Molecular dynamics and atomic charge calculations in the study of heparin conformation in aqueous solution

Becker, Camila Franco; Guimarães, Jorge A.; Verli, Hugo

doi:10.1016/j.carres.2005.03.018

Cited by 43 publications

(43 citation statements)

References 33 publications

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“…Based on such information, these structures were described in GROMOS96 43a1 force field parameters. Afterwards, both mono-and disaccharide topologies were further modified to include some refinements: (1) improper dihedrals, employed to preserve the conformational state of the hexopyranose rings in 4 C 1 (D-Glc, D-GlcA, D-Gal, D-Man and D-Rha), 1C 4 (L-Rha and L-6dTal), or 5 C 2 (Kdo) forms; (2) proper dihedrals, as described in GROMOS96 43a1 force field for glucose, to support stable simulations, 32 and (3) Löwdin HF/6-31G ** -derived atomic charges, which were either obtained from previous works of the group, 27,28 or calculated (as in the case of O-acetyl group, presented in Supplementary data, Fig. S1).…”

Section: Topology Constructionmentioning

confidence: 99%

“…The employed MD protocol was based on previous studies, 42 as described. [27][28][29] The Lincs method 43 was applied to constrain covalent bond lengths, allowing an integration step of 2 fs after an initial energy minimization using Steepest Descents algorithm. Electrostatic interactions were calculated with Particle Mesh Ewald method.…”

Section: Simulationsmentioning

confidence: 99%

“…23 These studies built the polysaccharides from the disaccharide level, that is, employing vacuum minimumenergy structures of isolated disaccharides obtained from adiabatic contour maps. [23][24][25] Likewise, our group has been employing parameters based on the GROMOS96 43a1 force field, 26 added by Löwdin HF/6-31G ** -derived atomic charges, 27,28 in the study of glycosaminoglycans as heparin, 27,29 fucans, and galactans, 30,31 as well as N-or O-linked glycans. 32,33 Moreover, the solution conformation of disaccharides, obtained from such proceedings, was observed to be adequate starting conformations to build models of glycans.…”

Section: Introductionmentioning

confidence: 99%

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Solution conformation and dynamics of exopolysaccharides from Burkholderia species

Pol-Fachin

Serrato

Verli

2010

Carbohydrate Research

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Section: Topology Constructionmentioning

confidence: 99%

Section: Simulationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Solution conformation and dynamics of exopolysaccharides from Burkholderia species

Pol-Fachin

Serrato

Verli

2010

Carbohydrate Research

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“…These topologies were supplied with Löwdin HF/6 -31G** atomic charges (23,24) and submitted to conformational analysis by varying the and dihedral angles from Ϫ180 to 180°, with a 30°step, in a total of 144 conformers for each linkage. Each conformation was further refined in a 20-ps molecular dynamics at 10 K, with an integration step of 0.5 fs (25).…”

Section: Extraction Of Sulfated Galactan From Egg Jelly Of Sea Urchins-mentioning

confidence: 99%

“…The relative stabilities of the conformations were used to construct relaxed energy contour plots. The minimum energy conformations described in these plots were submitted to 0.1 s molecular dynamics (MD) simulations in aqueous solutions using the SPC water model (26) following a protocol previously described (23,24,27). A triclinic water box under periodic boundary conditions was employed using a 10-Å minimum distance from solute to the box faces.…”

Section: Extraction Of Sulfated Galactan From Egg Jelly Of Sea Urchins-mentioning

confidence: 99%

A Unique 2-Sulfated β-Galactan from the Egg Jelly of the Sea Urchin Glyptocidaris crenularis

Castro

Pomin

Santos

et al. 2009

Journal of Biological Chemistry

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Sulfated polysaccharides from the egg jelly of sea urchins act as species-specific inducers of the sperm acrosome reaction, which is a rare molecular mechanism of carbohydrate-induced signal-transduction event in animal cells. The sea urchin polysaccharides differ in monosaccharide composition (L-fucose or L-galactose), glycosylation, and sulfation sites, but they are always in the ␣-anomeric configuration. Herein, structural analysis of the polysaccharide from the sea urchin Glyptocidaris crenularis surprisingly revealed a unique sulfated ␤-D-galactan composed by (3-␤-D-Galp-2(OSO 3 )-133-␤-D-Galp-1) n repeating units. Subsequently, we used the G. crenularis galactan to compare different 2-sulfated polysaccharides as inducers of the acrosome reaction using homologous and heterologous sperm. We also tested the effect of chemically over-sulfated galactans. Intriguingly, the anomeric configuration of the glycosidic linkage rather than the monosaccharide composition (galactose or fucose) is the preferential structural requirement for the effect of these polysaccharides on sea urchin fertilization. Nuclear magnetic resonance and molecular dynamics indicate that sulfated ␣-galactan or ␣-fucan have less dynamic structural behavior, exhibiting fewer conformational populations, with an almost exclusive conformational state with glycosidic dihedral angles ⌽/⌿ ‫؍‬ ؊102°/131°. The preponderant conformer observed in the sulfated ␣-galactan or ␣-fucan is not observed among populations in the ␤-form despite its more flexible structure in solution. Possibly, a proper spatial arrangement is required for interaction of the sea urchin-sulfated polysaccharides with the specific sperm receptor.The evolution of barriers to inter-specific hybridization is a crucial step in the fertilization of free-spawning marine invertebrates. In sea urchins the molecular recognition between sperm and egg ensures species recognition. The jelly coat surrounding sea urchin eggs is not a simple accessory structure; it is considerably complex on a molecular level and intimately involved in gamete recognition. It contains sulfated polysaccharides, sialoglycans, and peptides.Structural changes in the sulfated polysaccharide from the egg jelly of sea urchins modulate cell-cell recognition and species specificity leading to exocytosis of the acrosomal vesicle, the acrosome reaction. This is a crucial event for the recognition between male and female gametes, leading to the fertilization success, and is also what prevents intercrosses. The sulfated polysaccharide from the egg jelly recognizes its specific receptor present in the sperm. Apart from the sialoglycans that act in synergy with the sulfated polysaccharides, other components of the egg jelly do not possess acrosome reaction-inducing activity (1). The sulfated polysaccharide-mediated mechanism of sperm-egg recognition co-exists with that of bindin and its receptor in the egg (2-4).The sulfated polysaccharides from sea urchin show speciesspecific structures composed of repetitive units (mono-, tri-, ...

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Water Uptake, Distribution, and Mobility in Amorphous Poly( d , l ‐Lactide) by Molecular Dynamics Simulation

Xiang

Anderson

2014

Journal of Pharmaceutical Sciences

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Molecular dynamics and atomic charge calculations in the study of heparin conformation in aqueous solution

Cited by 43 publications

References 33 publications

Solution conformation and dynamics of exopolysaccharides from Burkholderia species

Solution conformation and dynamics of exopolysaccharides from Burkholderia species

A Unique 2-Sulfated β-Galactan from the Egg Jelly of the Sea Urchin Glyptocidaris crenularis

Water Uptake, Distribution, and Mobility in Amorphous Poly( d , l ‐Lactide) by Molecular Dynamics Simulation

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