Importance of IdoA and IdoA(2S) ring conformations in computational studies of glycosaminoglycan–protein interactions

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.

Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins

Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.

In silico insights into procathepsin S maturation mediated by glycosaminoglycans

Procathepsins, inactive precursors of cathepsins are present in the extracellular matrix (ECM) and in lysosomes. Their active forms are involved in a number of biologically relevant processes, including bone resorption, intracellular proteolysis and regulation of programmed cell death. These processes might be mediated by glycosaminoglycans (GAGs), long unbranched periodic negatively charged polysaccharides. GAGs are also present in ECM and play important role in anticoagulation, angiogenesis and tissue regeneration. GAGs not only mediate the enzymatic activity of cathepsins but can also regulate the process of procathepsin maturation, as it was shown for procathepsin B and S. In this study, we propose the molecular mechanism underlying the biological role of GAGs in procathepsin S maturation and compare our findings with computational data obtained for procathepsin B. We rigorously analyse procathepsin S-GAG complexes in terms of their dynamics, free energy and potential allosteric regulation. We conclude that the GAG binding region might have an effect on the dynamics of procathepsin S structure and so affect its maturation by two different mechanisms.

Capillary Zone Electrophoresis-Electrospray Ionization Tandem Mass Spectrometry for Total Analysis of Chondroitin/Dermatan Sulfate Oligosaccharides

Proteoglycans are heavily glycosylated proteins, covalently linked to one or more glycosaminoglycan (GAG) chains, abundantly expressed in the extracellular matrix (ECM). Among GAGs, chondroitin sulfate (CS) and dermatan sulfate (DS) play an essential role at the ECM level; however, the composition of the hybrid CS/DS as well as the distribution of the sulfate groups along the chain were also shown to influence biological activities in brain. The elevated structural diversity of CS/DS motifs, in which sulfation may occur at GalNAc and/or IdoA/GlcA in various combinations, requires the development of specific high performance analytical methods for reliable elucidation. Due to its sensitivity, reproducibility, and efficiency, capillary zone electrophoresis (CZE) for separation of CS/DS oligosaccharides coupled to electrospray ionization mass spectrometry (ESI-MS) for their structure determination contributed an essential progress to this field.In the present chapter, two powerful methods based on CZE for separation and ESI-MS for identification and structural analysis of CS/DS are presented. The first part is devoted to offline CZE-ESI-MS based on fraction collection, screening by negative ion mode nanoESI, and fragmentation analysis in tandem MS using collision-induced dissociation (CID) at low ion acceleration energies. In the second part of the chapter, a strategy for online CZE-ESI-MS in normal polarity and negative mode ESI followed by tandem MS in real-time data-dependent acquisition mode for CS/DS separation, screening, and fragmentation is described in detail. The latter method entails the in-laboratory manufacturing of a simple yet sturdy interface for the online CZE coupling to ESI-MS and the optimization of the coupled system for total analysis of regularly sulfated and irregularly, i.e., under- and oversulfated CS/DS domains.

Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship

The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.

Role of Oligosaccharide Chain Polarity in Protein-Glycosaminoglycan Interactions

Glycosaminoglycans (GAGs) are long unbranched anionic polysaccharides made up of repetitive disaccharide units involved in biologically relevant processes in the extracellular matrix such as cell proliferation and communication. A GAG can be bound in antiparallel energetically comparable orientations on the protein surface, and these orientations are, therefore, difficult to distinguish both experimentally and computationally. In this study, for the first time we analyzed the impact of the GAG chain polarity on the interactions with Fibroblast Growth Factors-1 and -2 (FGF-1 and FGF-2). We performed a series of 1 μs molecular dynamics simulations of the FGF-1 and FGF-2 complexes with heparin (HP), a GAG representative, of different length. We analyzed the relationship between the HP orientation, energetic, and conformational space characteristics of FGF-1-HP and FGF-2-HP complexes. We concluded that HP can be bound by these proteins in the same binding sites but in different orientations, while the orientation present in the experimental structure might be favorable. Our data presented in this study provide a novel view on the impact of GAG polarity on the specificity of protein-GAG complex formation, which is an essential aspect for the proper understanding of the intermolecular interactions in these systems.

Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study

Procathepsins are an inactive, immature form of cathepsins, predominantly cysteine proteases present in the extracellular matrix (ECM) and in lysosomes that play a key role in various biological processes such as bone resorption or intracellular proteolysis. The enzymatic activity of cathepsins can be mediated by glycosaminoglycans (GAGs), long unbranched periodic negatively charged polysaccharides found in ECM that take part in many biological processes such as anticoagulation, angiogenesis, and tissue regeneration. In addition to the known effects on mature cathepsins, GAGs can mediate the maturation process of procathepsins, in particular, procathepsin B. However, the detailed mechanism of this mediation at the molecular level is still unknown. In this study, for the first time, we aimed to unravel the role of GAGs in this process using computational approaches. We rigorously analyzed procathepsin B–GAG complexes in terms of their dynamics, energetics, and potential allosteric regulation. We revealed that GAGs can stabilize the conformation of the procathepsin B structure with the active site accessible for the substrate and concluded that GAGs most probably bind to procathepsin B once the zymogen adopts the enzymatically active conformation. Our data provided a novel mechanistic view of the maturation process of procathepsin B, while the approaches elaborated here might be useful to study other procathepsins. Furthermore, our data can serve as a rational guide for experimental work on procathepsin–GAG systems that are not characterized in vivo and in vitro yet.

Protein interactome analysis of iduronic acid-containing glycosaminoglycans reveals a novel flagellar invasion factor MbhA

Pathogens are able to exploit specific glycosaminoglycans (GAGs), especially iduronic acid (IdoA)-containing GAGs, to invade the host. By analyzing Escherichia coli proteome chip data, we identified the interactomes of three IdoA-containing GAGs: heparin, heparin sulfate (HS), and chondroitin sulfate B (CSB). Using non-IdoA-containing GAG, chondroitin sulfate C, as a negative control, 157 proteins specifically binding with IdoA-containing GAGs were revealed in the present study. These proteins showed functional enrichment in protein synthesis and metabolism. Fifteen proteins which commonly interacts with three IdoA-containing GAGs were further examined. The regular expression for motif showed these common IdoA interactome shared a conserved sequence. Among them, we identified a second flagellar system outer membrane protein, MbhA. The MbhA has Kd values of 8.9 × 10^-8 M, 5.3 × 10^-7 M, and 1.79 × 10^-7 M to interact with heparin, HS, and CSB, respectively. Using flow cytometry, we confirmed that the MbhA protein can bind to human epithelial cells HCT-8. Overexpression of mbhA increased the percentage of invasion in E. coli which lacks a second flagellar system. Moreover, pre-blocking of HCT-8 cells with MbhA inhibited the bacterial invasion, implying the importance of the direct interaction of MbhA and the host cell surface on bacterial invasion. SIGNIFICANCE: We analyzed the Escherichia coli proteomic data to elucidate the interactomes of three different IdoA-containing GAGs (heparin, HS, and CSB) because these IdoA-containing GAGs can mediate bacterial invasion to the host. Through proteomic and systematic analysis, a second flagellar system outer membrane protein, MbhA, was also identified in the present study. Affinity assay confirmed that MbhA can bind to three IdoA-containing GAGs heparin, HS, and CSB. The result of flow cytometry also showed MbhA can interact with human epithelial cells HCT-8. Results of bacteria invasion assay showed overexpression of mbhA promoted the bacterial invasion. Moreover, pre-blocking of HCT-8 cells with MbhA also reduced the percentage of bacterial invasion. These findings correspond well that MbhA is one of invasion factors.

Docking software performance in protein-glycosaminoglycan systems

We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned. Our results suggest that Dock program performs best in terms of the pose placement, has the most suitable scoring function, and its performance did not depend on the ligand size. This suggests that the implementation of the electrostatics as well as the shape complementarity procedure in Dock are the most suitable for docking glycosaminoglycan ligands. We also analyzed how free energy patterns of the benchmarking complexes affect the performance of the evaluated docking software.

