A library approach to investigate the correlation between peptide rigidity and binding affinity

肽作为抑制剂的能力取决于其对目标蛋白的亲和力。通过这一奖项，化学学部的生命过程化学项目资助了弗吉尼亚联邦大学的Matthew Hartman博士和加州大学圣巴巴拉分校的Irene Chen博士，以研究肽的分子硬度如何决定它们与蛋白质的结合亲和力。这个项目使用新的和强大的技术来创建分子集合，或库，包含数万亿个具有不同范围的定义刚度的分子。这些肽库测试了它们对具有刚性结合口袋或具有更灵活结合表面的蛋白质的亲和力。由此产生的趋势将简化对抑制生物学和临床重要蛋白质的肽分子的发现。该项目为研究生和本科生提供跨学科研究培训和职业指导的机会，包括来自代表性不足的少数群体的学生。此外，还开发了一个模块，利用乐高积木玩具向高年级学生介绍分子多样性的概念和力量。肽库是开发蛋白质配体和蛋白质-蛋白质相互作用抑制剂的强大仓库；标准小分子文库中缺少的分子。该项目解决了在肽库中引入构象约束的潜在好处，以回答关于肽柔韧性和靶标亲和力关系的两个问题：僵化是否内在地提高了结合亲和力；并且，与库中具有相似亲和力的柔性结构相比，具有刚性结构的高亲和力粘合剂是否更罕见？为了回答这些问题，建立了具有匹配的疏水性和序列多样性的肽库，但增加了刚性水平。这些文库将针对链霉亲和素（具有紧凑和刚性的结合位点，并识别连续的氨基酸基序）和一个原型SH3结构域（具有扩展和灵活的结合表面）进行测试，以研究对蛋白质靶点结构的依赖性。这种从每个文库中选择的粘合剂和亲和肽的流行度的批发分析回答了有关刚性与亲和关系的指导性问题。哈特曼博士通过这个项目为弗吉尼亚联邦大学的本科生和研究生提供化学生物学方面的培训。他和他的团队也在开发以plickers为基础的活动，让小学生（包括那些来自代表性不足的少数群体的学生）学习分子相互作用和机制。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。

The ability of a peptide to serve as an inhibitor depends on the affinity for its targeted protein. With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Matthew Hartman at Virginia Commonwealth University and Dr. Irene Chen at University of California-Santa Barbara to investigate how the molecular rigidities of peptides determine their binding affinities to proteins. This project uses new and powerful technologies to create molecular collections, or libraries, containing trillions of molecules with diverse ranges of defined rigidities. These peptide libraries are tested for their affinities to proteins with rigid binding pockets or with more flexible binding surfaces. The resulting trends will streamline the discovery of peptide molecules that inhibit biologically and clinically important proteins. This project provides opportunities for interdisciplinary research training and career mentoring to a diverse population of graduate and undergraduate students, including students from underrepresented minority groups. In addition, a module is developed that uses Lego construction toys to introduce upper elementary students to the concept and power of molecular diversity.Peptide libraries are powerful storehouses for the development of protein ligands and inhibitors of protein-protein interactions; molecules that are scarce in standard small molecule libraries. This project addresses the potential benefits of introducing conformational constraints into peptide libraries to answer two questions about the relationship of peptide flexibility and target affinity: does rigidification inherently improve binding affinity; and, are high-affinity binders with rigid structures more rare compared to flexible structures of similar affinity within a library? To answer these questions, peptide libraries are created with matched hydrophobicity and sequence diversity, but increasing levels of rigidity. These libraries will be tested against streptavidin (with a compact and rigid binding site and that recognizes contiguous amino acid motifs), and a prototypical SH3 domain (with an extended and flexible binding surface) to study the dependence on the structure of the protein targets. This wholesale analysis of the prevalence of binders and affinities of peptides selected from each library answers the guiding questions concerning the relationship of rigidity to affinity. Dr. Hartman through this project provides training in chemical biology to a diverse group of undergraduate and graduate students at Virginia Commonwealth University. He and his group are also developing the Plickers-based activities to engage elementary school students (including those from underrepresented minority groups) in learning about molecular interactions and mechanisms.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.