Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth

Intermediate molecular weight-fucosylated chondroitin sulfate from sea cucumber Cucumaria frondosa is a promising anticoagulant targeting intrinsic factor IXa

Thromboembolic diseases pose a serious risk to human health worldwide. Fucosylated chondroitin sulfate (FCS) is reported to have good anticoagulant activity with a low bleeding risk. Molecular weight plays a significant role in the anticoagulant activity of FCS, and FCS smaller than octasaccharide in size has no anticoagulant activity. Therefore, identifying the best candidate for developing novel anticoagulant FCS drugs is crucial. Herein, native FCS was isolated from sea cucumber Cucumaria frondosa (FCScf) and depolymerized into a series of lower molecular weights (FCScfs). A comprehensive assessment of the in vitro anticoagulant activity and in vivo bleeding risk of FCScfs with different molecule weights demonstrated that 10 kDa FCScf (FCScf-10 K) had a greater intrinsic anticoagulant activity than low molecular weight heparin (LMWH) without any bleeding risk. Using molecular modeling combined with experimental validation, we revealed that FCScf-10 K can specifically inhibit the formation of the Xase complex by binding the negatively charged sulfate group of FCScf-10 K to the positively charged side chain of arginine residues on the specific surface of factor IXa. Thus, these data demonstrate that the intermediate molecular weight FCScf-10 K is a promising candidate for the development of novel anticoagulant drugs.

Hindbrain boundaries as niches of neural progenitor and stem cells regulated by the extracellular matrix proteoglycan chondroitin sulphate

The interplay between neural progenitors and stem cells (NPSCs), and their extracellular matrix (ECM) is a crucial regulatory mechanism that determines their behavior. Nonetheless, how the ECM dictates the state of NPSCs remains elusive. The hindbrain is valuable to examine this relationship, as cells in the ventricular surface of hindbrain boundaries (HBs), which arise between any two neighboring rhombomeres, express the NPSC marker Sox2, while being surrounded with the membrane-bound ECM molecule chondroitin sulphate proteoglycan (CSPG), in chick and mouse embryos. CSPG expression was used to isolate HB Sox2+ cells for RNA-sequencing, revealing their distinguished molecular properties as typical NPSCs, which express known and newly identified genes relating to stem cells, cancer, the matrisome and cell cycle. In contrast, the CSPG- non-HB cells, displayed clear neural-differentiation transcriptome. To address whether CSPG is significant for hindbrain development, its expression was manipulated in vivo and in vitro. CSPG manipulations shifted the stem versus differentiation state of HB cells, evident by their behavior and altered gene expression. These results provide further understanding of the uniqueness of hindbrain boundaries as repetitive pools of NPSCs in-between the rapidly growing rhombomeres, which rely on their microenvironment to maintain their undifferentiated state during development.

Novel Genetic and Biochemical Insights into the Spectrum of NEFL-Associated Phenotypes

Background

NEFL encodes for the neurofilament light chain protein. Pathogenic variants in NEFL cause demyelinating, axonal and intermediate forms of Charcot-Marie-Tooth disease (CMT) which present with a varying degree of severity and somatic mutations have not been described yet. Currently, 34 different CMT-causing pathogenic variants in NEFL in 174 patients have been reported. Muscular involvement was also described in CMT2E patients mostly as a secondary effect. Also, there are a few descriptions of a primary muscle vulnerability upon pathogenic NEFL variants.

Objectives

To expand the current knowledge on the genetic landscape, clinical presentation and muscle involvement in NEFL-related neurological diseases by retrospective case study and literature review.

Methods

We applied in-depth phenotyping of new and already reported cases, molecular genetic testing, light-, electron- and Coherent Anti-Stokes Raman Scattering-microscopic studies and proteomic profiling in addition to in silico modelling of NEFL-variants.

Results

We report on a boy with a muscular phenotype (weakness, myalgia and cramps, Z-band alterations and mini-cores in some myofibers) associated with the heterozygous p.(Phe104Val) NEFL-variant, which was previously described in a neuropathy case. Skeletal muscle proteomics findings indicated affection of cytoskeletal proteins. Moreover, we report on two further neuropathic patients (16 years old girl and her father) both carrying the heterozygous p.(Pro8Ser) variant, which has been identified as 15% somatic mosaic in the father. While the daughter presented with altered neurophysiology,neurogenic clump feet and gait disturbances, the father showed clinically only feet deformities. As missense variants affecting proline at amino acid position 8 are leading to neuropathic manifestations of different severities, in silico modelling of these different amino acid substitutions indicated variable pathogenic impact correlating with disease onset.

