Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans

A mytilectin from Mytilus californianus: Study of its unique galactoside interactions, oligomerization patterns, and antifungal activity

In marine invertebrate such as bivalve mollusks, lectins play a critical rol in the immune system, defending against pathogens. A novel family of lectins, named mytilectins, has been discovered in these organisms. They are noted for their antifungal, antibacterial, and anticancer properties, suggesting substantial potential for biomedical and biotechnological applications. In this study, we describe rMcL-1, a mytilectin from the mussel Mytilus californianus. We explored the binding mechanisms using crystallographic data with five different galactosides, highlighting rMcL-1's preference for α-galactosides. By analyzing amino acid variations in its three carbohydrate-binding sites, we assessed their impact on binding affinity and specificity. Interestingly, rMcL-1 is capable of binding non-galactosides, and ligands with lower affinity, such as lactose, induce significant conformational changes in specific binding sites. A novel binding site at the dimer interface was identified in the presence of lactulose. Co-crystallization experiments demonstrated that ligand binding promotes oligomerization, with the resulting quaternary structure varying depending on the sugar involved. An analysis of the puckering parameters and transglycosidic dihedral angles of the glycan moieties associated with oligomeric rMcL-1 revealed consistent conformational preferences in lactulose moieties, while raffinose and lactose exhibited greater variability. Additionally, rMcL-1 exhibited antifungal activity against several phytopathogenic fungi, including Alternaria alternata, Fusarium oxysporum, Phytophthora capsici, and Pythium aphanidermatum. Overall, this study enhances our understanding of the molecular mechanisms underlying the diverse activities of mytilectins and may aid in the design of artificial lectins with specific and improved binding properties.

The synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles

Understanding the dynamic behavior of glycoproteins is crucial for deciphering their biological roles. This review explores the synergistic use of experimental and computational methods to address this complex challenge. Glycans, with their inherent flexibility and structural diversity, pose significant obstacles to traditional structural analysis. Innovative experimental techniques offer valuable snapshots of glycan conformations, but often lack the context of a physiological environment. Computational simulations provide atomic-level detail and explore the full range of dynamic motions, but require extensive resources and validation. Integrating these approaches, by using experimental data to refine and validate computational models, is essential for accurately capturing the complex interplay between glycans and proteins. This combined strategy promises to unlock a deeper understanding of glycoprotein function and inform the design of novel therapeutics.

Physicochemical characteristics of chitosan molecules: Modeling and experiments

Chitosan, a biocompatible polysaccharide, finds a wide range of applications, inter alia as an antimicrobial agent, stabilizer of food products, cosmetics, and in the targeted delivery of drugs and stem cells. This work represents a comprehensive review of the properties of chitosan molecule and its aqueous solutions uniquely combining theoretical modeling and experimental results. The emphasis is on physicochemical aspects which were sparsely considered in previous reviews. Accordingly, in the first part, the explicit solvent molecular dynamics (MD) modeling results characterizing the conformations of chitosan molecule, the contour length, the chain diameter and the density are discussed. These MD data are used to calculate several parameters for larger chitosan molecules using a hybrid approach based on continuous hydrodynamics. The dependencies of hydrodynamic diameter, frictional ratio, radius of gyration, and intrinsic viscosity on the molar mass of molecules are presented and discussed. These theoretical predictions, comprising useful analytical solutions, are used to interpret and rationalize the extensive experimental data acquired by advanced experimental techniques. In the final part, the molecule charge, acid-base, and electrokinetic properties, comprising the electrophoretic mobility and the zeta potential, are reviewed. Future research directions are defined and discussed.

The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times

The separation and structural identification of glycans are of great bioanalytical importance. To obtain a good understanding of the structural flexibility of glycans, replica exchange molecular dynamics (REMD) simulations were used based on AMBER force field calculations to create ensembles of glycan structures. Nonpolar surface area (NPSA) calculations based on continuum solvation (CS) models (Dhakal, R., et al. Int. J. Mass Spectrom. 2021, 461, 116495) were used to quantitatively characterize the polarity of the glycans. Retention times determined by tandem liquid chromatography-mass spectrometry (LC-MS) were correlated with CS-NPSA results obtained from analysis of the investigated glycan ensembles. Three classes of glycans with increasingly complex structures were investigated: linear glycans, fucosylated and sialylated biantennary glycans, and sialylated triantennary glycans. The linear and biantennary structures displayed bimodal distributions in their energies and CS-NPSA values, suggesting two sets of structures, while the more complex triantennary glycans displayed only a single distribution. The peak values of the CS-NPSA distributions (histogram structures) were selected as representatives to be correlated with the experimental retention times. For comparison, the most stable ensemble structures and those obtained from straightforward geometry optimizations were considered, as well. Overall, the histogram structures were found to correlate well with the retention times. In the case of the linear glycans, the CS-NPSA values for all three structural choices correlated very well with the retention times. For the biantennary glycans, the histogram data missed the retention-time ordering in one case but predicted the correct ordering for the triantennary case. Principal component analysis was performed to characterize the main glycan modes of the molecular dynamics.

Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.