Solution Structures of Glycosaminoglycan-bound CXCL8 Complexes Determined by Small-Angle X-Ray Scattering (SAXS).

Distinct Molten-Globule Conformations in an Interacting Protein Domain Resolved by 19F NMR of Fluoroproline Residues.

This study illustrates how subtle residue-localized conformational bias can affect the overall protein conformational dynamics influencing protein-protein interactions that are important for cellular functions and related to diseases.

How glycosaminoglycans mediate procathepsin K maturation: New insights from computational studies.

Cathepsins are predominantly cysteine proteases that function in lysosomes and the extracellular matrix, where they regulate essential proteolytic processes. They are synthesised as inactive zymogens (procathepsins), in which an N-terminal propeptide blocks access to the active site and is removed during maturation. Glycosaminoglycans (GAGs), a class of linear, sulfated polysaccharides composed of repeating disaccharide units, are known to modulate both cathepsin activity and proenzyme processing. Here, we use molecular modelling to elucidate the role of GAGs in the maturation of procathepsin K. Molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations identify putative allosteric sites on the procathepsin surface that mediate GAG recognition. Microsecond-scale MD simulations of the most stable complexes, analysed via principal component analysis (PCA), reveal GAG-dependent shifts in the conformational landscape of the proenzyme. To probe environmental effects, we further simulate apo and GAG-bound procathepsin K under lysosomal conditions (pH 4). These simulations demonstrate a synergistic interplay between acidification and GAG binding in promoting activation. While low pH destabilises propeptide secondary structure, GAG binding at a distinct allosteric hotspot amplifies this effect, promoting helix unwinding and facilitating propeptide dissociation. Overall, our results provide a molecular-level framework for GAG-assisted maturation of procathepsin K, highlighting cooperative environmental and allosteric regulation of zymogen activation.

Understanding Fibroblast Growth Factor-Heparan Sulfate Recognition by Molecular Dynamics Approaches.

Glycosaminoglycans, linear periodic anionic polysaccharides composed of repeating disaccharide units, are highly heterogeneous with respect to their chemical composition, sulfation patterns, conformational, dynamic and functional properties. The "sulfation code," which links specific sulfation patterns of these molecules to their biological function, is a key concept for understanding their structure-function relationships. However, both experimental and computational approaches face significant challenges in deciphering this code. In this computational study, we focus on fibroblast growth factor-glycosaminoglycan interactions, which play crucial roles in numerous biologically relevant processes. First, we evaluate the sensitivity and predictive power of currently available computational protocols for studying these systems. We then rigorously investigate the effects of heparin 6-O-desulfation on its interactions with several fibroblast growth factors. We conclude that, depending on the 6-O-sulfation pattern and the length of the oligosaccharide, either predominantly electrostatic interactions or a more complex interplay between electrostatic and hydrophobic interactions determines the specificity of the resulting protein-glycosaminoglycan complex. Finally, we demonstrate that a previously developed coarse-grained model successfully reproduces both the structural and thermodynamic properties of the analysed molecular systems. The results obtained in this study may contribute to the understanding of the fundamental mechanisms underlying protein-glycosaminoglycan interactions and represent a further step toward deciphering the glycosaminoglycan "sulfation code."

Quantitative Mapping of Glycosaminoglycan Secondary Structure Driven by Sulfation and Iduronic Acid.

Recent advances in the chemical synthesis of Glycosaminoglycans.

Glycosaminoglycans (GAGs) are complex carbohydrates ubiquitously expressed on cell surfaces and within the extracellular matrix, where they regulate essential biological processes through sequence- and sulfation-dependent interactions. Major GAG classes, including heparan sulfate (HS), chondroitin sulfate (CS), dermatan sulfate (DS), keratan sulfate (KS), and hyaluronic acid (HA), exhibit diverse sulfation patterns that encode specific molecular recognition events. Deciphering their structure-activity relationships has been hindered by intrinsic heterogeneity and limited access to well-defined materials. This review focuses on the recent advances in the chemical synthesis of GAGs, highlighting strategies that enable precise control over GAG structure and sulfation patterns. Recent innovations in protecting group design, stereoselective glycosylation, and automated assembly have significantly improved synthetic efficiency, facilitating the construction of increasingly complex and biologically relevant structures and advancing the rational design of GAG-based tools and therapeutics.

Protein Recognition and Amyloid Remodeling Governed by Paddlewheel Diruthenium Coordination Chemistry

Paddlewheel diruthenium (Ru2) complexes are promising modulators of protein aggregation due to their tunable coordination chemistry and dual-action properties. Here, we investigate the interaction of five Ru2 complexes with hen egg white lysozyme (HEWL), an amyloid model, to elucidate their antiaggregation capabilities. High-resolution X-ray crystallography shows that all complexes preferentially bind to Asp119 and, in some cases, Asp101, through coordination to the Ru2 core while preserving the overall protein fold. Both covalent and noncovalent interactions are observed, depending on ligand environment and steric effects. Solution studies confirm the formation of HEWL–Ru2 adducts under both neutral and acidic conditions. Functional assays demonstrate that all Ru2 complexes effectively inhibit HEWL fibrillogenesis, as indicated by reduced ThT fluorescence and the absence of large aggregates in dynamic light scattering measurements. Disaggregation of preformed fibrils was more variable, with the complex bearing vacant axial sites showing the highest activity. Circular dichroism and scanning electron microscopy analyses reveal that these compounds redirect aggregation toward noncanonical morphologies rather than fully dissolving fibrils. Cytotoxicity assays confirm reduced HEWL-induced cellular toxicity. Overall, our findings establish a correlation between ligand composition, coordination behavior, protein binding, and antiamyloid activity, providing a framework for designing Ru2-based multifunctional modulators of protein aggregation.