Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study - Fig 3

<p>(A) Community analysis. Correlated motion of the sub-domains in the glycosylated and non-glycosylated forms of proMMP-9. Sub-domains that are moving together are represented in the same color. (B) Left and right panel represents the comparison of RMSDs of the pro and catalytic domains of glycosylated proMMP-9 and Gal-8N domain and the solvent-accessible surface area (SASA in Ų) of two proteolytic fragments for the complex composed of Gal-8N and glycosylated proMMP-9, respectively. (C) Structural model of the complex composed of Gal-8N and proMMP-9.</p

Illustration of the conformational changes occurring in the proteolytic region of the prodomain, solvent-accessible surface area and multiple structure alignments.

<p>(A) Superimposition of the prodomain proteolytic region (top panel) shows significant conformational changes (R51-A70) in the glycosylated in contrast to non-glycosylated proMMP-9. The right top panel represents times-series of the distance between the Cα atoms of E59-R106 in the glycosylated (black) and non-glycosylated (red) proMMP-9, demonstrating the mobility of the loop. The lower left panel represents the glycosylated proMMP-9 prodomain in closed conformation (first cleavage region protects the second one and the distance between them is 10.9 Å). Lower right panel represents the non-glycosylated proMMP-9 prodomain in open conformation (both cleavages regions are exposed and the distance between them is 24.6 Å). (B) Left and right panel represents the solvent-accessible surface area (SASA in Ų) of two proteolytic fragments for glycosylated and non-glycosylated form of proMMP-9, respectively. (C) Superimposition of seven snapshots, each at 80ns intervals out of the 500ns MD trajectory. Glycans are represented according to the Consortium For Glycomics nomenclature.</p

Hydrogen bond analysis.

<p>Hydrogen bond analysis.</p

Carbohydrate-Conjugated Amino Acid-Based Fluorescent Block Copolymers: Their Self-Assembly, pH Responsiveness, and/or Lectin Recognition

An effective strategy has been documented to combine both carbohydrate and amino acid biomolecules in a single synthetic polymeric system via a reversible addition–fragmentation chain transfer (RAFT) polymerization technique. The resultant unique block copolymer was engineered to form uniform micelles with the desired projection of either selective or both amino acid/sugar residues on the outer surface with multivalency, providing pH-based stimuli-responsiveness and/or lectin recognition. The self-assembly process was studied in detail by field emission scanning electron microscopy (FE-SEM), dynamic light scattering (DLS), and UV–visible spectroscopy. The enhanced lectin binding behavior was observed for glyconanoparticles with both amino acid/sugar entities on the shell as compared to the only glycopolymer nanoparticle because of the higher steric hindrance factor in the case of only the glycopolymer nanoparticle. Fluorophore conjugation by postpolymerization functionalization was further exploited by fluorescence spectroscopy for evidencing the lectin recognition process

Understanding the Specificity of Human Galectin-8C Domain Interactions with Its Glycan Ligands Based on Molecular Dynamics Simulations

<div><p>Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.</p> </div

Set of oligosaccharide ligands.

<p>List of oligosaccharides used in MD simulations for study of interactions with the Gal-8C domain.</p

Multiple sequence alignments of the human galectin members.

<p>Conserved amino acids are shown in bold, amino acids which play important roles in interactions apart from conserved residues in Gal-8C are shown in red and in blue for Gal-8N. This multiple sequence alignment was carried out by MAFFT web server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059761#pone.0059761-Katoh1" target="_blank">[48]</a>.</p

Torsional analysis of bound ligands.

<p>Average glycosidic torsion angles for bound ligands in the Gal-8C domain (standard deviation). φ and ψ values for glycosidic linkages using the NMR definition as H1-C1-O1-C_x and C1-O1-C_x-H_x respectively.</p

Structure superimposition and degree of sequence identity.

<p>Three-dimensional structural alignments and sequence identity of members of the galectin family based on RMSD calculated by using the PDBeFold webserver <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059761#pone.0059761-Krissinel1" target="_blank">[49]</a>.</p

Superimposition of Gal-8N and -C domain.

<p>Ribbon representation of superimposed Gal-8N and -C domain. The N domain is shown in pink color code whereas the C domain is in cyan. Lactose is shown as stick model in yellow color. The variable loop between S3–S4 shows difference in length between Gal-8C and -N.</p