Computational Methods for Requirement-Driven Protein Design

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 DESCRIPTION (provided by applicant): Protein design is a rigorous test of our understanding of protein folding and stability, and a variety of design methods have been used to create proteins that have valuable applications in research and medicine. Almost all efforts in de novo protein design have been focused on creating idealized proteins composed of canonical structural elements. Examples include the design of coiled-coils, up-down helical bundles, and α/β proteins with very short connections between the secondary structural elements. These studies are excellent for exploring the minimal determinants of protein structure, but idealized structures may not be the most effective starting points for engineering novel protein functions. Functional sites in proteins are often located in pockets, grooves or loops that are created from assemblies of secondary structure that are not forming canonical or symmetric patterns. Here, we propose to create and test a computer-based strategy for designing proteins, called SEWING, that is not focused on creating a particular idealized structure, but rather can produce a diverse array of structures that all meet a set of predefined requirements. For instance, in one of our specific aims we will require that all the designs contain functional EF-hand calcium-binding sites, but beyond this requirement there will not be predefined goals for the final tertiar structures of the proteins. With SEWING, tertiary structures are assembled from structural motifs found in naturally occurring proteins. Motifs can be continuous or discontinuous in primary sequence, and generally contain two or three elements of secondary structure. Motifs are stitched together by superimposing regions of structural similarity in two motifs. Advantages of this approach include the use of building blocks that are inherently designable and the ability to incorporate functional motifs from naturally occurring proteins, for instance protein and ligand binding sites. To explore the utility of SEWING we will pursue several design goals including: the creation of helical bundles with diverse structural features such as clefts and binding pockets, embedding functional motifs in proteins to create protein binders, and creating proteins that contain multiple binding sites.