Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program

By Sharon L. Guffy, Frank D. Teets, Minnie I Langlois, Brian Kuhlman. 2018

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We have developed a set of protocols in the molecular modeling program Rosetta for performing requirement-driven protein design. First, the user specifies a set of structural features that they wish to be present in the designed protein. These requirements can be general, e.g. create a protein with five helices, or they can be very specific and require the correct placement of a set of amino acids to bind a ligand. Next, a large set of protein models are generated that satisfy the design requirements. The models are built using a method we recently introduced into Rosetta, called SEWING, that rapidly assembles novel protein backbones by combining pieces of naturally occurring proteins. In the last step of the process, rotamer-based sequence optimization and backbone refinement are performed with Rosetta, and a variety of quality metrics are used to pick sequences for experimental characterization. Here, we describe the input files and user options needed to run SEWING and perform requirement-driven design, and provide detailed instructions for two specific applications of the process: the design of new structural elements at a protein-protein interface and the design of ligand binding sites.

Subfields: Materials Chemistry, Molecular Biology

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