Division of Molecular and Cellular Biosciences: Investigator-initiated research projects (MCB)

在过去的十年里，动态无序在蛋白质组中的表现已经变得很明显。尤其是，内源性无序蛋白(IDPs)广泛参与信号转导。在这个角色中，他们绑定到他们的(结构化)目标；在这样做的过程中，他们自己获得了一种结构秩序的衡量标准。因此，约束性进程的细节具有根本性和实际重要性。结合机制的显著特征是它经常依赖于静电相互作用。最初，IDP被远程静电力拉向目标，形成了所谓的静电遭遇复合体。从这一点开始，它会迅速找到正确的构象，并与目标紧密结合。为了深入了解静电遭遇复合体的结构/动力学，PI将研究富含Pro的多肽(作为IDP的最小模型)与适配蛋白(c-Crk N-SH3结构域)的结合。通过在适配蛋白SH3结构域的疏水沟槽中引入一个或两个点突变来改变原始系统。这取消了紧束缚，并使平衡向中间态移动。由此导致的相遇复合体种群的增加使得它适合于使用化学位移、顺磁约束和弛豫数据进行核磁共振(核磁共振)研究。该实验数据集被用来构建该系统的计算机模型。为了实现这一目标，产生了许多~1微秒的络合物分子动力学(MD)轨迹。这些MD数据被用作一个源池，以形成“MD轨迹集合”，该集合是为复制实验测量的核磁共振参数而量身定制的。值得注意的是，该模型可以严格预测本质上是动态的数据。这种经过实验校准的MD集合有望为无序蛋白质系统的结构和动力学提供许多新的见解。尽管国内流离失所者构成了一个广泛的和基本重要的蛋白质类别，但他们在大学教科书中很少或根本没有得到报道。从这个意义上说，在研究实验室中出现的概念与课堂教学之间存在着明显且越来越大的差距。国际和平研究所将通过以下方式为弥合这一差距做出贡献：(I)在布拉德利学院、卡尔顿学院、欧柏林学院、巴特勒学院和朱尼亚塔学院等几个本科院校发表演讲，所有这些院校在历史上都与普渡大学有联系；(Ii)开发可供其他教师使用的视觉材料；(Ii)由招募到国际和平研究所实验室的本科生设计和呈现该项目的主要成果；(Iii)在“科学美国人”和/或“化学教育杂志”上发表文章(S)，向广大受众介绍国内流离失所者。当与学生讨论国内流离失所者时，PI将强调导致蛋白质科学中这一新概念出现的“跳出框框的思维”的元素。认识到积极的研究不断挑战教科书的教条，应该为感兴趣的学生提供灵感的来源，并帮助引导他们中的一些人走向科学事业。特别是，国际学生联合会将利用这一特殊机会吸引来自代表性不足群体的学生。在这项工作中，他将依靠NOBCChE(全国黑人化学家和化学工程师专业促进组织)地方分会的持续支持。

In the last decade it has become clear that dynamic disorder is prominently represented in the proteome. In particular, intrinsically disordered proteins (IDPs) are widely involved in signal transduction. In this role, they bind to their (structured) targets; in doing so they themselves acquire a measure of structural order. The details of the binding process are, therefore, of both fundamental and practical importance. The salient feature of the binding mechanism is that it often relies on electrostatic interactions. Initially, the IDP is pulled toward its target by long-range electrostatic forces, forming what is termed an electrostatic encounter complex. Starting from this point, it quickly finds the correct conformation and binds tightly to the target. To obtain insight into the structure/dynamics of the electrostatic encounter complex, the PI will study the binding of a proline-rich peptide (which serves as a minimal model for an IDP) to an adapter protein (the c-Crk N-SH3 domain). The original system is altered by introducing one or two point mutations into hydrophobic grooves of the adapter protein SH3 domain. This abolishes tight binding and shifts the equilibrium toward the intermediate state. The resulting increase in the population of the encounter complex makes it amenable to a nuclear magnetic resonance (NMR) study using chemical shifts, paramagnetic restraints, and relaxation data. This experimental dataset is used to construct an in silico model of the system. Toward this goal, a number of ~1 micro sec molecular dynamics (MD) trajectories of the complex are generated. These MD data are used as a source pool to form an "ensemble of MD trajectories", which is tailored to reproduce the experimentally measured NMR parameters. Of note, this model can rigorously predict the pieces of data that are inherently dynamic. Such experimentally calibrated MD ensembles are expected to provide a number of new insights into the structure and dynamics of disordered protein systems. Although IDPs constitute a broad and fundamentally important class of proteins, they receive little or no coverage in college textbooks. In this sense there is a perceptible and growing gap between the concepts emerging in the research laboratories and the classroom teaching. The PI will contribute to bridging this gap by (i) making presentations at several undergraduate institutions, namely Bradley, Carleton, Oberlin, Butler, and Juniata College, all of which are historically connected to Purdue; (ii) developing visual materials that can be used by other teachers; the main findings of this project will be presented in a form of MD-based movies, designed and rendered by undergraduate students recruited into the PI's laboratory; (iii) publishing article(s) in Scientific American and/or the Journal of Chemical Education to provide a broad audience with an accessible introduction to IDPs. When discussing IDPs with students, the PI will stress the element of "thinking outside the box" that led to the emergence of this new concept in protein science. The realization that active research constantly challenges the textbook dogmas should provide a source of inspiration for interested students and help to steer some of them toward a career in science. In particular, the PI will use this special opportunity to engage the students from underrepresented groups. In this effort he will rely on the continuing support from the local chapter of NOBCChE (National Organization for the Professional Advancement of Black Chemists and Chemical Engineers).