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Chimeragenesis of distantly-related proteins by noncontiguous recombination

Smith, Matthew A. and Romero, Philip A. and Wu, Timothy and Brustad, Eric M. and Arnold, Frances H. (2013) Chimeragenesis of distantly-related proteins by noncontiguous recombination. Protein Science, 22 (2). pp. 231-238. ISSN 0961-8368. PMCID PMC3588919. doi:10.1002/pro.2202.

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We introduce a method for identifying elements of a protein structure that can be shuffled to make chimeric proteins from two or more homologous parents. Formulating recombination as a graph-partitioning problem allows us to identify noncontiguous segments of the sequence that should be inherited together in the progeny proteins. We demonstrate this noncontiguous recombination approach by constructing a chimera of β-glucosidases from two different kingdoms of life. Although the protein's alpha–beta barrel fold has no obvious subdomains for recombination, noncontiguous SCHEMA recombination generated a functional chimera that takes approximately half its structure from each parent. The X-ray crystal structure shows that the structural blocks that make up the chimera maintain the backbone conformations found in their respective parental structures. Although the chimera has lower β-glucosidase activity than the parent enzymes, the activity was easily recovered by directed evolution. This simple method, which does not rely on detailed atomic models, can be used to design chimeras that take structural, and functional, elements from distantly-related proteins.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Romero, Philip A.0000-0002-2586-7263
Brustad, Eric M.0000-0002-7031-5433
Arnold, Frances H.0000-0002-4027-364X
Additional Information:© 2012 The Protein Society. Received 3 October 2012; Revised 21 November 2012; Accepted 26 November 2012. Article first published online: 29 Dec. 2012. Grant sponsors: Institute for Collaborative Biotechnologies and US Army Research Office (Grant number: W911NF-09-D-0001); The National Central University, Taiwan (Cooperative Agreement for Energy Research Collaboration); Grant sponsor: Gordon and Betty Moore Foundation, the Beckman Institute and Caltech (the Sanofi-Aventis Bioengineering Research Program); Grant sponsor: US DOE and NIH (Beamline operations at SSRL); Grant sponsor: Resnick Sustainability Institute (fellowship; M.A.S.). The authors thank A. Wang of the Academia Sinica, Taiwan, for providing the TrBgl2 gene and T. Gloster and G. Davies of the University of York, UK, for providing the TmBglA gene. The authors also acknowledge the Molecular Observatory at Caltech for their support with X-ray crystallography. The content of the information in this document does not necessarily reflect the position or the policy of the sponsoring agencies, and no official endorsement should be inferred.
Group:Resnick Sustainability Institute
Funding AgencyGrant Number
Army Research Office (ARO)W911NF-09-D-0001
National Central University (Taiwan)UNSPECIFIED
Gordon and Betty Moore FoundationUNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
Resnick Sustainability InstituteUNSPECIFIED
Sanofi-Aventis Bioengineering Research ProgramUNSPECIFIED
Subject Keywords:chimeragenesis; protein recombination; eukaryotic-prokaryotic chimera; GH1; structural conservation; graph partitioning
Issue or Number:2
PubMed Central ID:PMC3588919
Record Number:CaltechAUTHORS:20130226-103727663
Persistent URL:
Official Citation:Smith, M. A., Romero, P. A., Wu, T., Brustad, E. M. and Arnold, F. H. (2013), Chimeragenesis of distantly-related proteins by noncontiguous recombination. Protein Science, 22: 231–238. doi: 10.1002/pro.2202
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:37144
Deposited On:26 Feb 2013 19:33
Last Modified:09 Nov 2021 23:27

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