Conclusions

Our findings provide new morphological and biochemical insights into the vulnerability of denervated muscle (upon NEFL-associated neuropathy) as well as novel genetic findings expanding the current knowledge on NEFL-related neuromuscular phenotypes and their clinical manifestations. Along this line, our data show that even subtle expression of somatic NEFL variants can lead to neuromuscular symptoms.

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.

Nanoarchitectonics of cellulose nanocrystal conjugated with a tetrasaccharide-glycoprobe for targeting oligodendrocyte precursor cells

Demyelination is a serious complication of neurological disorders, which can be reversed by oligodendrocyte precursor cell (OPC) as the available source of myelination. Chondroitin sulfate (CS) plays key roles in neurological disorders, which still attracted less attention on how CS modulates the fate of OPCs. Nanoparticle coupled with glycoprobe is a potential strategy for investigating the carbohydrate-protein interaction. However, there is lack of CS-based glycoprobe with enough chain length that interact with protein effectively. Herein, we designed a responsive delivery system, in which CS was the target molecule, and cellulose nanocrystal (CNC) was the penetrative nanocarrier. A coumarin derivative (B) was conjugated at the reducing end of an unanimal-sourced chondroitin tetrasaccharide (4mer). This glycoprobe (4B) was grafted to the surface of a rod-like nanocarrier, which had a crystalline core and a poly(ethylene glycol) shell. This glycosylated nanoparticle (N4B-P) displayed a uniform size, improved water-solubility, and responsive release of glycoprobe. N4B-P displayed strong green fluorescence and good cell-compatibility, which imaged well the neural cells including astrocytes and OPCs. Interestingly, both of glycoprobe and N4B-P were internalized selectively by OPCs when they were incubated in astrocytes/OPCs mixtures. This rod-like nanoparticle would be a potential probe for studying carbohydrate-protein interaction in OPCs.

Tools for mammalian glycoscience research

Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.

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.

Functions of chondroitin/dermatan sulfate containing GalNAc4,6-disulfate

Chondroitin sulfate (CS) and dermatan sulfate (DS) containing GalNAc4,6-disulfate (GalNAc4S6S) were initially discovered in marine animals. Following the discovery, these glycosaminoglycans have been found in various animals including human. In the biosynthesis of CS/DS containing GalNAc4S6S, three groups of sulfotransferases are involved; chondroitin 4-sulfotransferases (C4STs), dermatan 4-sulfotransferase-1 (D4ST-1) and GalNAc 4-sulfate 6-O-sulfotransferase (GalNAc4S-6ST). GalNAc4S-6ST and its products have been shown to play important roles in the abnormal pathological conditions such as central nervous system injury, cancer development, abnormal tissue fibrosis, development of osteoporosis, and infection with viruses or nematodes. CS/DS containing GalNAc4S6S has been shown to increase with the functional differentiation of mast cells, macrophages and neutrophils. Genetic approaches using knockout or knockdown of GalNAc4S-6ST, blocking of the epitopes containing GalNAc4S6S by specific antibodies and chemical technology that enabled the synthesis of oligosaccharides with defined sulfation patterns have been applied successfully to these investigations. These studies contributed significantly to the basic understanding of the functional roles of CS/DS containing GalNAc4S6S in various abnormal conditions, and appear to provide promising clues to the development of possible measures to treat them.

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses

Inspired by the role of cell-surface glycoproteins as coreceptors for pathogens, we report the development of GlycoGrip: a glycopolymer-based lateral flow assay for detecting SARS-CoV-2 and its variants. GlycoGrip utilizes glycopolymers for primary capture and antispike antibodies labeled with gold nanoparticles for signal-generating detection. A lock-step integration between experiment and computation has enabled efficient optimization of GlycoGrip test strips which can selectively, sensitively, and rapidly detect SARS-CoV-2 and its variants in biofluids. Employing the power of the glycocalyx in a diagnostic assay has distinct advantages over conventional immunoassays as glycopolymers can bind to antigens in a multivalent capacity and are highly adaptable for mutated strains. As new variants of SARS-CoV-2 are identified, GlycoGrip will serve as a highly reconfigurable biosensor for their detection. Additionally, via extensive ensemble-based docking simulations which incorporate protein and glycan motion, we have elucidated important clues as to how heparan sulfate and other glycocalyx components may bind the spike glycoprotein during SARS-CoV-2 host-cell infection. GlycoGrip is a promising and generalizable alternative to costly, labor-intensive RT-PCR, and we envision it will be broadly useful, including for rural or low-income populations that are historically undertested and under-reported in infection statistics.

