Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins

Journal of Molecular Biology

Volumn 350, Issue 4, 2005, Pages 806-816

  Drummond, D Allan ^a   Iverson, Brent L ^b   Georgiou, George ^c   Arnold, Frances H ^d  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c The University of Texas at Austin   (United States)

^d California Institute of Technology   (United States)

Author keywords

Mutagenesis; Neutrality; Optimal mutation rate; PCR; Poisson distribution

Indexed keywords

AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; GENE LIBRARY; MUTAGENESIS; MUTATION; MUTATION RATE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS MODEL; PROTEIN FUNCTION; WILD TYPE;

EID: 20544449855     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.05.023     Document Type: Article

References (25)

1. J. Maynard Smith Natural selection and the concept of a protein space Nature 225 1970 563 564
2. M. Suzuki, F.C. Christians, B. Kim, A. Skandalis, M.E. Black, and L.A. Loeb Tolerance of different proteins for amino acid diversity Mol. Divers. 2 1996 111 118
3. P.S. Daugherty, G. Chen, B.L. Iverson, and G. Georgiou Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies Proc. Natl Acad. Sci. USA 97 2000 2029 2034
4. S. Shafikhani, R.A. Siegel, E. Ferrari, and V. Schellenberger Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization Biotechniques 23 1997 304 310
5. J.D. Bloom, J.J. Silberg, C.O. Wilke, D.A. Drummond, C. Adami, and F.H. Arnold Thermodynamic prediction of protein neutrality Proc. Natl Acad. Sci. USA 102 2005 606 611
6. F.H. Arnold Enzyme engineering reaches the boiling point Proc. Natl Acad. Sci. USA 95 1998 2035 2036
7. G. Georgiou Analysis of large libraries of protein mutants using flow cytometry Advan. Protein Chem. 55 2001 293 315
8. K. Kunichika, Y. Hashimoto, and T. Imoto Robustness of hen lysozyme monitored by random mutations Protein Eng. 15 2002 805 809
9. M. Zaccolo, and E. Gherardi The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase J. Mol. Biol. 285 1999 775 783
10. C.O. Wilke, and C. Adami Interaction between directional epistasis and average mutational effects Proc. Roy. Soc. ser. B 268 2001 1469 1474
11. S.F. Elena, and R.E. Lenski Epistasis between new mutations and genetic background and a test of genetic canalization Evol. Int. J. Org. Evol. 55 2001 1746 1752
12. A.S. Kondrashov Deleterious mutations and the evolution of sexual reproduction Nature 336 1988 435 440
13. J.A. Francisco, R. Campbell, B.L. Iverson, and G. Georgiou Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface Proc. Natl Acad. Sci. USA 90 1993 10444 10448
14. F. Sun The polymerase chain reaction and branching processes J. Comput. Biol. 2 1995 63 86
15. G. Weiss, and A. von Haeseler Modeling the polymerase chain reaction J. Comput. Biol. 2 1995 49 61
16. G. Weiss, and A. von Haeseler A coalescent approach to the polymerase chain reaction Nucl. Acids Res. 25 1997 3082 3087
17. E. Bornberg-Bauer, and H.S. Chan Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space Proc. Natl Acad. Sci. USA 96 1999 10689 91064
18. D.A. Drummond, J.J. Silberg, C.O. Wilke, and F.H. Arnold On the conservative nature of intragenic recombination Proc. Natl Acad. Sci. USA 102 2005 5380 5385
19. M. Fromant, S. Blanquet, and P. Plateau Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction Anal. Biochem. 224 1995 347 353
20. P. Flajolet, F. Gardy, and L. Thimonier Birthday paradox, coupon collectors, caching algorithms, and self-organizing search Discrete Appl. Mathematics 39 1992 207 229
21. G.L. Moore, and C.D. Maranas Modeling DNA mutation and recombination for directed evolution experiments J. Theoret. Biol. 205 2000 483 503
22. M. Zaccolo, D.M. Williams, D.M. Brown, and E. Gherardi An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues J. Mol. Biol. 255 1996 589 603
23. M.F. Goodman Error-prone repair DNA polymerases in prokaryotes and eukaryotes Annu. Rev. Biochem. 71 2002 17 50
24. A. Crameri, S.A. Raillard, E. Bermudez, and W.P. Stemmer DNA shuffling of a family of genes from diverse species accelerates directed evolution Nature 391 1998 288 291
25. T.D. Andrews, and T. Gojobori Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis Genetics 166 2004 25 32