Catalytic halogen bonds in enzymatic bond breaking and making in DNA

DNA 中酶促键断裂和形成中的催化卤素键

• 批准号: 2203161
• 负责人: Pui Ho
• 金额: $ 60万
• 依托单位: Colorado State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2203161&HistoricalAwards=false
• 关键词: Catalytic; halogen; bonds; enzymatic; bond

With this award, the Chemistry of Life Processes Program of the Chemistry Division is funding Professors Pui S. Ho and Anthony K. Rappé at Colorado State University to determine how halogens can replace magnesium in the design of catalytic proteins (enzymes) that break and make the bonds in DNA. Magnesium is the metal typically used by enzymes to help cut or join DNA in cells. Dr. Ho’s group has shown that the catalytic magnesium in an enzyme found in mice can be replaced by an unnatural chlorinated or iodinated amino acid. This project will determine how an interaction called halogen-bonding allows elements on opposite ends of the periodic table to catalyze the same DNA-modifying reactions. This science probes the idea of using halogen-bonding as a design tool to engineer synthetic enzymes for biotechnology applications. This project will provide training in structural and computational chemistry to graduate and undergraduate students, including those from underrepresented groups. Finally, an outreach project will help middle school and high school students learn how scientists use “X-ray vision” see the atoms in three dimensions in DNA and proteins.The making and breaking of the bonds along the DNA backbone are critical reactions in a broad range of genomic processes. Endonucleases and ligases typically use magnesium ion or similar metal cations as catalysts to specifically cut and rejoin DNA fragments. The Ho and Rappé groups have shown that the essential catalytic divalent magnesium ion in mouse endonuclease G (mEndoG) can be functionally replaced by a chlorinated or iodinated tyrosine. The resulting halogenated construct recapitulates the activity of the wild type mEndoG to specifically cleave four-stranded DNA Holliday junctions that contain a 5-hydroxymethylcytosine base. This cleavage reaction is catalyzed by a hydrogen bond (H-bond) enhanced halogen bond (X-bond), or HBeXB, for short. In addition, the halogenated enzyme was found to catalyze a unique ATP-independent DNA joining reaction that is also seen in the wild type mEndoG. This research project will characterize the structural and mechanistic properties that allow this metal-free, X-bond catalyzed enzyme (or cX-Zyme) to act as a site-specific endonuclease and an ATP-independent ligase. From a broad scientific perspective, this work raises the interesting possibility that one may be able to exploit X-bonding quite generally as a novel method to promote specific catalytic chemistry in enzyme active sites.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

有了这个奖项，化学司的化学过程计划是科罗拉多州立大学的Pui S. Ho和Anthony K.Rappé教授，以确定卤素如何在催化蛋白（酶）设计中替代镁，这些蛋白质（酶）破裂并在DNA中产生键。镁是酶通常用来帮助切割或连接DNA在细胞中的金属。 Ho博士的组表明，在小鼠中发现的酶中的催化镁可以用非天然的氯化或碘化氨基酸代替。该项目将确定一种称为卤素键合的相互作用如何允许元素周期表相对端的元素催化相同的DNA修改反应。该科学预测了将卤素键入用作设计工具来设计生物技术应用的设计工具。该项目将为研究生和本科生提供结构和计算化学的培训，包括来自代表性不足的小组的培训。最后，一个外展项目将帮助中学和高中生学习科学家如何使用“ X射线视觉”，请参见DNA和蛋白质中三个维度的原子。沿DNA骨架的键和破坏键是广泛基因组过程中的关键反应。核酸内切酶和连接酶通常使用镁离子或类似的金属阳离子作为催化剂，以专门切割和重新加入DNA片段。 Ho和Rappé组表明，小鼠核酸内切酶G（Mendog）中必需的催化二价镁离子可以在功能上用氯化或碘化的酪氨酸代替。所得的卤代构建体概括了野生型门托的活性，以明确清除含有5-羟基甲基环胞嘧啶碱基的四链DNA Holliday连接。该裂解反应由氢键（H键）增强的卤素键（X键）或HBEXB催化。此外，发现卤代酶可以催化独特的ATP独立的DNA连接反应，在野生型Mendog中也可以看到。该研究项目将表征结构和机械性能，这些特性允许这种无金属，X键催化的酶（或CX-zyme）充当特定位点特异性核酸酶和非ATP独立的连接酶。从广义的科学角度来看，这项工作提出了有趣的可能性，即人们可能能够完全探索X键，这是一种新颖的方法，作为一种新的方法来促进酶的活性场所中特定的催化化学反应。该奖项反映了NSF的法定任务，并被认为是通过评估基金会的知识和更广泛的影响来通过评估的支持来珍贵的，这是珍贵的。