Halogen bonds in biomolecular design

对卤素键（x键）的研究在化学和材料科学的几乎所有领域都在增长。在生物学和生物化学中，x -键具有促进合理设计针对酶靶点的新型卤化抑制剂的巨大潜力。本项目采用综合策略来研究结构如何影响DNA和蛋白质中生物分子x键的能量。这个项目正在开发一种独特的计算工具，生物学家、生物化学家和化学生物学家可以使用它来合理地设计针对重要酶的新抑制剂。该工具还将用于帮助设计新的生物基材料。该项目对社会的影响是通过教育外展项目让K-12年级的学生参与体验式学习，提高未来劳动力的科学素养。这个拓展项目向高中学生介绍结构生物学中的两个重要概念：1)三维蛋白质结构的基本原理，2)这些结构是如何通过实验确定的。最后，研究培训提供给不同群体的学生，从高中到博士后水平，包括性别，种族和经济背景。提出的研究的驱动假设是，一旦将生物卤素键力场（ffBXB）纳入分子力学/动力学程序，就可以准确有效地应用于设计用于生物工程应用的新型卤化分子。该项目在一个标准的分子模拟程序中实现并测试了ffBXB。该程序经过测试，因为它能够准确地模拟x键的结构和能量，这些x键涉及先前表征的实验模型DNA连接中正式带负电荷的氧受体。新程序被独立地交叉验证，因为它能够准确地模拟模型DNA连接和T4溶菌酶中涉及正式中性氧受体的x键的结构和能量。验证研究是通过x射线晶体学原子水平结构测定这些分子体系，并通过差示扫描量热法（DSC）在溶液中测量它们的相互作用能。利用自由能微扰方法研究了工程x键对生物体系构象和溶剂动力学的影响。通过应用ffBXB来设计新的蛋白质-蛋白质界面，验证了主要假设。设计了一种螺旋状多肽模型系统，其中引入卤化氨基酸作为x键提供“旋钮”，适合工程受体“孔”。由此产生的“x -拉链”作为一个概念的证明，x键可以用来促进以合理的方式特定组装的蛋白质。

The study of halogen bonds (X-bonds) is growing in nearly all fields of chemistry and material science. In biology and biochemistry, X-bonds have great potential to facilitate the rational design of new halogenated inhibitors against enzyme targets. This project applies a comprehensive strategy to study how structure affects the energy of biomolecular X-bonds in DNA and proteins. This project is developing a unique computational tool that can be used by biologists, biochemists and chemical biologists to rationally design new inhibitors against important enzymes. The tool would also be used to aid design of new biologically-based materials. The impact of this project on society is to improve the scientific literacy of the future workforce by engaging students at the K-12 level with experiential learning through an educational outreach project. This outreach project is introducing high school students to two important concepts in structural biology: 1) the fundamentals of 3-dimensional protein structures and 2) how those structures are experimentally determined. Finally, research training is provided to diverse groups of students, ranging from high school to postdoctoral levels, inclusive of gender, ethnicity and economic background. The driving hypothesis of the proposed studies is that a force field for biological halogen bonds (ffBXB), once incorporated into a molecular mechanics/dynamics program, can be accurately and efficiently applied to design novel halogenated molecules for bioengineering applications. The project implements and tests the ffBXB in a standard molecular simulation program. The program is tested for its ability to accurately model the structures and energies of X-bonds that involve formally negatively charged oxygen acceptors in a previously-characterized experimental model DNA junction. The new program is independently cross-validated for its ability to accurately model the structures and energies of X-bonds that involve formally neutral oxygen acceptors in the model DNA junction and in T4 lysozyme. The validation studies are performed by X-ray crystallographic atomic level structure determination of these molecular systems and measuring their energies of interaction by differential scanning calorimetry (DSC) in solution. Free energy perturbation methods are used to study the effects of engineered X-bonds on the conformational and solvent dynamics of a biological system. The primary hypothesis is tested by applying the ffBXB to design new protein-protein interfaces. A coiled-coil polypeptide model system has been designed in which halogenated amino acids are introduced to serve as X-bond donating "knobs" that fit into engineered acceptor "holes". The resulting "X-Zipper" serves as a proof of concept that X-bonds can be used to facilitate specific assembly of proteins in a rational manner.