Computationally focusing the directed evolution of proteins - PubMed (original) (raw)
Review
Computationally focusing the directed evolution of proteins
C A Voigt et al. J Cell Biochem Suppl. 2001.
Abstract
Directed evolution has proven to be a successful strategy for the modification of enzyme properties. To date, the preferred experimental procedure has been to apply mutations or crossovers randomly throughout the gene. With the emergence of powerful computational methods, it has become possible to develop focused combinatorial searches, guided by computer algorithms. Here, we describe several computational methods that have emerged to aid the optimization of mutant libraries, the targeting of specific residues for mutagenesis, and the design of recombination experiments.
Copyright 2002 Wiley-Liss, Inc.
Similar articles
- Fast and Flexible Synthesis of Combinatorial Libraries for Directed Evolution.
Sadler JC, Green L, Swainston N, Kell DB, Currin A. Sadler JC, et al. Methods Enzymol. 2018;608:59-79. doi: 10.1016/bs.mie.2018.04.006. Epub 2018 May 24. Methods Enzymol. 2018. PMID: 30173773 - Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries.
Wong TS, Roccatano D, Schwaneberg U. Wong TS, et al. Environ Microbiol. 2007 Nov;9(11):2645-59. doi: 10.1111/j.1462-2920.2007.01411.x. Environ Microbiol. 2007. PMID: 17922750 Review. - Advances in generating functional diversity for directed protein evolution.
Shivange AV, Marienhagen J, Mundhada H, Schenk A, Schwaneberg U. Shivange AV, et al. Curr Opin Chem Biol. 2009 Feb;13(1):19-25. doi: 10.1016/j.cbpa.2009.01.019. Epub 2009 Mar 2. Curr Opin Chem Biol. 2009. PMID: 19261539 Review. - Combination of computational prescreening and experimental library construction can accelerate enzyme optimization by directed evolution.
Funke SA, Otte N, Eggert T, Bocola M, Jaeger KE, Thiel W. Funke SA, et al. Protein Eng Des Sel. 2005 Nov;18(11):509-14. doi: 10.1093/protein/gzi062. Epub 2005 Oct 3. Protein Eng Des Sel. 2005. PMID: 16203748 - Combinatorial Evolution of DNA with RECODE.
Kang Z, Ding W, Jin P, Du G, Chen J. Kang Z, et al. Methods Mol Biol. 2018;1772:205-212. doi: 10.1007/978-1-4939-7795-6_11. Methods Mol Biol. 2018. PMID: 29754230
Cited by
- Computationally mapping sequence space to understand evolutionary protein engineering.
Armstrong KA, Tidor B. Armstrong KA, et al. Biotechnol Prog. 2008 Jan-Feb;24(1):62-73. doi: 10.1021/bp070134h. Epub 2007 Nov 17. Biotechnol Prog. 2008. PMID: 18020358 Free PMC article. - Structural and functional roles of coevolved sites in proteins.
Chakrabarti S, Panchenko AR. Chakrabarti S, et al. PLoS One. 2010 Jan 6;5(1):e8591. doi: 10.1371/journal.pone.0008591. PLoS One. 2010. PMID: 20066038 Free PMC article. - Model-guided mechanism discovery and parameter selection for directed evolution.
Stainbrook SC, Tyo KEJ. Stainbrook SC, et al. Appl Microbiol Biotechnol. 2019 Dec;103(23-24):9697-9709. doi: 10.1007/s00253-019-10179-5. Epub 2019 Nov 4. Appl Microbiol Biotechnol. 2019. PMID: 31686141 Free PMC article. - Expanding the nucleotide and sugar 1-phosphate promiscuity of nucleotidyltransferase RmlA via directed evolution.
Moretti R, Chang A, Peltier-Pain P, Bingman CA, Phillips GN Jr, Thorson JS. Moretti R, et al. J Biol Chem. 2011 Apr 15;286(15):13235-43. doi: 10.1074/jbc.M110.206433. Epub 2011 Feb 11. J Biol Chem. 2011. PMID: 21317292 Free PMC article. - Computational design of affinity and specificity at protein-protein interfaces.
Karanicolas J, Kuhlman B. Karanicolas J, et al. Curr Opin Struct Biol. 2009 Aug;19(4):458-63. doi: 10.1016/j.sbi.2009.07.005. Epub 2009 Jul 29. Curr Opin Struct Biol. 2009. PMID: 19646858 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources