Dynamics of intermolecular ion pairs at protein-DNA interfaces

通过这一奖项，化学系生命过程化学计划资助德克萨斯大学加尔维斯顿分校(UTMB)的岩原俊二博士研究离子对动力学在蛋白质-DNA关联中的作用。这项工作是与UTMB-Galveston的B.Montgomery Pettitt博士和UTHSC-Houston的David Gorenstein博士合作的。该团队将研究HoxD9同源结构域-DNA复合体中赖氨酸和精氨酸侧链与DNA磷酸基团相互作用的离子对动力学。这项研究项目的中心假设是，通过允许相关原子的高迁移率，离子对动力学对蛋白质-DNA相互作用具有极大的重要性。研究小组将使用核磁共振光谱学、生物物理化学、有机化学和计算化学的方法来验证这一假设。需要追求的三个具体目标是：1)表征蛋白质与DNA之间分子间离子对的动力学，2)描述由于与DNA形成离子对而引起的蛋白质侧链阳离子的运动变化，以及3)阐明DNA磷酸盐中氧硫取代增强蛋白质-DNA亲和力的机制。通过提供具有重要生物学意义的大分子界面上离子对动力学的原子水平信息，该项目将极大地加深我们对离子对及其在蛋白质功能中的作用的理解。尽管离子对在化学和生命科学中具有普遍的重要性，但人们对离子对在分子识别和催化等生命过程中的动力学性质还没有很好的了解。该项目旨在阐明这一根本问题，特别关注蛋白质和DNA之间的离子对。通过解开这些分子间离子对的动力学及其对大分子缔合的熵效应，该项目有望促进蛋白质和/或核酸的工程。关于相对较小的蛋白质-DNA复合体的离子对动力学的实验数据将允许计算化学界验证和改进分子动力学力场。此外，在该项目中，研究活动将纳入若干教育/宣传活动。国际核磁共振协会将为墨西哥湾沿岸联盟组织一系列核磁共振研讨会和一次当地核磁共振研讨会，该联盟由大休斯顿地区的科学家组成。该项目的成果将被纳入国际和平协会正在开发的一门跨学科课程，并计划向该地区的高中生推广。

With this award, the Chemistry of Life Processes Program in the Division of Chemistry is funding Dr. Junji Iwahara of the University of Texas Medical Branch (UTMB)-Galveston to study the roles of the ion-pair dynamics in protein-DNA association. The work is collaborative with Dr. B. Montgomery Pettitt from UTMB-Galveston and Dr. David Gorenstein from UTHSC-Houston. The team will study the ion-pair dynamics for lysine and arginine side chains interacting with DNA phosphate groups in the HoxD9 homeodomain-DNA complex. The central hypothesis in this research project is that by allowing high mobility of involved atoms, the ion-pair dynamics are entropically important for protein-DNA interactions. The research team will test this hypothesis by using approaches of NMR spectroscopy, biophysical chemistry, organic chemistry, and computational chemistry. Three specific objectives to be pursued are: 1) characterizing the dynamics of intermolecular ion pairs between protein and DNA, 2) delineating motional changes of protein side-chain cations due to ion-pair formation with DNA, and 3) elucidating the mechanism by which oxygen-to-sulfur substitution in DNA phosphate enhances protein-DNA affinity. By providing the atomic-level information on the ion-pair dynamics at the biologically important macromolecular interfaces, this project will substantially deepen our understanding of ion pairs and their roles in protein function.Despite the universal importance of ion pairs in chemical and life sciences, dynamic properties of the ion pairs in life processes such as molecular recognition and catalysis are not well understood. This project aims to shed light on this fundamental problem, with a particular focus on ion pairs between protein and DNA. By unraveling the dynamics of these intermolecular ion pairs and their entropic effects on macromolecular association, this project is expected to facilitate the engineering of proteins and/or nucleic acids. The experimental data on the ion-pair dynamics for the relatively small protein-DNA complex will allow the computational chemistry community to validate and improve the molecular dynamics force fields. Moreover, in this project, research activities will be integrated into several educational/outreach activities. The PI will organize an NMR seminar series and a local NMR workshop for the Gulf Coast Consortium comprising scientists in the Greater Houston area. Results from this project are to be incorporated into an interdisciplinary course being developed by the PI, and outreach to high school students in the area is planned.