Newman projections of the gauche-gauche (gg), gauche-trans (gt) and trans-gauche (tg) rotameric conformers of the ω dihedral angle. The gg, gt and tg conformers are defined relative to the O5-C5-C6-O6 and C4-C5C6-O6 torsions. 

Contexts in source publication

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... described in the previous section ( figure 5). With these data, we weighted the ensembles of Φ and Ψ values on the populations of 1 C4 and 2 SO conformers at 278 K (figure 5 and Appendix). The results indicated that for the GlcN-IdoA linkages, the population-weighted distributions of Φ and Ψ were centred at -65º and -50º, respectively, in a narrow fashion (rigid) and without apparent influence of sulphation pattern (figure 7a). In tar-MD simulations, a slight shift of the frequency distributions was observed, centered at -45º and -30º for the Φ and Ψ torsions, respectively, with the latter showing a slightly wider distribution ( figure 7c). Again, the sulphation pattern did not seem to eject any noticeable ...

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... experiment is carried out by first registering a spectrum under conditions of thermal equilibrium with the irradiation frequency set at a value that is far from any ligand or protein signal (e.g. 40 ppm), i.e, the so-called off-resonance spectrum (figure 7, top), which is used as reference with signal intensities I0. A second experiment is then recorded, in which the protein is selectively saturated (on-resonance spectrum; see figure 7, middle), giving rise to ligand signals with Isat intensities. In general, the selective irradiation consists of a cascade of Gaussian-shaped pulses (low power) that saturate only a region of the spectrum that contains a few protein resonances (but not ligand signals), e.g., the aliphatic (from 0 to -1 ppm) or aromatic region (around 7 ppm), for a specific period of time (saturation time; typically from 0.5 to 5-6 seconds). The selective saturation is transferred to the whole protein via spin diffusion through the vast network of intra-molecular 1 H-1 H cross-relaxation pathways (intra-molecular NOE; see figure 7, middle), being a quite efficient processes due to the typical large molecular weight of the receptor. Also, saturation is transferred from the protein to the bound ligand via spin diffusion through inter-molecular NOEs. The dissociation of the ligand will then transfer this saturation into the bulk solution where it accumulates during the saturation time of the experiment, as a result of the much slower relaxation in the unbound that the bound state. In particular, as in fast-exchanging protein-ligand systems the enthalpic relaxation (R1) of fast-tumbling molecules (small) in the free state is much slower than the kinetic off-rate constant of binding Furthermore, for those hydrogen atoms of the ligand establishing close contacts to the protein surface (4-5 Å) these Isat values will be lower than the I0 intensities, i.e, negative inter-molecular NOE, due to the transfer of the relaxation properties of the macromolecule to the small ligand in the bound state (figure 7, middle). By subtracting the off-resonance from the on-resonance spectrum (I0-Isat) the difference or STD spectrum is obtained, which will just contain the proton signals of the ligand in close contact to the protein surface ( figure 7, bottom), and where any signal coming from non-binding compounds is cancelled ...

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... to define the global geometries of the trisaccharides, we analysed the dynamic behaviour of their two glycosidic linkages by monitoring the torsions Φ (H1'-C1'-O-C4) and Ψ (C1'-O-C4-H4) along free-MD and tar-MD simulations. In this regard, the relative distribution curves obtained from free-MD (a, b) and tar-MD (c, d) are shown in figure ...

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... the IdoA-GlcN linkages, the population-weighted distributions (free-MD) were centred at 40º for the Φ torsion, and 0º and -45º (two sub-minima) for the Ψ torsion, with the former being quite rigid and the latter behaving more flexibly (-80º to 30º range; figure 7b), as it is the common flexible behaviour of the IdoA-GlcN linkage [78] . On the other hand, tar-MD simulations predicted a narrow (rigid) distribution around 40º for the Φ torsion, and a flexible Ψ torsion with two maximums centered at 15º and -30º ( figure 7d). Furthermore, both MD approaches indicated that the sulphation pattern did not seem to notably affect the conformational space sampled around the IdoA-GlcN linkages ( figure 7, b and d). It has to be noted that no anti-Ψ conformations have been observed during tar-MD simulations. This is not surprising since the simulation time employed (8 ns) is too short for a thorough sampling around the glycosidic ...

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... the IdoA-GlcN linkages, the population-weighted distributions (free-MD) were centred at 40º for the Φ torsion, and 0º and -45º (two sub-minima) for the Ψ torsion, with the former being quite rigid and the latter behaving more flexibly (-80º to 30º range; figure 7b), as it is the common flexible behaviour of the IdoA-GlcN linkage [78] . On the other hand, tar-MD simulations predicted a narrow (rigid) distribution around 40º for the Φ torsion, and a flexible Ψ torsion with two maximums centered at 15º and -30º ( figure 7d). Furthermore, both MD approaches indicated that the sulphation pattern did not seem to notably affect the conformational space sampled around the IdoA-GlcN linkages ( figure 7, b and d). It has to be noted that no anti-Ψ conformations have been observed during tar-MD simulations. This is not surprising since the simulation time employed (8 ns) is too short for a thorough sampling around the glycosidic ...

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... into details, the structural elements that determine the molecular recognition of these heparin-like GAG trisaccharides have been identified. First, the Ca 2+ -coordination by oxygens O3 and O4 of the non-reducing glucosamine ring explains the Ca 2+ dependency of the binding. Furthermore, as we would expect, the docking calculations showed up that the interactions with the calcium ion act as major stabilizing contributors to ligand binding affinity in all cases (highly negative per residue scores). Second, all the trisaccharides showed a double salt bridge involving the coordination of the carboxylate group of the central iduronate ring by the ammonium groups of the side chains of Lys299 and Lys313 ( figure 7, ...

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... -group), OR (oxygen ring) and O4 of the iduronate ring ( figure 7, down). In addition, the oxygen ...

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... third, in all the cases the ammonium group of the Lys299 side chain occupies the region below the plane of the iduronate ring ( figure 7, down), in a location that had been previously identified as a specific site for the interaction with calcium ions [77b] . This ammonium group coordinates the oxygen atoms ...