring Ring Conformation in Uronate Monosaccharides: Insights from Ab Initio Calculations and Classical Molecular Dynamics Simulations

The study focuses on the conformational properties of biologically relevant monosaccharides belonging to the group of uronates: α-l-iduronate, O2-sulfated-α-l-iduronate, and O2-sulfated-α-l-guluronate, either unfunctionalized or O1-methylated. We applied the previously proposed two-step methodology, combining classical MD simulations and subsequent ab initio (QM) calculations, performed on a rationally subsampled set of molecular configurations. We found that, regardless of the number of molecular configurations considered, the level of theory, and the weighting scheme applied, none of the QM approaches is capable of predicting the correct conformational equilibrium of sulfated iduronates as long as the tight counterion binding is not considered. Multicenter, ring-shape-specific binding of either Na+ or Ca2+ ions drastically shifts the conformational equilibrium of the pyranose ring in sulfated iduronates toward 1C4 but does not significantly affect the conformation of non-sulfated compounds. A similar shift is observed upon the protonation of carboxyl groups in all iduronates. In addition, we report a set of average J-coupling constant values related to vicinal protons bound to the pyranose ring of iduronates and corresponding to each of the three main groups of ring conformers, i.e., 4C1, B/S (boat/skew boat), and 1C4. In combination with the conformational energies or with the experimental data, these values allowed the relative proportions of the ring conformers to be estimated and the Karplus-type equations linking the 3JHH-coupling constants to the torsion angles within the pyranose ring to be refined.

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.

Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides

Analysis of crystal structures of hexose monosaccharides α-d-mannose (α-MAN), β-d-mannose (β-MAN), α-d-glucose (α-GLC), β-d-glucose (β-GLC), α-d-galactose (α-GAL), β-d-galactose (β-GAL), α-d-altrose (α-ALT), β-d-altrose (β-ALT), α-d-idose (α-IDO), and β-d-idose (β-IDO) reveals that the monosaccharide ring adopts multiple ring conformations. These ring conformations can be broadly classified as chair, half-chair, envelope, boat, and skew-boat conformations. The ability of the monosaccharide ring to adopt multiple conformations has been closely tied with their bioactivity. However, it has been difficult to capture the dynamic information of these conformations from experimental studies. Even from simulations, capturing these different conformations is challenging because of the energy barriers involved in the transitions between the stable ⁴C₁ and ¹C₄ chair forms. In this study, we analyze the influence of the polarizable force field on the ring dynamics of five major types of unsubstituted aldohexoses─glucose, mannose, galactose, altrose, and idose─and their anomers. We simulate microsecond trajectories to capture the influence of the CHARMM36 additive and polarizable carbohydrate force fields on the ring dynamics. The microsecond trajectories allow us to comment on the issues associated with equilibrium molecular dynamics simulations. Further, we use the extended system adaptive biasing force (eABF) method to compare the conformational sampling efficiencies of the additive and polarizable force fields. Our studies reveal that inclusion of polarization enhances the sampling of ring conformations and lowers the energy barriers between the ⁴C₁ and ¹C₄ conformations. Overall, the CHARMM36 additive force field is observed to be rigid and favor the ⁴C₁ conformations. Although the inclusion of polarizability results in enhancing ring flexibility, we observe sampling that does not agree with experimental results, warranting a revision of the polarizable Drude parameters.

Multifaceted Computational Modeling in Glycoscience

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.

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.

Carbohydrate structure database (CSDB) oligosaccharide conformation tool

Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database (CSDB). Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 inter-residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to four torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html.

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations

In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (⁴C₁ to ¹C₄) of each monosaccharide except mannose are sampled in our simulations, although the ⁴C₁ chair form is energetically more favorable than ¹C₄. In N-glycan1, the 1-6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks.

