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

Arizona State University, Scottsdale AZ

Investigators

Abstract

Title: Mapping Sequence-Structure Function Landscape by Integrating Evolutionary Landscape Inference with Folding and Dynamics Protein-­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.