Solution conformation and dynamics of exopolysaccharides from Burkholderia species

Pol-Fachin, Laércio; Serrato, Rodrigo Vassoler; Verli, Hugo

doi:10.1016/j.carres.2010.06.010

Cited by 16 publications

(14 citation statements)

References 61 publications

(96 reference statements)

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“…Both disulfated ((l-Arap2,4S-(133)-l-Arap2,4S) 4 ) and non-sulfated arabinan ((l-Arap-(133)-l-Arap) 4 ) octasaccharides were constructed based on the most prevalent conformations of their composing disaccharides, obtained from solution MD simulations, as described previously (25,26). For these calculations, the pyranosic arabinose was only considered in its most abundant form (i.e.…”

mentioning

confidence: 99%

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin

Fernández

Quintana

Cerezo

et al. 2013

Journal of Biological Chemistry

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Background: Many seaweed polysaccharides have anticoagulant activity, but the mechanism of action was elucidated in a few cases. Results: A highly sulfated pyranosic ␤-arabinan exerts its activity through direct and indirect inhibition of thrombin. Conclusion:The structure and mechanism of action of the arabinan are different from those found for other polysaccharides. Significance: This arabinan could be an alternative anticoagulant in certain specific cases.

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confidence: 99%

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin

Fernández

Quintana

Cerezo

et al. 2013

Journal of Biological Chemistry

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“…The most abundant conformational states of each glycosidic linkage were then used as starting geometries for the construction of complete models of structures 1 – 4 , previously described as a successful approach to obtain 3D models of glycan chains in solution, [11,12,13,15] and submitted to MD simulations for further geometry refinement in the whole molecule scaffold as well as for conformational sampling.…”

Section: Resultsmentioning

confidence: 99%

“…The strategy employed for conformational characterization of ipomotaosides was previously described [11] and validated against NMR data for compounds such as saponins [12], exopolysaccharides [13], galactans and fucans [14], and a series of glycoproteins and glycopeptides [11,15], based on building glycan chains from most abundant conformational states in solution, as determined by MD simulations. The built molecules were submitted to additional simulations in order to account to potential inter-residue interactions and, consequently, conformational effects.…”

Section: Introductionmentioning

confidence: 99%

Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2

et al. 2014

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Abstract:The aerial parts of Ipomoea batatas are described herein to produce four new resin glycosides, designated as ipomotaosides A, B, C, and D. Ipomotaoside A was found to present inhibitory activity on both cyclooxygenases. However, the conformational elucidation of these molecules may be difficult due to their high flexibility. In this context, the current work presents a conformational characterization of ipomotaosides A-D in aqueous and nonaqueous solvents. The employed protocol includes metadynamics evaluation and unrestrained molecular dynamics simulations (MD). The obtained data provided structural models for the ipomotaosides in good agreement with previous ROESY distances measured in pyridine. Accordingly, the most abundant conformation of ipomotaoside A in solution was employed in flexible docking studies, providing a structural basis for the compound's inhibition of COX enzymes. The so-obtained complex supports resin glycosides' role as original scaffolds for future studies, aiming at structural optimization and development of potential new anti-inflammatory agents.

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“…The disaccharidic or monosacharide-aglycone glycosydic linkages presented by QS-21 had their torsion angles rotated between −180° and 150°, in steps of 30°, thus generating 144 conformers for each torsion, allowing us to obtain a conformational description of the molecule. We used a constant restriction force in the φ and ψ proper dihedrals in this energy minimization process, which permitted the exploration of the conformational space by all of the unit’s linkages [13]. Thus, these minimized conformations were submitted to MD simulations in vacuum for 20 ps at 10 K, with an integration step of 0.5 fs, further improving the minimum-energy conformations investigation.…”

Section: Methodsmentioning

confidence: 99%

“…Structure-based investigations can help understand the molecular basis concerning these compounds’ dynamics [12], conformation [13], and function [14]. However, obtaining 3D atomic models remains a challenge, since efficient approaches that accurately describe the biological conformational states of saponins and glycoconjugates are still scarce.…”

Section: Introductionmentioning

confidence: 99%

Atomic Model and Micelle Dynamics of QS-21 Saponin

et al. 2014

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QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD) simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS). Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the OPEN ACCESSMolecules 2014, 19 3745 first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.

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Solution conformation and dynamics of exopolysaccharides from Burkholderia species

Cited by 16 publications

References 61 publications

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin

Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2

Atomic Model and Micelle Dynamics of QS-21 Saponin

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