Extension of a de novo TIM barrel with a rationally designed secondary structure element. (20th March 2021)

• Record Type: Journal Article
• Authors: Wiese, Jonas Gregor; Shanmugaratnam, Sooruban; Höcker, Birte
• Is Part Of: Protein science. Volume 30:Number 5(2021)
• Page Start: 982
• Page End: 989
• Publication Date: 2021-03-20
• Subjects: (βα)8‐barrel -- ab initio folding -- computational protein design -- enzyme design -- sTIM11 -- TIM barrel; Proteins -- Periodicals; 572.6
• DOI: 10.1002/pro.4064
• Languages: English
• ISSNs: 0961-8368

Abstract

Abstract: 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. Abstract : PDB Code(s): 7A8S ;