Accelerating conformational transitions in binding flexible proteins

蛋白质是生物大分子，几乎控制着细胞功能的方方面面，从酶催化、对外界刺激的反应，到控制细胞周期和细胞命运的决定。在功能方面，蛋白质已经进化成具有独特的三维(3D)结构属性。该项目专注于一类重要的新发现的蛋白质，这些蛋白质利用高度灵活的3D结构来实现功能。这些蛋白质包括所谓的固有无序蛋白质(IDPs)，约占所有真核蛋白质的三分之一，是细胞信号和调控网络的关键组成部分。该项目将开发有效的计算方法来模拟柔性蛋白质，并揭示结构无序如何调节蛋白质功能的基本原理。新的计算工具将提供给广泛的科学界，并可用于研究生物分子动力学和相互作用。除了培训研究生和本科生外，PI还将为马萨诸塞州西部的各种外联项目做出贡献，这些项目在STEM领域吸引妇女和其他代表性不足的少数族裔。他还将帮助扩大一个名为“分子游乐场”的非正式科学教育项目，该项目在学校、博物馆、购物中心和机场等公共场所安装交互式分子显示器。这个项目将增加蛋白质动力学方面急需的内容，例如说明国内流离失所者极端的构象灵活性如何支持功能这一迷人的现象。该项目的主要研究目标是确定基本原则，使灵活的蛋白质，如内源性蛋白，经历快速结合诱导折叠或解折叠，以获得可行的细胞信号。更多地利用灵活的蛋白质，如IDPs，与复杂的多细胞生物体中日益复杂的信号转导有关。然而，结合柔性蛋白的大规模构象转换的频繁要求可能会导致一个潜在的动力学瓶颈，不利于有效的细胞信号传递。假设IDPs上的富集电荷与其结合靶标之间的长程静电相互作用在促进易化结合方面发挥了关键作用。一个需要检验的具体假设是，远程静电力不仅加速了IDP相遇，而且还促进了具有折叠能力的相遇拓扑，以允许在相遇时有效地折叠。该项目还将解决细胞信号中一种被称为受调控的展开的新现象，并确定瞬时疏水相互作用如何减少转换障碍，并有助于有效地耦合结合、折叠和展开Bcl-2家族蛋白质。为了验证这些假设，将开发新的GPU加速的、基于隐式溶剂的原子模拟技术，以便能够有效地计算结合诱导的大规模蛋白质构象转变的自由能、途径和动力学。平衡和动力学模拟的结果将使用现有的力学和动力学数据以及与实验实验室合作进行的新测量进行验证。该项目由分子和细胞生物科学部的分子生物物理组支持，部分联合资金来自化学部的化学理论、模型和计算方法(CTMC)计划。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Proteins are biological macromolecules that control virtually all aspects of cellular functions, ranging from enzyme catalysis, response to external stimuli, to control of cell cycle and cell fate decision. For function, proteins have evolved to possess unique three-dimensional (3D) structural properties. This project focuses on an important newly recognized class of proteins that exploit highly flexible 3D structures for function. These proteins include so-called intrinsically disordered proteins (IDPs) that account for about one-third of all eukaryotic proteins and are key components of cellular signaling and regulatory networks. This project will develop efficient computational methods for simulating flexible proteins and uncover the fundamental principles of how structural disorder mediates protein function. The new computational tools will be made available to the broad scientific community and can be applied to study biomolecular dynamics and interactions in general. Besides training of graduate and undergraduate students, the PI will contribute to various outreach programs in western Massachusetts that engage women and other under-represented minorities in STEM fields. He will also help expand an informal science education project known as the "Molecular Playground", which installs interactive molecular displays in public spaces such as schools, museums, shopping malls and airports. This project will add much-needed contents with protein dynamics, such as to illustrate the fascinating phenomenon how extreme conformational flexibility of IDPs support function. The overarching research objective of this project is to determine the fundamental principles that allow flexible proteins such as IDPs to undergo rapid binding-induced folding or unfolding for viable cellular signaling. Greater utilization of flexible proteins such as IDPs have been associated with increasingly sophisticated signaling in complex multicellular organisms. However, the frequent requirement of large-scale conformational transitions for binding flexible proteins can lead to a potential kinetic bottleneck detrimental to effective cellular signaling. It is hypothesized that long-range electrostatic interactions between enriched charges on IDPs and their binding targets play a key role in promoting facile binding. A specific hypothesis to be tested is that long-range electrostatic forces not only accelerate IDP encounter, but also promote folding-competent encounter topologies to allow efficient folding upon encounter. This project will also tackle an emerging phenomenon known as regulated unfolding in cellular signaling and determine how transient hydrophobic interactions may reduce transition barriers and contribute to efficient coupled binding, folding and unfolding in Bcl-2 family proteins. To test these hypotheses, new GPU-accelerated, implicit solvent-based atomistic simulation techniques will be developed to enable efficient calculation of the free energy, pathway and kinetics of binding-induced large-scale protein conformational transitions. Results from equilibrium and kinetic simulations will be validated using existing mechanistic and kinetic data as well as new measurements performed in collaboration with experimental labs. This project is supported by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences with partial co-funding from the Chemical Theory, Models and Computational methods (CTMC) Program in the Division of Chemistry.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.