COMPUTER MODELING AND OTHER THEORETICAL STUDIES OF BIOPO

摘要：对辛基葡萄糖苷（OG）胶束在5 ~ 100个聚集数范围内的分子动力学模拟表明，在3ns时间尺度上，10个及以上的团簇是稳定的。稳定的团簇表现为形状波动大，氢键头基团网络清晰，大的疏水性斑块暴露，偶尔与溶剂交换脂质。对添加肽的27-mer的初步模拟表明，上述特征增强了胶束/肽和胶束/肽复合物的稳定性。这项工作启动了实验室对表面活性剂为基础的佐剂结构的模拟研究。对几种细菌外壳多糖进行朗格万动力学模拟，以了解它们在共同官能团之间距离的基础上的交叉反应性。结果表明，在CHARMM2力场模拟中，为了避免聚合物的坍塌，要么需要明确的溶剂，要么需要调节良好的平均力势（pmf）；利用光散射的结果开发PMF的努力正在进行中。流体力学计算用于估计五糖乳酸- n -岩藻戊二糖-1和蛋白质溶菌酶的旋转扩散张量。在这两种情况下，结果都解决了从核磁共振弛豫测量中获得的有序参数和异构化率解释中的歧义。

ABSTRACT: Molecular dynamics computer simulations of octylglucoside (OG) micelles over a range of aggregation number from 5 to 100 indicated that clusters of 10 and above were stable on the 3 ns time scale. The stable clusters showed large undulations in shape, clear networks of hydrogen bonded headgroups, large exposed hydrophobic patches, and occasional exchange lipids with solvent. Preliminary simulations of a 27-mer with an added peptide suggest that the preceding features enhance the stability of micelle/peptide and micelle/peptide complexes. This work initiates the Laboratory's simulation study of the structure of surfactant based adjuvants. Langevin dynamics simulations were carried out on segments of several bacterial coat polysaccharides in an effort to understand their cross reactivity on the basis of distances between common functional groups. It was deduced that either explicit solvent or a well tuned potential of mean force (pmf) is required to avoid polymer collapse in simulations using CHARMM2 force field; efforts to develop a pmf using results from light scattering underway. Hydrodynamic calculations were used to estimate rotational diffusion tensors for the pentassaccharide lacto-N-fucopentaose-1 and the protein lysozyme. In both cases the results resolved ambiguities in the interpretation of order parameters and isomerization rates obtained from NMR relaxation measurements.