Department of Chemistry, Simon Fraser University, Burnaby, B.C., V5A 1S6, Canada.
Chemistry. 2011 Oct 4;17(41):11438-45. doi: 10.1002/chem.201101464. Epub 2011 Sep 2.
X-ray crystallographic data of the carbohydrate mimic MDWNMHAA when bound to an anti-Shigella flexneri Y mAb SYA/J6 indicate the immobilization of water molecules, that is, the presence of "bound" waters, in the active site. Water Ligand Observed via Gradient Spectroscopy (WaterLOGSY) was used in conjunction with saturation transfer difference (STD)-NMR spectroscopy to probe the existence of immobilized water molecules in the complex of MDWNMHAA 1 bound to mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD Molecular Dynamics platform were then used to specify the likely locations of these water molecules. Of note, those waters involved in providing complementarity between the peptide and mAb SYA/J6 remained throughout the course of the simulation. Together, the experimental and computational protocols have been used to identify the bound water molecules present in the antibody-peptide complex.
当结合到抗福氏志贺菌 Y 单克隆抗体 SYA/J6 时，碳水化合物类似物 MDWNMHAA 的 X 射线晶体学数据表明，在活性部位存在固定的水分子，即“结合”水。通过梯度光谱（WaterLOGSY）观察到的水配体与饱和转移差异（STD）-NMR 光谱结合使用，以探测在 MDWNMHAA 1 与 mAb SYA/J6 结合的复合物中固定水分子的存在。然后使用 ZymeCAD 分子动力学平台进行分子动力学模拟，以指定这些水分子的可能位置。值得注意的是，在整个模拟过程中，那些参与提供肽和 mAb SYA/J6 之间互补性的水分子仍然存在。这些实验和计算方案一起用于鉴定存在于抗体-肽复合物中的结合水分子。