Chondroitin Sulfate/Dermatan Sulfate-Protein Interactions and Their Biological Functions in Human Diseases: Implications and Analytical Tools

Chondroitin sulfate (CS) and dermatan sulfate (DS) are linear anionic polysaccharides that are widely present on the cell surface and in the cell matrix and connective tissue. CS and DS chains are usually attached to core proteins and are present in the form of proteoglycans (PGs). They not only are important structural substances but also bind to a variety of cytokines, growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillary glycoproteins to execute series of important biological functions. CS and DS exhibit variable sulfation patterns and different sequence arrangements, and their molecular weights also vary within a large range, increasing the structural complexity and diversity of CS/DS. The structure-function relationship of CS/DS PGs directly and indirectly involves them in a variety of physiological and pathological processes. Accumulating evidence suggests that CS/DS serves as an important cofactor for many cell behaviors. Understanding the molecular basis of these interactions helps to elucidate the occurrence and development of various diseases and the development of new therapeutic approaches. The present article reviews the physiological and pathological processes in which CS and DS participate through their interactions with different proteins. Moreover, classic and emerging glycosaminoglycan (GAG)-protein interaction analysis tools and their applications in CS/DS-protein characterization are also discussed.

A Bittersweet Computational Journey among Glycosaminoglycans

Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge.

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.

Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans

Glycosaminoglycans (GAGs), long linear periodic anionic polysaccharides, are key molecules in the extracellular matrix (ECM). Therefore, deciphering their role in the biologically relevant context is important for fundamental understanding of the processes ongoing in ECM and for establishing new strategies in the regenerative medicine. Although GAGs represent a number of computational challenges, molecular docking is a powerful tool for analysis of their interactions. Despite the recent development of GAG-specific docking approaches, there is plenty of room for improvement. Here, replica exchange molecular dynamics with repulsive scaling (REMD-RS) recently proved to be a successful approach for protein-protein complexes, was applied to dock GAGs. In this method, effective pairwise radii are increased in different Hamiltonian replicas. REMD-RS is shown to be an attractive alternative to classical docking approaches for GAGs. This work contributes to setting up of GAG-specific computational protocols and provides new insights into the nature of these biological systems.

Glycosaminoglycan-Protein Interactions and Their Roles in Human Disease

Glycosaminoglycans (GAGs) are a family of linear and negatively charged polysaccharides that exist ubiquitously on the human cell surface as well as in the extracellular matrix. GAGs interact with a wide range of proteins, including proteases, growth factors, cytokines, chemokines and adhesion molecules, enabling them to mediate many physiological processes, such as protein function, cellular adhesion and signaling. GAG-protein interactions participate in and intervene in a variety of human diseases, including cardiovascular disease, infectious disease, neurodegenerative diseases and tumors. The breakthrough in analytical tools and approaches during the last two decades has facilitated a greater understanding of the importance of GAG-protein interactions and their roles in human diseases. This review focuses on aspects of the molecular basis and mechanisms of GAG-protein interactions involved in human disease. The most recent advances in analytical tools, especially mass spectrometry-based GAG sequencing and binding motif characterization methods, are introduced. An update of selected families of GAG binding proteins is presented. Perspectives on development of novel therapeutics targeting specific GAG-protein interactions are also covered in this review.

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.

Sulfated glycans engage the Ang-Tie pathway to regulate vascular development

The angiopoietin (Ang)/Tie pathway is essential for the proper maturation and remodeling of the vasculature. Despite its importance in disease, the mechanisms that control signal transduction through this pathway are poorly understood. Here, we demonstrate that heparan sulfate glycosaminoglycans (HS GAGs) regulate Ang/Tie signaling through direct interactions with both Ang ligands and the Tie1 receptor. HS GAGs bound to Ang1/4 ligands and formed ternary Ang-Tie2 receptor complexes, thereby potentiating endothelial survival signaling. In addition, we found that HS GAGs are novel ligands for the orphan receptor Tie1. The HS-Tie1 interaction promoted Tie1-Tie2 heterodimerization and enhanced Tie1 stability within the mature vasculature. Loss of HS-Tie1 binding using CRISPR/Cas9-mediated mutagenesis in vivo led to decreased Tie protein levels, pathway suppression, and aberrant retinal vascularization. Together, these results reveal that sulfated glycans use dual mechanisms to regulate Ang/Tie signaling and are important for the development and maintenance of the vasculature.

