Computational Introduction of Catalytic Activity into Proteins

Steve J Bertolani; Dylan Alexander Carlin; Justin B Siegel

doi:10.1007/978-1-4939-3569-7_13

Computational Introduction of Catalytic Activity into Proteins

Methods Mol Biol. 2016:1414:213-31. doi: 10.1007/978-1-4939-3569-7_13.

Authors

Steve J Bertolani¹, Dylan Alexander Carlin², Justin B Siegel^{3

4

5}

Affiliations

¹ Department of Chemistry, University of California Davis, One Shields Avenue, Davis, CA, USA.
² Biophysics Graduate Group, University of California Davis, One Shields Avenue, Davis, CA, USA.
³ Department of Chemistry, University of California Davis, One Shields Avenue, Davis, CA, USA. jbsiegel@ucdavis.edu.
⁴ Genome Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA. jbsiegel@ucdavis.edu.
⁵ Department of Biochemistry and Molecular Medicine, University of California Davis, One Shields Avenue, Davis, CA, USA. jbsiegel@ucdavis.edu.

PMID: 27094294
DOI: 10.1007/978-1-4939-3569-7_13

Abstract

Recently, there have been several successful cases of introducing catalytic activity into proteins. One method that has been used successfully to achieve this is the theozyme placement and enzyme design algorithms implemented in Rosetta Molecular Modeling Suite. Here, we illustrate how to use this software to recapitulate the placement of catalytic residues and ligand into a protein using a theozyme, protein scaffold, and catalytic constraints as input.

Keywords: De novo enzyme design; Enzyme design; Rosetta; Theozyme.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Catalysis
Crystallography, X-Ray
Models, Molecular
Proteins / chemistry
Proteins / metabolism*

Substances

Proteins