DOMAIN-LIGAND BINDING FREE ENERGY CALCULATIONS ON PDC109, A TWO-DOMAIN PROTEIN

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 PDC 109是一种10.6 kDa的模块化蛋白，含有两个由柔性接头连接的II型纤连蛋白（Fn 2）重复序列。它通过与精子细胞膜的相互作用在牛精子与输卵管上皮的结合中起主要作用。这些相互作用刺激磷酸胆碱（PhC）的流出，精子细胞膜脂质的可溶性头部基团，导致与PDC 109结构域的特异性结合。长时间尺度的分子动力学模拟PDC 109表明，PhC的结合与结构域之间的相互作用。我们建议通过计算平均力（PMF）的潜力作为每个域和配体的结合位点之间的距离的函数，使用自适应偏置力（ABF）的方法来估计PhC结合亲和力。将在单个结构域和完整的PDC 109上计算自由能曲线。这项研究将改善对PDC 109和磷脂膜之间相互作用的实验结果的解释，并提供相关系统中结构域-结构域相互作用对配体结合的作用的见解。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. PDC109 is a 10.6 kDa modular protein containing two fibronectin type II (Fn2) repeats joined by a flexible linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with the sperm cell membrane. These interactions stimulate the efflux of phosphorylcholine (PhC), the soluble head group of the sperm cell membrane lipids, resulting in the specific binding to the PDC109 domains. Long timescale molecular dynamics simulation on PDC109 suggests that PhC binding is correlated with domain-domain interactions. We propose to estimate PhC binding affinity by calculating a potential of mean force (PMF) as a function of distance between binding sites of each domain and the ligand using the adaptive biasing force (ABF) method. The free energy profiles will be calculated on the individual domains and on the intact PDC109. This study will improve interpretation of reported experimental results for the interaction between PDC109 and phospholipid membranes and provide insight into roles of domain-domain interactions on ligand binding in related systems.