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

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 PDC109是一个10.6 kDa的模块化蛋白，含有两个纤维连接蛋白II(Fn2)重复序列，由一个柔性连接子连接。它通过与精子细胞膜的相互作用，在公牛精子与输卵管上皮结合的过程中发挥重要作用。这些相互作用刺激磷胆碱(PHC)的外流，导致与PDC109结构域的特异性结合。对PDC109的长时间分子动力学模拟表明，PHC的结合与结构域-结构域相互作用有关。我们建议通过使用自适应偏向力(ABF)方法计算作为每个结构域与配体结合位置之间距离的函数的平均力势(PMF)来估计PHC结合亲和力。自由能分布将在各个区域和完整的PDC109上计算。这项研究将改进对已报道的PDC109与磷脂膜相互作用的实验结果的解释，并为深入了解结构域-结构域相互作用在相关系统中配体结合中的作用提供依据。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.