Modeling large protein-glycosaminoglycan complexes using a fragment-based approach

Glycosaminoglycans (GAGs), a major constituent of the extracellular matrix, participate in cell-signaling by binding specific proteins. Structural data on protein-GAG interactions are crucial to understand and modulate these signaling processes, with potential applications in regenerative medicine. However, experimental and theoretical approaches used to study GAG-protein systems are challenged by GAGs high flexibility limiting the conformational sampling above a certain size, and by the scarcity of GAG-specific docking tools compared to protein-protein or protein-drug docking approaches. We present for the first time an automated fragment-based method for docking GAGs on a protein binding site. In this approach, trimeric GAG fragments are flexibly docked to the protein, assembled based on their spacial overlap, and refined by molecular dynamics. The method appeared more successful than the classical full-ligand approach for most of 13 tested complexes with known structure. The approach is particularly promising for docking of long GAG chains, which represents a bottleneck for classical docking approaches applied to these systems. © 2019 Wiley Periodicals, Inc.

Solution Conformation of Heparin Tetrasaccharide. DFT Analysis of Structure and Spin⁻Spin Coupling Constants

Density functional theory (DFT) has provided detailed information on the molecular structure and spin⁻spin coupling constants of heparin tetrasaccharide (GlcNS,6S-IdoA2S-GlcNS,6S-IdoA2S-OMe) representing the predominant heparin repeating-sequence. The fully optimised molecular structures of two tetrasaccharide conformations (differing from each other in the conformational form of the sulphated iduronic acid residue⁻one ¹C₄ and the other ²S₀) were obtained using the B3LYP/6-311+G(d,p) level of theory and applying explicit water molecules to simulate the presence of a solvent. The theoretical data provided insight into variations of the bond lengths, bond angles and torsion angles, formations of intra- and intermolecular hydrogen bonds and ionic interactions. Optimised molecular structures indicated the formation of a complex hydrogen bond network, including interresidue and intraresidue bonds. The ionic interactions strongly influence the first hydration shell and, together with hydrogen bonds, play an important role in shaping the 3D tetrasaccharide structure. DFT-derived indirect three⁻bond proton⁻proton coupling constants (³J_H-C-C-H) showed that the best agreement with experiment was obtained with a weighted average of 67:33 (¹C₄:²S₀) of the IdoA2S forms. Detailed analysis of Fermi-contact contributions to ³J_H-C-C-H showed that important contributions arise from the oxygen lone pairs of neighbouring oxygen atoms. The analysis also showed that the magnitude of diamagnetic spin⁻orbit contributions are sufficiently large to determine the magnitude of some proton⁻proton coupling constants. The data highlight the need to use appropriate quantum-chemical calculations for a detailed understanding of the solution properties of heparin oligosaccharides.

So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again!

Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.

Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges

Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.

Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions

Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.

Computational drill down on FGF1-heparin interactions through methodological evaluation

Glycosaminoglycans (GAGs) exhibit a key role in cellular communication processes through interactions with target proteins of the extracellular matrix (ECM). The sandwich-like interaction established between Fibroblast growth factor (FGF) and heparin (HE) represents quite a peculiar protein-GAG-protein system, which has been both structurally and functionally intensively studied. The molecular recognition characteristics of this system have been exploited in various computational studies in order to deepen understanding of GAG-protein interactions. Here, we drill down on the interactions established in this peculiar macromolecular complex by analyzing the applicability of docking techniques and molecular dynamics (MD)-based approaches, and we dissect the molecular recognition properties exhibited by FGF towards a series of HE derivatives. We examine the sensitivity of MM-GBSA free energy calculations in terms of receptor conformational space sampling and changes in the ligand structures. Furthermore, we investigate its predictive power in combination with other computational methods, namely the well-established Autodock3 (AD3) and dynamic molecular docking (DMD), a targeted MD-based docking method specifically developed to account for flexibility and solvent in computer simulations of protein-GAG systems. Our results show that a site-mapping approach can be effectively combined with AD3 and DMD calculations to accurately reproduce available experimental data and, furthermore, to determine specific GAG recognition patterns. This study deepens our understanding of the applicability of available theoretical approaches to the investigation of molecular recognition in protein-GAG systems.

