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首页> 外文期刊>Chemistry: A European journal >Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations
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Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations

机译：通过STD-NMR光谱和分子动力学模拟研究模拟碳水化合物的肽与其互补的抗碳水化合物抗体的结合

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Saturation transfer difference (STD)-NMR spectroscopy was used to probe experimentally the bioactive solution conformation of the carbohydrate mimic MDWNMHAA 1 of the O-polysaccharide of Shigella flexneri Y when bound to its complementary antibody, mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD? Molecular Dynamics platform were also undertaken to give a more accurate picture of the conformational flexibility and the possibilities for bound ligand conformations. The ligand topology, or the dynamic epitope, was mapped with the CORCEMA-ST (COmplete Relaxation and Conformational Exchange Matrix Analysis of Saturation Transfer) program that calculates a total matrix analysis of relaxation and exchange effects to generate predicted STD-NMR intensities from simulation. The comparison of these predicted STD enhancements with experimental data was used to select a representative binding mode. A protocol that employed theoretical STD effects calculated at snapshots during the entire course of a molecular dynamics (MD) trajectory of the peptide bound to the Fv portion of the antibody, and not the averaged atomic positions of receptor-ligand complexes, was also examined. In addition, the R factor was calculated on the basis of STD (fit) to avoid T1 bias, and an effective R factor, R_(eff), was defined such that if the calculated STD (fit) for proton k was within error of the experimental STD (fit) for proton k, then that calculated STD (fit) for proton k was not included in the calculation of the R factor. This protocol was effective in deriving the antibody-bound solution conformation of the peptide which also differed from the bound conformation determined by X-ray crystallography; however, several discrepancies between experimental and calculated STD (fit) values were observed. The bound conformation was therefore further refined with a simulated annealing refinement protocol known as STD-NMR intensity-restrained CORCEMA optimization (SICO) to give a more accurate representation of the bound peptide epitope. Further optimization was required in this case, but a satisfactory correlation between experimental and calculated STD values was obtained. Attempts were also made to obtain STD enhancements with a synthetic pentasaccharide hapten, corresponding to the O-polysaccharide, while bound to the antibody. However, unfavorable kinetics of binding in this system prevented sufficient STD build-up, which, in turn, hindered a rigorous analysis via full STD build-up curves.
机译：当饱和志贺氏菌Y的O-多糖结合其互补抗体mAb SYA / J6时，使用饱和转移差异（STD）-NMR光谱从实验上探测碳水化合物模拟物MDWNMHAA 1的生物活性溶液构象。使用ZymeCAD？进行分子动力学模拟还进行了分子动力学平台，以提供构象灵活性和结合的配体构象的可能性的更准确的图片。用CORCEMA-ST（饱和转移的完全弛豫和构象交换矩阵分析）程序绘制了配体拓扑图或动态表位，该程序计算了弛豫和交换效应的总矩阵分析，以通过模拟生成预测的STD-NMR强度。将这些预测的STD增强与实验数据进行比较，以选择代表性的结合模式。还检查了一种协议，该协议采用了在与抗体Fv部分结合的肽的分子动力学（MD）轨迹的整个过程中，按快照计算的理论STD效应，而不是受体-配体复合物的平均原子位置。此外，基于STD（拟合）来计算R因子以避免T1偏差，并定义有效R因子R_（eff），使得如果计算出的质子k STD（拟合）在误差范围内质子k的实验性STD（拟合），则计算出的质子k的性病STD（拟合）不包括在R因子的计算中。该方案有效地衍生了肽的抗体结合溶液构象，该构象也不同于通过X射线晶体学测定的结合构象。但是，观察到实验值和计算出的STD（拟合）值之间存在一些差异。因此，结合的构象用称为STD-NMR强度限制的CORCEMA最优化（SICO）的模拟退火优化方案进一步完善，以给出结合肽表位的更准确表示。在这种情况下，需要进一步优化，但是在实验值和计算出的STD值之间获得了令人满意的相关性。还尝试用与抗体结合的对应于O-多糖的合成五糖半抗原获得STD增强。但是，该系统中不利的结合动力学阻止了足够的STD积累，进而阻碍了通过完整的STD积累曲线进行严格的分析。

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