Engineering new RNA-binding proteins by selection and design

University Of Washington, Seattle WA

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Abstract

RNA-binding proteins perform essential functions in every aspect of RNA biogenesis. These functions are a fundamental aspect of basic cellular physiology, and numerous human diseases arise from defects in the function of these proteins. The biological activity of the very numerous RNA-coding genes in higher eukaryotes also rely on their interaction with RNA-binding proteins responsible for their biogenesis and localization. A detailed understanding of how these proteins function in RNA metabolism is therefore central to understanding gene expression and its regulation. In turn, this goal requires understanding the molecular basis for the specificity of relatively few but ubiquitous RNA-binding protein domains. Understanding protein specificity means to be able to predict what RNA a protein binds to from its sequence and structure, and to re-direct the specificity of that protein by rational methods. By designing proteins with new specificity, we would not only understand the function of these proteins to an unprecedented level, but would also generate new activities to control gene expression. These are our goals, and we propose to use new computational approaches conjointly with experimental methods to achieve them. Specifically, we propose to: 1. Evaluate our ability to predict the specificity of RNA-binding proteins using new experimental methods 2. Develop existing potential functions for protein-RNA interfaces to incorporate the contribution of protein-protein interactions and protein side chain flexibility 3. Alter the specificity of paradigmatic RNA-binding proteins using in vitro evolution conjointly with rational protein design methods We are not aware of any other sustained effort at using computational and experimental methods conjointly to predict the specificity of RNA-binding proteins and to design proteins with new activity.