Glycosaminoglycanomics: where we are

Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging. We give here an overview of the experimental approaches used in glycosaminoglycomics, of the major GAG-protein interactomes characterized so far, and of the computational tools and databases available to analyze and store GAG structures and interactions.

Pharmacology of Heparin and Related Drugs

Heparin has been recognized as a valuable anticoagulant and antithrombotic for several decades and is still widely used in clinical practice for a variety of indications. The anticoagulant activity of heparin is mainly attributable to the action of a specific pentasaccharide sequence that acts in concert with antithrombin, a plasma coagulation factor inhibitor. This observation has led to the development of synthetic heparin mimetics for clinical use. However, it is increasingly recognized that heparin has many other pharmacological properties, including but not limited to antiviral, anti-inflammatory, and antimetastatic actions. Many of these activities are independent of its anticoagulant activity, although the mechanisms of these other activities are currently less well defined. Nonetheless, heparin is being exploited for clinical uses beyond anticoagulation and developed for a wide range of clinical disorders. This article provides a "state of the art" review of our current understanding of the pharmacology of heparin and related drugs and an overview of the status of development of such drugs.

Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes

Glycosaminoglycans represent a class of linear anionic periodic polysaccharides, which play a key role in a variety of biological processes in the extracellular matrix via interactions with their protein targets. Computationally, glycosaminoglycans are very challenging due to their high flexibility, periodicity and electrostatics-driven nature of the interactions with their protein counterparts. In this work, we carry out a detailed computational characterization of the interactions in protein-glycosaminoglycan complexes from the Protein Data Bank (PDB), which are split into two subsets accounting for their intrinsic nature: non-enzymatic-protein-glycosaminoglycan and enzyme-glycosaminoglycan complexes. We apply molecular dynamics to analyze the differences in these two subsets in terms of flexibility, retainment of the native interactions in the simulations, free energy components of binding and contributions of protein residue types to glycosaminoglycan binding. Furthermore, we systematically demonstrate that protein electrostatic potential calculations, previously found to be successful for glycosaminoglycan binding sites prediction for individual systems, are in general very useful for proposing protein surface regions as putative glycosaminoglycan binding sites, which can be further used for local docking calculations with these particular polysaccharides. Finally, the performance of six different docking programs (Autodock 3, Autodock Vina, MOE, eHiTS, FlexX and Glide), some of which proved to perform well for particular protein-glycosaminoglycan complexes in previous work, is evaluated on the complete protein-glycosaminoglycan data set from the PDB. This work contributes to widen our knowledge of protein-glycosaminoglycan molecular recognition and could be useful to steer a choice of the strategies to be applied in theoretical studies of these systems.

Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics, and nuclear magnetic resonance

Glycosaminoglycans (GAGs) play an important role in many biological processes in the extracellular matrix. In a theoretical approach, structures of monosaccharide building blocks of natural GAGs and their sulfated derivatives were optimized by a B3LYP6311ppdd//B3LYP/6-31+G(d) method. The dependence of the observed conformational properties on the applied methodology is described. NMR chemical shifts and proton-proton spin-spin coupling constants were calculated using the GIAO approach and analyzed in terms of the method's accuracy and sensitivity towards the influence of sulfation, O1-methylation, conformations of sugar ring, and ω dihedral angle. The net sulfation of the monosaccharides was found to be correlated with the ¹H chemical shifts in the methyl group of the N-acetylated saccharides both theoretically and experimentally. The ω dihedral angle conformation populations of free monosaccharides and monosaccharide blocks within polymeric GAG molecules were calculated by a molecular dynamics approach using the GLYCAM06 force field and compared with the available NMR and quantum mechanical data. Qualitative trends for the impact of sulfation and ring conformation on the chemical shifts and proton-proton spin-spin coupling constants were obtained and discussed in terms of the potential and limitations of the computational methodology used to be complementary to NMR experiments and to assist in experimental data assignment.

Enforced conformational changes in the structural units of glycosaminoglycan (non-sulfated heparin-based oligosaccharides)

The conformational transitions in the structural units of glycosaminoglycans (GAGs) were the subject of many theoretical and experimental studies.