The Role of Thioamides in Natural and Designed Proteins

在化学系生命科学化学（CLP）项目的支持下，宾夕法尼亚大学的E. James Petersson教授正在研究硫酰胺的作用，即蛋白质中肽键的氧到硫取代。这些研究结果将进一步发展硫酰胺作为生物物理和药物化学的工具，为合理设计或不影响稳定性的硫酰胺蛋白提供规则。这项工作还将有助于解释在某些天然蛋白质中发现的硫胺的进化价值。对硫酰胺基本特性的计划研究可以影响多种领域，如表观遗传学、蛋白质折叠的生物物理学、酶抑制剂的设计，甚至使用硫酰胺稳定肽作为肿瘤显像剂的荧光引导手术。这项工作的广泛影响包括在多学科实验室环境中培养本科生和研究生，利用有机合成和物理化学，以及分子和细胞生物学来研究生物现象。此外，Petersson教授和他的研究小组将参加面对面和虚拟的展览，向K-12组和感兴趣的成年人展示他们的发现。他们还将帮助建立宾夕法尼亚大学化学暑期研究学院（Penn Chemistry Summer Research Academy），以便更多来自科学领域代表性不足的群体的学生有机会体验科学并参与科学研究。在本项目下，硫酰胺的物理性质和反应性将作为模型肽中氨基酸序列的函数进行研究。这将有助于对环境相关特性（如pKa）的机制理解，以及对量子力学（QM）计算进行基准测试。例如，有必要更好地开发三肽或多肽的分子力学参数，而不是像以前那样使用基于小分子值的参数。将进行反应性研究，有可能开发出鉴定新的天然含硫酰胺蛋白质的工具。Petersson教授的实验室还将研究硫酰胺对肽、肽/蛋白主客体系统和全长蛋白的二级和三级结构的影响。利用模型系统的数据，新的PyRosetta程序将被开发出来，以努力预测硫胺对蛋白质稳定性的影响。这些预测将在含硫酰胺的蛋白质上进行测试，这些蛋白质将通过x射线晶体学和/或核磁共振以及溶液相稳定性测量来表征。综上所述，这些实验有望更好地系统地了解硫酰胺对蛋白质性质的影响，从局部序列效应到二级、三级甚至四级结构的影响。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

With the support of the Chemistry of Life Sciences (CLP) program in the Division of Chemistry, Professor E. James Petersson from the University of Pennsylvania is studying the effects of thioamides, oxygen-to-sulfur substitutions of the peptide bond found in proteins. The results of these studies will further the development of thioamides as tools for biophysical and medicinal chemistry by providing rules for the rational design of thioamide proteins with or without affecting stability, as desired. The work will also help to explain the evolutionary value of the thioamides found in certain natural proteins. The planned investigations of the fundamental properties of thioamides can impact areas as diverse as epigenetics, the biophysics of protein folding, the design of enzyme inhibitors, or even fluorescence-guided surgery using thioamide-stabilized peptides as tumor imaging agents. The broader impacts of this work include training undergraduate and graduate students in a multidisciplinary laboratory environment that makes use of organic synthesis and physical chemistry, as well as molecular and cellular biology, to investigate biological phenomena. In addition, Professor Petersson and his research group will participate in expositions both in-person, and virtual, to demonstrate their findings to K-12 groups and interested adults. They will also help to build the Penn Chemistry Summer Research Academy so that more students from groups under-represented in science have opportunities to experience science and participate in scientific research.Under this project, the physical properties and reactivity of thioamides will be studied as a function of amino acid sequence in model peptides. This will aid in the mechanistic understanding of environment-dependent properties such as pKa, and in benchmarking quantum mechanical (QM) calculations. For example, there is a need to better develop in molecular mechanics parameters for tripeptides or polypeptides, rather than use parameters based on small molecule values as has been done heretofore. Reactivity studies will be performed that have the potential to develop tools to identify new natural thioamide-containing proteins. Professor Petersson’s laboratory will also study thioamide effects on the secondary and tertiary structure of peptides, peptide/protein host-guest systems, and full-length proteins. Using data from model systems, novel PyRosetta programs will be developed in an effort to predict the effects of thioamides on protein stability. These predictions will be tested on thioamide-containing proteins, which will be characterized through X-ray crystallography and/or NMR as well as solution-phase stability measurements. Taken together, these experiments are expected to provide a better systematic understanding of the effects of thioamides on protein properties from local sequence-based effects, to effects on secondary, tertiary, and even quaternary structure.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.