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Publication Abstract from PubMed

The ability to construct novel enzymes is a major aim in de novo protein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recent de novo design of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a short de novo helix on top of the barrel. Due to the size of the protein, we developed a design pipeline based on computational ab initio folding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites.

Extension of a de novo TIM barrel with a rationally designed secondary structure element.,Wiese JG, Shanmugaratnam S, Hocker B Protein Sci. 2021 Mar 15. doi: 10.1002/pro.4064. PMID:33723882^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.