Photoaffinity Probes for the Identification of Sequence-Specific Glycosaminoglycan-Binding Proteins

Glycosaminoglycan (GAG)-protein interactions mediate critical physiological and pathological processes, such as neuronal plasticity, development, and viral invasion. However, mapping GAG-protein interaction networks is challenging as these interactions often require specific GAG sulfation patterns and involve transmembrane receptors or extracellular matrix-associated proteins. Here, we report the first GAG polysaccharide-based photoaffinity probes for the system-wide identification of GAG-binding proteins in living cells. A general platform for the modular, efficient assembly of various chondroitin sulfate (CS)-based photoaffinity probes was developed. Systematic evaluations led to benzophenone-containing probes that efficiently and selectively captured known CS-E-binding proteins in vitro and in cells. Importantly, the probes also enabled the identification of >50 new proteins from living neurons that interact with the neuroplasticity-relevant CS-E sulfation motif. Several candidates were independently validated and included membrane receptors important for axon guidance, innate immunity, synapse development, and synaptic plasticity. Overall, our studies provide a powerful approach for mapping GAG-protein interaction networks, revealing new potential functions for these polysaccharides and linking them to diseases such as Alzheimer's and autism.

Age-related functional changes of total thyroid hormones and glycosaminoglycans in growing calves

Background and Aim:

During the physiological growing, thyroid and proteoglycan glycosaminoglycan (GAG) changes dynamically occur, according to genetic and non-genetic factors. The purpose of this research was to compare the effects of early postnatal development (10 days) until 210 days of life on the triiodothyronine (T₃), thyroxine (T₄), the relative T₄:T₃ ratio, and GAGs profile, and to define the different reference intervals of the calf’s development through the various growing phases.

Materials and Methods:

The effect of growing on total thyroid hormones and GAG profiles was studied from 10 days to 210days of age in 64 clinically healthy Brown calves, 30males and 34females. Blood samples were collected at 10, 20, 30, 60, 90, 120, 150, 180, and 210days of age.

Results:

The results showed a significant effect of a calf’s growth on T₃, T₄, and GAG values (p<0.0001). Significant correlations between T₃ and T₄ were observed. Compared to the previous time point, T₃ showed a significant decrease at 20days and at 60days (p<0.01), while a significant increase was observed at 90days and 210days (p<0.05); T₄ showed a significant decrease at 20days (p<0.01), while significant increases were observed at both 180days and 210days (p<0.05); GAGs showed a significant increase at 120days and 210days (p<0.05). Positive and significant correlations between BW and GAGs in both males (p<0.0057) and females (p<0.0059) were observed.

Conclusion:

It can be concluded that the highest T₃ and T₄ concentrations have been associated with the early growing process (10days), with an increasing trend also at 210days, it is possible to hypothesize a probable metabolic effect of thyroid function in anabolic and/or catabolic directions during the calves’ development. Likewise, it can be reasonably inferred that the highest plasma GAGs at 210days may be due to their metabolic role during the development of growing calves. Taken together, these findings suggest the potential and relative contribution made by thyroid and GAGs effects on the dynamics of growing calves.

Operation spinal cord regeneration: Patterning information residing in extracellular matrix glycosaminoglycans

INTRODUCTION

Spinal cord injuries are devastating, with many complications beyond paralysis and loss of sensory function. Although spinal cord regeneration can revolutionize treatment for spinal cord injuries, the goal has not yet been achieved. The regenerative mechanism of axolotls demonstrates that the regeneration is a repeat of developmental process that all animals have all the genes, but axolotls have both the genes and the patterning information to do it at the adult stage.

METHODS

A narrative review was conducted. Relevant studies were collected via an English-language PubMed database search and those known to the authors.

RESULTS

Research during the past 30 years reveals that growth factors, along with spinal cord extracellular matrix, especially glycosaminoglycans, regulates axonal regrowth. Degrading chondroitin sulfate glycosaminoglycans by injecting the bacterial enzyme chondroitinase improves axonal sprouting and functional recovery after spinal cord injury in both rodents and rhesus monkeys. Furthermore, the brain is one of the first organs to develop during the embryonic period, and heparan sulfate glycosaminoglycans are key molecules required for brain development.

CONCLUSIONS

Patterning information residing in glycosaminoglycans might be key elements in restricting spinal cord regeneration. A recommended solution is not to edit the human genome, considering the conserved signaling pathways between animals, but to take advantage of the regenerative mechanism of axolotls and the current knowledge about the pattern-forming glycosaminoglycans for successful spinal cord regeneration and clinical applications.

New SDC function prediction based on protein-protein interaction using bioinformatics tools

The precise roles for SDC have been complex to specify. Assigning and reanalyzing protein and peptide identification to novel protein functions is one of the most important challenges in postgenomic era. Here, we provide SDC molecular description to support, contextualize and reanalyze the corresponding protein-protein interaction (PPI). From SDC-1 data mining, we discuss the potential of bioinformatics tools to predict new biological rules of SDC. Using these methods, we have assembled new possibilities for SDC biology from PPI data, once, the understanding of biology complexity cannot be capture from one simple question.

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.

Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.