CAREER:Multiscale Thermodynamic Tools for Probing the Stability and Function of Natively Unfolded Proteins

摘要提案标题：职业：探索天然未折叠蛋白质稳定性和功能的多尺度热力学工具。Ashbaugh研究所：杜兰大学提案编号：CBET-0746955天然未折叠的蛋白质正在成为一类重要的生物大分子，尽管它们缺乏明确的三维结构，但它们仍具有必要的生物学功能，这与蛋白质形状和功能的传统观点相反。至于折叠蛋白质，多肽成为内在无序卷曲的倾向是在其氨基酸序列中编码的。为了将结构的缺乏与功能联系起来，必须首先鉴定天然未折叠的蛋白质。到目前为止，基于序列的相关性预测天然线圈的稳定性已经开发，只有通过经验数据库分析，几乎没有基本的基础。这些蛋白质的特殊功能包括：配体/DNA结合、细胞信号传导、细胞骨架成分的分散和跨核膜转运调节。不幸的是，预测未折叠蛋白质稳定性和功能的综合理论方法发展缓慢。PI建议开发新的模拟策略，用于模拟固有无序蛋白质的构象稳定性和未折叠核孔相关蛋白质在基于溶质大小调节跨核膜转运中的功能。最初的模拟将集中在天然未折叠蛋白质及其构象稳定性的多尺度建模。基础分子模拟将研究组分氨基酸和探针侧链相互作用的溶液热力学，这些相互作用使肽二级结构元件不稳定，有利于非结构化线圈。从这些模拟中确定的热力学平均值将被粗粒化，以剔除降低计算效率的非必要自由度，同时使用PI实验室开发的新约束技术保留肽构象自由度和化学保真度。这些粗粒度模型将提供一个更深层次的热力学和结构的理解天然未折叠蛋白质稳定性的经验预测。随后的模拟将利用本文开发的技术来模拟天然未折叠的蛋白质功能。具体而言，PI将研究未折叠核孔蛋白之间的相互作用，以区分尺寸选择性、虚拟门控与选择性相模型之间的冲突机制。建模工作将通过实验进行验证，生成的结果将用作我们的合作者开发的连续介质传输模型的输入。除了非结构化的生物大分子，该提案中开发的技术是通用的，并构成了一种从下而上建模聚合物和胶体材料特性的全新方法。此外，非结构化多肽工程的新兴应用，如促进转运膜的设计，需要对它们的稳定性和聚合物螺旋样性质如何依赖于氨基酸序列的基本理解。为了振兴新奥尔良的学术环境，PI正在通过引入一门新课程，在本科课程中启动一个服务学习部分，“化学和工程科学在社区。"在这门课程中，杜兰大学的学生与当地公立学校的学生互动，就科学方法的日常使用进行演示，以得出基于证据的解释。还努力通过新生研讨会系列和杜兰大学路易斯·斯托克斯路易斯安那州少数民族参与联盟计划招募本科生参与研究。希望通过外联活动鼓励来自不同群体的学生考虑终身从事科学和工程，同时为受卡特里娜飓风影响的当地化学工业提供积极的劳动力。

ABSTRACT Proposal Title: CAREER: Multi-scale Thermodynamic Tools for Probing the Stability andFunction of Natively Unfolded ProteinsPrincipal Investigator: Henry S. Ashbaugh Institution: Tulane University Proposal No: CBET-0746955Natively unfolded proteins are emerging as an important class of biomacromolecules that carry out necessary biological functions despite their lack of well-defined three-dimensional structures, contrary to traditional ideas linking protein shape and function. As for folded proteins, the propensity for a polypeptide to be an intrinsically disordered coil is encoded in its amino acid sequence. To relate lack of structure to function, natively unfolded proteins must first be identified. To date, sequence based correlations for the prediction of native coil stability have been developed only through empirical database analysis with little fundamental basis. Specific functions for these proteins that have been identified include: ligand / DNA binding, cell signaling, the dispersion of cytoskeletal components, and trans-nuclear membrane transport regulation.Unfortunately, a comprehensive theoretical approach for predicting unfolded protein stability and function has been slow to develop.Intellectual Merit. The PIs propose to develop new simulation strategies for modeling the conformational stability of intrinsically disordered proteins and the function of unfolded nuclear pore associated proteins in regulating trans-nuclear membrane transport based on solute size. Initial simulations will focus on the multiscale modeling of natively unfolded proteins and their conformational stability. Foundational molecular simulations will investigate the solution thermodynamics of component amino acids and probe side chain interactions that destabilize peptide secondary structural elements in favor of unstructured coils. Thermodynamic averages determined from these simulations will be coarse-grained to winnow non-essential degrees-of freedom that diminish computational efficiency, while retaining peptide conformational degrees of-freedom and chemical fidelity using new constraint techniques developed in the PIs lab. Thesecoarse-grained models will provide a deeper thermodynamic and structural understanding of empirical predictors for natively unfolded protein stability. Subsequent simulations will take advantage of the techniques developed herein to model natively unfolded protein function. Specifically, the PIs will investigate interactions between unfolded nuclear pore proteins to discriminate between conflicting mechanisms for size selectivity, virtual gating versus the selective phase model. The modeling efforts will be validated against experiments, and results generated will be used as inputs to continuum transport models developed by our collaborators.Broader Impacts. Beyond unstructured bio-macromolecules, the techniques developed in this proposal are general and constitute a fundamentally new approach towards modeling the properties of polymeric and colloidal materials from the bottom-up. Moreover, the engineering of unstructured polypeptides for emerging applications, like the design of facilitated transport membranes, requires a fundamental understanding of how their stability and polymer coil-like properties depend on amino acid sequence.In an effort to revitalize the academic environment of New Orleans, the PI is initiating aservice-learning component in the undergraduate curriculum through the introduction of a new course, "Chemistry and Engineering Science in the Community." In this course, Tulane students interact with local public school students, making presentations on the everyday use of the scientific method to arrive at evidence based explanations. Efforts are also being directed towards recruiting undergraduate participation in research through a freshman seminar series and the Louis Stokes Louisiana Alliance for Minority Participation program at Tulane University. It is hoped through the outreach activities to encourage students from diverse groups to consider lifelong careers in science and engineering, while providing a motivated work force for the local chemical industry effected by Hurricane Katrina.