Mapping Sequence-Structure Function Landscape by Integrating Evolutionary Landscape Inference with Folding and Dynamics

标题：通过整合进化景观推断与折叠和动态蛋白质-蛋白质相互作用来绘制序列-结构功能景观在所有细胞功能中都是至关重要的，因为它们支撑着细胞内的所有信号网络。这些相互作用是由小蛋白相互作用结构域(PID)介导的，这些结构域以严格调控的方式将结合伙伴聚集在一起。这些ID的序列编码了它们功能所需的所有特征，包括在特有的3D结构中正确折叠，以及特定而动态地识别它们的伴侣的能力。所有这些特征都是进化的结果，因此编码在PID的进化史中。在这个项目中，PI将开发良好集成的计算和实验方法，分析现有的序列，以提取所有共同进化的位置，并定量评估它们对折叠和功能的贡献。他们将使用在细胞所涉及的各种信号网络中介导调节蛋白复合体的最丰富的功能结构域之一作为模型PID。他们的方法将能够识别共同进化的联系如何有助于这些领域的折叠。然后，PI将检查这些结构域的结合相互作用，以了解共同进化的位置如何有助于结合。该项目将计算方法和实验方法紧密结合，为参与其中的学生提供独特的学习机会。这个项目将为高中生提供教学模块、校园访问和研究实习。蛋白质相互作用域(PID)以独特的功能特征在信号网络中调节相互作用，例如(I)对随机突变表现出对新功能的进化的耐受性，(Ii)参与变构调节，(Iii)与多个伙伴相互作用，但在相互作用中表现出特异性。所有这些特征都编码在它们的进化史中。测序和进化推断方法的最新进展使我们能够确定共同进化的位置和保护概况。在这个项目中，新的计算方法将与实验突变分析相结合，以定量评估共同进化位置对折叠和功能的贡献。我们将会追求两个目标。首先，一小组共同进化的接触决定了折叠景观的深度和流畅度，确保了最小程度的挫折折叠景观将被确定。这将阐明ID的折叠原理。其次，通过将残基动态耦合方法与共同进化分析相结合，将确定支配结合识别和变构调节的共同进化接触机制。有了这些信息，该项目将阐明一组共同进化的位置如何以及为什么对折叠和功能至关重要，并提供ID的蓝图。WW域将用作型号PID。WW域是独立折叠的小型PID模块，概括了ID的所有独特特征。此外，它们是细胞中最丰富的功能模块之一，在涉及生理和疾病状态的各种信号网络中介导调节蛋白复合体。这项提议的长期目标是设计一种方法来预测决定折叠和结合识别的因素，这是所有细胞功能的基础。该项目得到了生物科学局分子和细胞生物科学司分子生物物理组的支持。

Title: Mapping Sequence-Structure Function Landscape by Integrating Evolutionary Landscape Inference with Folding and DynamicsProtein-­protein interactions are crucial in all cellular functions, as they underpin all signaling networks within the cell. These interactions are mediated by small protein interaction domains (PIDs) that bring together binding partners in a tightly regulated manner. The sequence of these PIDs encodes all the features necessary for their function, including proper folding in a characteristic 3D structure and the ability to recognize their partner specifically yet dynamically. All these features are the result of evolution, and thus are encoded in the evolutionary history of the PIDs. In this project, the PIs will develop well integrated computational and experimental methods that will analyze existing sequences to extract all the co-evolved positions and to evaluate quantitatively their contribution to folding and function. They will use one of the most abundant functional domains that mediate regulatory protein complexes in various signaling networks involved in cells as a model PID. Their methods will enable identification of how co­evolved contacts contribute to the folding of these domains. The PIs will then examine the binding interactions of these domains to understand how co-evolved positions contribute to binding. This project closely integrates computational and experimental approaches, offering unique learning opportunities to students involved. This project will provide teaching modules, campus visits, and research internships for high school students.Protein interaction domains (PIDs) mediate interactions in signaling networks with unique functional characteristics such as (i) displaying tolerance to random mutations yet evolving for new functions, (ii) being involved in allosteric regulations, (iii) interacting with more than one partner yet showing specificity in their interaction. All these features are encoded in their evolutionary history. Recent advancements in sequencing and in evolutionary inference methods enable us to identify co-evolved positions and also conservation profiles. In this project, novel computational methods will be integrated with experimental mutagenesis analysis to evaluate quantitatively the contribution of co-evolved positions to folding and function. Two objectives will be pursued. First, a small set of co-evolved contacts that dictates the depth and smoothness of the folding landscape, ensuring a minimally frustrated folding landscape will be determined. This will elucidate folding principles of PIDs. Second, by integrating the residue dynamic coupling method with the co-evolutionary analysis, the mechanism of co-evolved contacts that govern binding recognition and allosteric regulations in PIDs will be determined. With this information, the project will elucidate the how and why a set of co-evolved positions are critical for fold and function, and provide the blueprints of PIDs. The WW domain will be used as a model PID. WW domains are independently folded, small PID modules that recapitulate all the unique characteristics of PIDs. Moreover, they are one of the most abundant functional modules in cell, mediating regulatory protein complexes in various signaling networks involved in physiological and disease states. The long term goal of this proposal is to devise means for predicting factors that dictate folding and binding recognition of PIDs, which underpin all cellular functions. This project is supported by the Molecular Biophysics Cluster of the Molecular and Cellular Biosciences Division in the Directorate for Biological Sciences.