Enantioselective Reductive Oligomerization of Carbon Dioxide into l-Erythrulose via a Chemoenzymatic Catalysis

A cell-free enantioselective transformation of the carbon atom of CO₂ has never been reported. In the urgent context of transforming CO₂ into products of high value, the enantiocontrolled synthesis of chiral compounds from CO₂ would be highly desirable. Using an original hybrid chemoenzymatic catalytic process, we report herein the reductive oligomerization of CO₂ into C₃ (dihydroxyacetone, DHA) and C₄ (l-erythrulose) carbohydrates, with perfect enantioselectivity of the latter chiral product. This was achieved with the key intermediacy of formaldehyde. CO₂ is first reduced selectively by 4e^- by an iron-catalyzed hydroboration reaction, leading to the isolation and complete characterization of a new bis(boryl)acetal compound derived from dimesitylborane. In an aqueous buffer solution at 30 °C, this compound readily releases formaldehyde, which is then involved in selective enzymatic transformations, giving rise either (i) to DHA using a formolase (FLS) catalysis or (ii) to l-erythrulose with a cascade reaction combining FLS and d-fructose-6-phosphate aldolase (FSA) A129S variant. Finally, the nature of the synthesized products is noteworthy, since carbohydrates are of high interest for the chemical and pharmaceutical industries. The present results prove that the cell-free de novo synthesis of carbohydrates from CO₂ as a sustainable carbon source is a possible alternative pathway in addition to the intensely studied biomass extraction and de novo syntheses from fossil resources.

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity

Lectin-glycan interactions facilitate inter- and intracellular communication in many processes including protein trafficking, host-pathogen recognition, and tumorigenesis promotion. Specific recognition of glycans by lectins is also the basis for a wide range of applications in areas including glycobiology research, cancer screening, and antiviral therapeutics. To provide a better understanding of the determinants of lectin-glycan interaction specificity and support such applications, this study comprehensively investigates specificity-conferring features of all available lectin-glycan complex structures. Systematic characterization, comparison, and predictive modeling of a set of 221 complementary physicochemical and geometric features representing these interactions highlighted specificity-conferring features with potential mechanistic insight. Univariable comparative analyses with weighted Wilcoxon-Mann-Whitney tests revealed strong statistical associations between binding site features and specificity that are conserved across unrelated lectin binding sites. Multivariable modeling with random forests demonstrated the utility of these features for predicting the identity of bound glycans based on generalized patterns learned from non-homologous lectins. These analyses revealed global determinants of lectin specificity, such as sialic acid glycan recognition in deep, concave binding sites enriched for positively charged residues, in contrast to high mannose glycan recognition in fairly shallow but well-defined pockets enriched for non-polar residues. Focused fine specificity analysis of hemagglutinin interactions with human-like and avian-like glycans uncovered features representing both known and novel mutations related to shifts in influenza tropism from avian to human tissues. As the approach presented here relies on co-crystallized lectin-glycan pairs for studying specificity, it is limited in its inferences by the quantity, quality, and diversity of the structural data available. Regardless, the systematic characterization of lectin binding sites presented here provides a novel approach to studying lectin specificity and is a step towards confidently predicting new lectin-glycan interactions.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.

Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta

Carbohydrate chains are ubiquitous in the complex molecular processes of life. These highly diverse chains are recognized by a variety of protein receptors, enabling glycans to regulate many biological functions. High-resolution structures of protein-glycoligand complexes reveal the atomic details necessary to understand this level of molecular recognition and inform application-focused scientific and engineering pursuits. When experimental challenges hinder high-throughput determination of quality structures, computational tools can, in principle, fill the gap. In this work, we introduce GlycanDock, a residue-centric protein-glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. We performed a benchmark docking assessment using a set of 109 experimentally determined protein-glycoligand complexes as well as 62 unbound protein structures. The GlycanDock algorithm can sample and discriminate among protein-glycoligand models of native-like structural accuracy with statistical reliability from starting structures of up to 7 Å root-mean-square deviation in the glycoligand ring atoms. We show that GlycanDock-refined models qualitatively replicated the known binding specificity of a bacterial carbohydrate-binding module. Finally, we present a protein-glycoligand docking pipeline for generating putative protein-glycoligand complexes when only the glycoligand sequence and unbound protein structure are known. In combination with other carbohydrate modeling tools, the GlycanDock docking refinement algorithm will accelerate research in the glycosciences.

Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution

In this work, by using molecular dynamic simulation we provide microscale structure information which helps to reveal the molecular mechanisms concerning the multi-chain conformational behavior of short curdlan. Through simulations starting with different conformations of curldan dodecasaccharides, it is found that the right-handed triple helix is thermodynamically the most stable conformation in aqueous solutions, which is well maintained and stabilized by an inter-strand hydrogen bonding network of the C₂ hydroxyls. Unlike any predicted forms, the inter-strand hydrogen bonds exhibit a left-handed double helix pattern with preferred global orientations. Temperature REMD results suggest that the formation of triple helix is temperature sensitive, but the already formed triple helix is not. Investigation of curdlan with numbers of repeating units from 3 to 12 captures a critical value of 6, which in a way elucidates the relationship between the formation of triple helix and the chain length.

Prebiotic Peptides Based on the Glycocodon Theory Analyzed with FRET

In modern protein–carbohydrate interactions, carbohydrate–aromatic contact with CH–π interactions are used. Currently, they are considered driving forces of this complexation. In these contacts, tryptophan, tyrosine, and histidine are preferred. In this study, we focus on primary prebiotic chemistry when only glycine, alanine, aspartic acid, and valine are available in polypeptides. In this situation, when the aromatic acids are not available, hydrogen-bonding aspartic acid must be used for monosaccharide complexation. It is shown here that (DAA)n polypeptides play important roles in primary “protein”–glucose recognition, that (DGG)n plays an important role in “protein”–ribose recognition, and that (DGA)n plays an important role in “protein”–galactose recognition. Glucose oxidase from Aspergillus niger, which still has some ancient prebiotic sequences, is chosen here as an example for discussion.

Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations

Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.

GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans

Glycosaminoglycans (GAGs) are a family of anionic carbohydrates that play an essential role in the physiology and pathology of all eukaryotic life forms. Experimental determination of GAG-protein complexes is challenging due to their difficult isolation from biological sources, natural heterogeneity, and conformational flexibility-including possible ring puckering of sulfated iduronic acid from ¹C₄ to ²S_O conformation. To overcome these challenges, we present GlycoTorch Vina (GTV), a molecular docking tool based on the carbohydrate docking program VinaCarb (VC). Our program is unique in that it contains parameters to model ²S_O sugars while also supporting glycosidic linkages specific to GAGs. We discuss how crystallographic models of carbohydrates can be biased by the choice of refinement software and structural dictionaries. To overcome these variations, we carefully curated 12 of the best available GAG and GAG-like crystal structures (ranging from tetra- to octasaccharides or longer) obtained from the PDB-REDO server and refined using the same protocol. Both GTV and VC produced pose predictions with a mean root-mean-square deviation (RMSD) of 3.1 Å from the native crystal structure-a statistically significant improvement when compared to AutoDock Vina (4.5 Å) and the commercial software Glide (5.9 Å). Examples of how real-space correlation coefficients can be used to better assess the accuracy of docking pose predictions are given. Comparisons between statistical distributions of empirical "salt bridge" interactions, relevant to GAGs, were compared to density functional theory (DFT) studies of model salt bridges, and water-mediated salt bridges; however, there was generally a poor agreement between these data. Water bridges appear to play an important, yet poorly understood, role in the structures of GAG-protein complexes. To aid in the rapid prototyping of future pose scoring functions, we include a module that allows users to include their own torsional and nonbonded parameters.

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

Molecular dynamic simulation: Conformational properties of single-stranded curdlan in aqueous solution

Recently, molecular dynamic simulation technique has been proved to be a powerful tool providing structural insights for better understanding the functionality of carbohydrates. Here, by using molecular dynamic simulation method we investigated the detailed conformational properties of the single-stranded curdlan with 12 glucose units. The results showed that the right-handed 6/1 helix structure was thermodynamically the most stable conformation in solution. The formation of the helix conformation was determined by many factors such as the glycosidic linkage, explicit water solvation and hydrogen bonds. When temperature was increased, the representative helix conformation was found becoming unstable giving rise to metastable conformations because when water mobility was accelerated with temperature, the hydrogen bonding strength between the curdlan chain and water went down, breaking the continuity of the hydrogen bonding network of water and hydroxyl groups. When the number of repeating glucose units varied from 6 to 24, the major helix conformation remained, but the conformational properties of longer chains were more apparently aff ;ected by chain flexibility.