Literature DB >> 26055155

Methods for the directed evolution of proteins.

Michael S Packer1, David R Liu1.   

Abstract

Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.

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Year:  2015        PMID： 26055155     DOI： 10.1038/nrg3927

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  133 in total

1.  Directed evolution of the peroxidase activity of a de novo-designed protein.

Authors:  Shona C Patel; Michael H Hecht
Journal:  Protein Eng Des Sel       Date:  2012-06-03       Impact factor: 1.650

Review 2.  Macromolecular modeling with rosetta.

Authors:  Rhiju Das; David Baker
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

3.  A general strategy for the evolution of bond-forming enzymes using yeast display.

Authors:  Irwin Chen; Brent M Dorr; David R Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-22       Impact factor: 11.205

4.  Mutagenic repair in Escherichia coli: products of the recA gene and of the umuD and umuC genes act at different steps in UV-induced mutagenesis.

Authors:  B A Bridges; R Woodgate
Journal:  Proc Natl Acad Sci U S A       Date:  1985-06       Impact factor: 11.205

5.  A de novo protein binding pair by computational design and directed evolution.

Authors:  John Karanicolas; Jacob E Corn; Irwin Chen; Lukasz A Joachimiak; Orly Dym; Sun H Peck; Shira Albeck; Tamar Unger; Wenxin Hu; Gaohua Liu; Scott Delbecq; Gaetano T Montelione; Clint P Spiegel; David R Liu; David Baker
Journal:  Mol Cell       Date:  2011-03-31       Impact factor: 17.970

Review 6.  Luminogenic cytochrome P450 assays.

Authors:  James J Cali; Dongping Ma; Mary Sobol; Daniel J Simpson; Susan Frackman; Troy D Good; William J Daily; David Liu
Journal:  Expert Opin Drug Metab Toxicol       Date:  2006-08       Impact factor: 4.481

7.  A novel genetic system to detect protein-protein interactions.

Authors:  S Fields; O Song
Journal:  Nature       Date:  1989-07-20       Impact factor: 49.962

8.  Molecular evolution by staggered extension process (StEP) in vitro recombination.

Authors:  H Zhao; L Giver; Z Shao; J A Affholter; F H Arnold
Journal:  Nat Biotechnol       Date:  1998-03       Impact factor: 54.908

9.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

10.  Rewiring yeast sugar transporter preference through modifying a conserved protein motif.

Authors:  Eric M Young; Alice Tong; Hang Bui; Caitlin Spofford; Hal S Alper
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-16       Impact factor: 11.205
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  196 in total

1.  How mutational epistasis impairs predictability in protein evolution and design.

Authors:  Charlotte M Miton; Nobuhiko Tokuriki
Journal:  Protein Sci       Date:  2016-01-22       Impact factor: 6.725

2.  Directed evolution methods for overcoming trade-offs between protein activity and stability.

Authors:  Samuel D Stimple; Matthew D Smith; Peter M Tessier
Journal:  AIChE J       Date:  2019-10-09       Impact factor: 3.993

3.  Evolution of a split RNA polymerase as a versatile biosensor platform.

Authors:  Jinyue Pu; Julia Zinkus-Boltz; Bryan C Dickinson
Journal:  Nat Chem Biol       Date:  2017-02-13       Impact factor: 15.040

4.  Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning.

Authors:  Derek M Mason; Simon Friedensohn; Cédric R Weber; Christian Jordi; Bastian Wagner; Simon M Meng; Roy A Ehling; Lucia Bonati; Jan Dahinden; Pablo Gainza; Bruno E Correia; Sai T Reddy
Journal:  Nat Biomed Eng       Date:  2021-04-15       Impact factor: 25.671

5.  Natural selection in compartmentalized environment with reshuffling.

Authors:  A S Zadorin; Y Rondelez
Journal:  J Math Biol       Date:  2019-07-13       Impact factor: 2.259

6.  Tools and systems for evolutionary engineering of biomolecules and microorganisms.

Authors:  Sungho Jang; Minsun Kim; Jaeseong Hwang; Gyoo Yeol Jung
Journal:  J Ind Microbiol Biotechnol       Date:  2019-05-27       Impact factor: 3.346

7.  Evolve and survive.

Authors:  Alena Pance
Journal:  Nat Rev Microbiol       Date:  2017-03-27       Impact factor: 60.633

8.  Polyclonal Antibodies in Microplates to Predict the Maximum Adsorption Activities of Enzyme/Mutants from Cell Lysates.

Authors:  Yiran Feng; Xiaolan Yang; Deqiang Wang; Xiaolei Hu; Huimin Chong; Juan Liao; Chang-Guo Zhan; Fei Liao
Journal:  Protein J       Date:  2017-06       Impact factor: 2.371

Review 9.  Biomolecular engineering for nanobio/bionanotechnology.

Authors:  Teruyuki Nagamune
Journal:  Nano Converg       Date:  2017-04-24

10.  Multiple mechanisms contribute to increased neutral lipid accumulation in yeast producing recombinant variants of plant diacylglycerol acyltransferase 1.

Authors:  Yang Xu; Guanqun Chen; Michael S Greer; Kristian Mark P Caldo; Geetha Ramakrishnan; Saleh Shah; Limin Wu; M Joanne Lemieux; Jocelyn Ozga; Randall J Weselake
Journal:  J Biol Chem       Date:  2017-09-12       Impact factor: 5.157
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