Protein interaction domains (PIDs) are the most important players in mediating protein networks in cell regulation. All PIDs come with exceptional features that make them ideal outlets in signaling networks. First, they recognize exposed short linear peptide stretches on their partners. This binding style creates a specific, yet fast and easily disrupted response, which is ideal for signaling pathways. Second, their flexibility/dynamics is a major determinant of binding specificity that makes them remarkably versatile: they can engage with several different ligands at different stages of signaling. These features also make them attractive as an evolvable unit to wire new protein networks in synthetic biology. Understanding these structural elements on the molecular level helps to explain specificity and dynamic regulation in cell signaling systems, and opens the way for genome-wide analysis of protein interaction networks. Furthermore, it provides insight into the evolution of cellular regulatory mechanisms, and may offer new promise for the development of therapeutic agents that target key regulatory interactions. However, understanding the sequence-structure-function (i.e. binding specificity) of PIDs presents several challenges, because PID interactions are context dependent: the same fold with small variations in sequence leads to different binding affinities and/or different allosteric regulations. Conventional experimental or theoretical approaches are insufficient to deal with this complexity. However, 10 billion years of evolution engraved the necessary information in the sequence variances of PID folds. Therefore, we propose to develop a novel approach that couples inference analysis using phylogenetics of PIDs with their biophysical characterization to elucidate critical contacts and how variations in these positions lead to a specific fold and binding affinity. Our goal is to provide the blue prints of recognition of the outlets of cellular interactions and to provide a recipe to generate synthetic PIDs. A distinguishing factor in the design of this project is the tightly coupled use of computational methods and detailed experimental characterization of PID. To this end, we will use WW domain as our PID system and generate artificially designed WW sequences based on their evolutionary and co-evolutionary inference of WW domain sequences. We will then characterize fold stability and binding affinity. This approach will enable us: (i) to identify co-evolved position pairs critical for the function and fold, (ii) to provide mechanistic insights on how the mutations in these co-evolved positions contribute to the fold/stability and binding specificity, (iii) to map sequence-structure-binding specificity(function) relationship of WW domains through iterative generation of functional artificial WW sequences, (iv) to provide design principles of artificially designed WW domains.
|Effective start/end date||8/1/16 → 7/31/19|
- NSF-ENG: Div Civil, Mech, Manufacturing Innovation (CMMI): $450,000.00
Protein Interaction Domains and Motifs
Protein Interaction Maps