Accelerating conformational transitions in binding flexible proteins

蛋白质是一种生物大分子，几乎控制着细胞功能的所有方面，从酶催化、对外部刺激的反应到细胞周期的控制和细胞命运的决定。就功能而言，蛋白质已经进化到具有独特的三维（3D）结构特性。这个项目的重点是一个重要的新认识的一类蛋白质，利用高度灵活的3D结构的功能。这些蛋白质包括所谓的内在无序蛋白（IDPs），约占所有真核蛋白的三分之一，是细胞信号传导和调节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，并揭示结构紊乱如何介导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，可以应用于研究生物分子动力学和一般的相互作用。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推广项目做出贡献，这些项目将吸引女性和其他未被充分代表的少数族裔参与STEM领域。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互动分子显示器。本项目将增加蛋白质动力学方面急需的内容，例如说明IDPs的极端构象灵活性如何支持功能的迷人现象。该项目的总体研究目标是确定允许柔性蛋白（如IDPs）进行快速结合诱导折叠或展开以实现可行的细胞信号传导的基本原理。在复杂的多细胞生物中，更多地利用柔性蛋白（如IDPs）与日益复杂的信号传导有关。然而，结合柔性蛋白频繁需要大规模的构象转变，这可能导致潜在的动力学瓶颈，不利于有效的细胞信号传导。假设IDPs上富集电荷与其结合靶之间的远距离静电相互作用在促进易结合中起关键作用。需要测试的一个具体假设是，远程静电力不仅加速了IDP相遇，而且还促进了折叠能力的相遇拓扑，从而允许在相遇时进行有效的折叠。该项目还将解决一个新兴现象，即细胞信号传导中的调节展开，并确定瞬态疏水相互作用如何减少过渡障碍，并有助于Bcl-2家族蛋白的有效偶联结合、折叠和展开。为了验证这些假设，新的gpu加速的、隐式的基于溶剂的原子模拟技术将被开发出来，从而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来验证。本项目由分子与细胞生物科学部分子生物物理集群支持，部分资金来自化学学部化学理论、模型和计算方法（CTMC）项目。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。

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.