Abstract
Reconstructing Evolutionary Adaptive Paths (REAP) is one of several methods to improve enzyme functionality. This approach incorporates computational and theoretical aspects of protein engineering to create a focused library of protein variety with a high degree of functionality. In contrast to other techniques like DNA shuffling, REAP allows a library to have diverse functionality among relatively few variants. REAP is a low-throughput method which takes advantage of natural selection and uses ancestral protein sequences to direct gene mutations, thereby creating a library with a high density of viable proteins. These proteins must then be assayed to characterize their functionality to identify which variants have the desired traits such as acid stability or thermostability.
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References
Cole MF, Gaucher EA (2011) Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol 72:193–203
Cole MF, Gaucher EA (2011) Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin Chem Biol 15:399–406
Fan Y, Fang W, Xiao Y et al (2007) Directed evolution for increased chitinase activity. Appl Microbiol Biotechnol 76:135–139
Chen F, Gaucher EA, Leal NA et al (2010) Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc Natl Acad Sci U S A 107:1948–1953
Benner SA, Gaucher EA (2001) Evolution, language and analogy in functional genomics. Trends Genet 17:414–418
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217
Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nat Rev Genet 13:303–314
Huelsenbeck JP, Ronquist F, Nielsen R et al (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314
Gaucher EA, Gu X, Miyamoto MM et al (2002) Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27:315–321
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591
Tawfik DS, Bershtein S, Goldin K (2008) Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 379:1029–1044
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Cole, M.F., Cox, V.E., Gratton, K.L., Gaucher, E.A. (2013). Reconstructing Evolutionary Adaptive Paths for Protein Engineering. In: Samuelson, J. (eds) Enzyme Engineering. Methods in Molecular Biology, vol 978. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-293-3_8
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DOI: https://doi.org/10.1007/978-1-62703-293-3_8
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Publisher Name: Humana Press, Totowa, NJ
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