Yan Z Y, Bush C A
Department of Chemistry, Illinois Institute of Technology, Chicago 60616.
Biopolymers. 1990 Mar-Apr;29(4-5):799-811. doi: 10.1002/bip.360290414.
Molecular dynamics simulations were carried out without explicit consideration of solvent to explore the conformational mobility of blood group A and H oligosaccharides. The potential energy force field of Rasmussen and co-workers was used with the CHARMM program on a number of disaccharide and trisaccharide models composed of fucose, galactose, glucose, N-acetyl glucosamine, and N-acetyl galactosamine chosen to represent various fragments of blood group oligosaccharides. In agreement with results of earlier studies, stable chair conformations were found for each pyranoside from which no transitions were detected in simulations as long as 800 ps. Exocyclic dihedral angles, including that of C5-C6, generally show numerous transitions on a time scale of approximately 5-30 ps. The dihedral angles of some but not all glycosidic linkages of blood group oligosaccharides show transitions on the time scale of 30-50 ps, implying that the extent of internal motion in blood group oligosaccharides depends strongly on linkage stereochemistry. For certain blood group A and H oligosaccharides that show limited internal motion in these simulations, we argue that the calculations are consistent with our previous analysis of 1H nuclear Overhauser enhancement (NOE) data that imply single conformations over a wide range of temperature and solvent conditions. While the trajectories are consistent with 13C T1 values that have been interpreted as indicating rigid conformations, measurements of 13C-NOE and T1 as a function of magnetic field strength are proposed as an improved method for experimental detection of the internal motion that is suggested for certain oligosaccharides in these simulations. The results of these simulations differ substantially from those of peptides of a similar molecular weight in that the oligosaccharides show much less internal motion.
为了探究A血型和H血型寡糖的构象流动性，我们进行了不明确考虑溶剂的分子动力学模拟。使用Rasmussen及其同事的势能力场，结合CHARMM程序，对一些由岩藻糖、半乳糖、葡萄糖、N - 乙酰葡糖胺和N - 乙酰半乳糖胺组成的二糖和三糖模型进行了模拟，这些模型被选来代表血型寡糖的各种片段。与早期研究结果一致，每个吡喃糖苷都发现了稳定的椅式构象，在长达800皮秒的模拟中未检测到构象转变。包括C5 - C6二面角在内的环外二面角通常在大约5 - 30皮秒的时间尺度上显示出大量转变。血型寡糖中一些但并非所有糖苷键的二面角在30 - 50皮秒的时间尺度上显示出转变，这意味着血型寡糖内部运动的程度强烈依赖于连接的立体化学。对于在这些模拟中显示出有限内部运动的某些A血型和H血型寡糖，我们认为这些计算与我们之前对1H核Overhauser增强（NOE）数据的分析一致，该分析表明在广泛的温度和溶剂条件下为单一构象。虽然这些轨迹与已被解释为表明刚性构象的13C T1值一致，但建议测量13C - NOE和T1作为磁场强度的函数，作为一种改进的实验方法来检测这些模拟中某些寡糖所暗示的内部运动。这些模拟结果与类似分子量的肽的结果有很大不同，因为寡糖显示出的内部运动要少得多。
