Woods R J, Pathiaseril A, Wormald M R, Edge C J, Dwek R A
Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, USA.
Eur J Biochem. 1998 Dec 1;258(2):372-86. doi: 10.1046/j.1432-1327.1998.2580372.x.
The conformational properties of oligosaccharides are important in determining their biological properties, such as recognition by proteins. The structural and dynamic properties of many oligosaccharides are poorly understood both because of a lack of experimental data (usually obtained from solution NMR parameters) and because of gross approximations frequently invoked in theoretical models. To characterise the oligomannose oligosaccharide Man,GlcNAc2 we have acquired a more extensive NMR data set and performed the first unrestrained molecular dynamics (MD) simulation in water of this large oligosaccharide (employing the GLYCAM_93 parameter set with the AMBER force field). Good agreement is seen between the computed dynamics data and the results of both an isolated spin pair (ISPA) analysis of short mixing time NOE data and NOE build-up curves for mixing times from 100 to 2000 ms. The number of experimental conformational constraints obtained in this study are in principle sufficient to fully define a rigid structure. The fact that this could not be done indicates a high degree of internal flexibility and/or the presence of multiple conformations about the glycosidic linkages. Independently, the same conclusions are reached from an analysis of the MD results. In addition, the theoretical results allow the overall topology of the molecule and its intra-molecular and solvent-mediated hydrogen bonding pattern to be defined. Extensive re-organisation of solvent and inter-residue hydrogen bonds is shown to be required for significant conformational changes to occur, resulting in relatively long life-times for distinct glycosidic linkage conformations, despite the high local flexibility of the glycosidic linkages. This factor is also seen in the overall topology of the molecule, where the considerable internal flexibility is not translated into gross changes in structure. The control exerted by the solvent over both the flexibility and overall topology of an oligosaccharide has important implications for recognition processes and for the conformational properties of glycans attached to glycoproteins.
寡糖的构象性质对于确定其生物学性质（如被蛋白质识别）很重要。由于缺乏实验数据（通常从溶液核磁共振参数获得）以及理论模型中经常采用的粗略近似，许多寡糖的结构和动力学性质了解甚少。为了表征低聚甘露糖寡糖Man₅GlcNAc₂，我们获取了更广泛的核磁共振数据集，并对这种大型寡糖在水中进行了首次无约束分子动力学（MD）模拟（采用带有AMBER力场的GLYCAM_93参数集）。计算得到的动力学数据与短混合时间NOE数据的孤立自旋对（ISPA）分析结果以及混合时间从100到2000毫秒的NOE积累曲线结果之间显示出良好的一致性。本研究中获得的实验构象约束数量原则上足以完全定义一个刚性结构。但无法做到这一点表明其具有高度的内部灵活性和/或糖苷键存在多种构象。独立地，从对MD结果的分析中也得出了相同的结论。此外，理论结果使我们能够定义分子的整体拓扑结构及其分子内和溶剂介导的氢键模式。结果表明，要发生显著的构象变化需要溶剂和残基间氢键进行广泛的重新组织，尽管糖苷键具有较高的局部灵活性，但不同糖苷键构象的寿命相对较长。这一因素在分子的整体拓扑结构中也可见，其中相当大的内部灵活性并未转化为结构上的总体变化。溶剂对寡糖的灵活性和整体拓扑结构的控制对于识别过程以及与糖蛋白相连的聚糖的构象性质具有重要意义。
