Characterizing the ion-pair dynamics and their roles in protein-DNA association

描述（申请人提供）：离子配对是生物大分子执行其功能的最基本的原子相互作用之一。许多大分子配合物的三维结构在功能重要位点上存在离子对（也称为盐桥），表明离子对在分子结合、识别和催化中起着重要作用。在许多蛋白质-药物复合物中也发现了关键的分子间离子对。因此，对离子对的深入了解可以为未来的人类治疗提供更成功的大分子工程和药物设计。为此，目前的项目汇集了三个具有互补专业知识的研究小组，以了解蛋白质- dna界面的离子对动力学及其在蛋白质- dna结合中的作用。蛋白质和DNA之间离子对的形成以及反离子的释放是许多蛋白质-DNA结合过程的主要驱动力。PI的小组最近开发了核磁共振方法来表征涉及氢键和离子对的侧链动力学。本项目的研究旨在验证我们的中心假设，即离子对动力学对蛋白质- dna结合具有熵上的重要性。利用核磁共振和其他溶液生物物理方法，结合计算和核酸化学，研究分子界面上自然和非自然离子对的动力学及其对蛋白质- dna结合的影响。该项目的具体目标是1)表征蛋白质和DNA之间离子对的动力学；2)描述DNA分子识别过程中电离基团的运动变化；3)阐明DNA磷酸盐中氧-硫取代增强蛋白质-DNA亲和力的机制。利用Egr-1、HoxD9和Antp蛋白的dna结合域作为模型系统，研究小组将研究两大类真核转录因子：锌指（Egr-1）和同源结构域（HoxD9和Antp）蛋白的离子对动力学及其在蛋白质- dna结合中的作用。比较人类HoxD9和果蝇Antp同源结构域的数据也将使我们能够检查离子对动力学在多大程度上在进化中是保守的。研究小组还将通过比较离子对动力学的实验结果和计算结果来验证分子动力学力场参数集。该项目将极大地推进生物大分子系统中离子对的知识。这些新知识将促进蛋白质和核酸工程用于人类治疗。基于实验的与离子对相关的力场参数验证可以改善涉及离子对的药物的硅筛选。因此，广泛的生物医学领域将从这个项目中受益。

DESCRIPTION (provided by applicant): Ion pairing is one of the most fundamental atomic interactions for biological macromolecules to execute their functions. Numerous three-dimensional structures of macromolecular complexes show the presence of ion pairs (also known as salt bridges) at functionally important sites, suggesting that ion pairs play significant roles in molecular association, recognition and catalysis. Crucial intermolecular ion pairs are also found in many protein-drug complexes. Thus, deeper knowledge of ion pairs can enable more successful macromolecular engineering and drug design for future human therapeutics. Toward this end, the current project brings together three research groups with complementary expertise to understand ion-pair dynamics at protein-DNA interfaces and their roles in protein-DNA association. Formation of ion pairs between protein and DNA along with the release of counterions is the major driving force for many protein-DNA association processes. The PI's group recently developed NMR methods for characterizing side-chain dynamics involving hydrogen bonds and ion pairs. The research in this project is designed to test our central hypothesis that the ion-pair dynamics is entropically important for protein-DNA association. Using NMR and other solution-biophysical methods together with computation and nucleic acid chemistry, the research team will study the dynamics of natural and unnatural ion pairs at molecular interfaces and their impact on protein-DNA association. The specific aims in this project are 1) to characterize the dynamics of ion pairs between protein and DNA; 2) to delineate motional changes of ionized groups in molecular recognition of DNA; and 3) to elucidate the mechanism by which oxygen-to-sulfur substitution in DNA phosphate enhances protein-DNA affinity. Using the DNA-binding domains of Egr-1, HoxD9, and Antp proteins as model systems, the research team will study the ion-pair dynamics and their roles in protein-DNA association for two major classes of eukaryotic transcription factors: zinc-finger (Egr-1) and homeodomain (HoxD9 and Antp) proteins. Comparison of data for human HoxD9 and fruit fly Antp homeodomains will also allow us to examine to what extent ion pair dynamics are conserved though evolution. The research team will also validate molecular dynamics force-field parameter sets by comparing the experimental and computational results on the ion-pair dynamics. This project will substantially advance knowledge of ion pairs in biological macromolecular systems. The new knowledge will facilitate engineering of proteins and nucleic acids for human therapeutics. Experiment-based validation of the force-field parameters relevant to ion pairs can lead to improvement of in silico screening of drugs involving ion pairs. Thus, a broad range of biomedical fields will benefit from this project.