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De novo enzyme design using Rosetta3
University of Washington, USA.
University of North Carolina, USA.
University of Washington, USA.
University of Washington, USA.
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2011 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 5Article in journal (Refereed) Published
Abstract [en]

The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest. The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction.

Place, publisher, year, edition, pages
2011. Vol. 6, no 5
National Category
Biochemistry and Molecular Biology
Research subject
Chemistry, Biochemistry
Identifiers
URN: urn:nbn:se:lnu:diva-50611DOI: 10.1371/journal.pone.0019230PubMedID: 21603656OAI: oai:DiVA.org:lnu-50611DiVA, id: diva2:911195
Available from: 2016-03-11 Created: 2016-03-11 Last updated: 2017-11-30Bibliographically approved

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Bjelic, Sinisa

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