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Extension of a de novo TIM barrel with a rationally designed secondary structure element

DOI zum Zitieren der Version auf EPub Bayreuth: https://doi.org/10.15495/EPub_UBT_00005976
URN to cite this document: urn:nbn:de:bvb:703-epub-5976-3

Title data

Wiese, Jonas Gregor ; Shanmugaratnam, Sooruban ; Höcker, Birte:
Extension of a de novo TIM barrel with a rationally designed secondary structure element.
In: Protein Science. Vol. 30 (May 2021) Issue 5 . - pp. 982-989.
ISSN 1469-896X
DOI der Verlagsversion: https://doi.org/10.1002/pro.4064

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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.

Further data

Item Type: Article in a journal
Keywords: (βα)8-barrel; TIM barrel; ab initio folding; computational protein design; enzyme design; sTIM11
DDC Subjects: 500 Science > 500 Natural sciences
500 Science > 570 Life sciences, biology
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry > Chair Biochemistry - Univ.-Prof. Dr. Birte Höcker
Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry
Language: English
Originates at UBT: Yes
URN: urn:nbn:de:bvb:703-epub-5976-3
Date Deposited: 09 Feb 2022 09:15
Last Modified: 09 Feb 2022 09:15
URI: https://epub.uni-bayreuth.de/id/eprint/5976

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