GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins

Solution conformation and dynamics of exopolysaccharides from Burkholderia species

“…2F-G, 3A, G-H, and 4F). These data agree to previous results 33,53 indicating that the inclusion of water molecules may be capable of promoting the occurrence of specific conformers, especially in b-linked glycosidic linkages, as well as to stabilize additional regions of the energy maps. As well, such solution simulations appeared to be capable of disclosing conformations closer to those obtained by experimental techniques, as it will be further discussed below.…”

“…30,33,40 This was performed by using a constant force to restrict only the U and W proper dihedrals during energy minimization in each of the above-mentioned values, allowing the search of the conformational space associated with the given linkage. Then, using the minimized output conformations, a series of MD simulations were performed for 20 ps at 10 K, with an integration step of 0.5 fs, to further support the search for minimum-energy conformations within GROMACS package and GROMOS96 43a1 parameters.…”

“…[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. 33 Based on the above-mentioned methodology, the current work intends to evaluate the conformation and dynamics of three EPSs from Burkholderia species through MD simulations in aqueous solutions.…”

“…32,33 Moreover, the solution conformation of disaccharides, obtained from such proceedings, was observed to be adequate starting conformations to build models of glycans. 33 Based on the above-mentioned methodology, the current work intends to evaluate the conformation and dynamics of three EPSs from Burkholderia species through MD simulations in aqueous solutions. The studied compounds include B. caribensis, B. cepacia, and B. pseudomallei, for which the obtained solution ensembles were compared to available experimental NOE contacts.…”

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

“…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.…”