Amino acid alphabet size in protein evolution experiments: Better to search a small library thoroughly or a large library sparsely?

Protein Engineering, Design and Selection

Volumn 21, Issue 5, 2008, Pages 311-317

  Muñoz, Enrique ^a,b   Deem, Michael W ^a,b  

^a Rice University   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

Antibody engineering; Directed evolution; Generalized NK model; Protein engineering; Reduced amino acid code

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; EXPERIMENTS; LIBRARIES; MODELS; ORGANIC ACIDS;

ALPHABET-SIZE; ANTIBODY ENGINEERING; CELL SELECTION; DIRECTED EVOLUTION; GENERALIZED NK MODEL; HUMAN ANTIBODIES; PHYSICAL MODEL; PROTEIN ENGINEERING; PROTEIN EVOLUTION; REDUCED AMINO ACID CODE;

ANTIBODIES;

AMINO ACID; ABC TRANSPORTER; CDR3 PROTEIN, CANDIDA ALBICANS; PEPTIDE LIBRARY; PROTEIN;

AMINO ACID SEQUENCE; ANTIBODY ENGINEERING; ARTICLE; EVOLUTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; SIMULATION; T LYMPHOCYTE; CHEMISTRY; COMPUTER SIMULATION; ENTROPY; GENE LIBRARY; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL;

AMINO ACIDS; ATP-BINDING CASSETTE TRANSPORTERS; COMPUTER SIMULATION; ENTROPY; EVOLUTION, MOLECULAR; GENE LIBRARY; MODELS, STATISTICAL; MONTE CARLO METHOD; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SACCHAROMYCES CEREVISIAE; T-LYMPHOCYTES;

EID: 48849109693     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzn007     Document Type: Article

References (39)

1. Anderson,J.C., Wu,N., Santoro,S.W., Lakshman,V., King,D.S. and Schultz,P.G. (2004) Proc. Natl Acad. Sci. USA, 101, 7566-7571.
2. Barbas,C.F. III, Kang,A.S., Lerner,R.A. and Benkovic,S.J. (1991) Proc. Natl Acad. Sci. USA, 88, 7978-7982.
3. Boder,E.T., Midelfort,K.S. and Wittrup,K.D. (2000) Proc. Natl Acad. Sci. USA, 97, 10701-10705.
4. Bogarad,L.D. and Deem,M.W. (1999) Proc. Natl Acad. Sci. USA, 96, 2591-2595.
5. Chemla,Y.R., Grossman,H.L., Poon,Y., McDermott,R., Stevens,R., Alper,M.D. and Clarke,J. (2000) Proc. Natl Acad. Sci. USA, 97, 14268-14272.
6. Collis,A.V.J., Brouwer,A.P. and Martin,A.C.R. (2003) J. Mol. Biol., 325, 337-354.
7. Deem,M.W. and Lee,H.Y. (2003) Phys. Rev. Lett., 91, 068101.
8. Earl,D.J. and Deem,M.W. (2004) Proc. Natl Acad. Sci. USA, 101, 11531-11536.
9. Fellouse,F.A., Wiesmann,C. and Sidhu,S.S. (2004) Proc. Natl Acad. Sci. USA, 101, 12467-12472.
10. Fellouse,F.A., Li,B., Compaan,D.M., Peden,A.A., Hymowitz,S.G. and Sidhu,S.S. (2005) J. Mol. Biol., 348, 1153-1162.
11. Fellouse,F.A., Barthelemy,P.A., Kelley,R.F. and Sidhu,S.S. (2006) J. Mol. Biol., 357, 100-114.
12. Gold,L. (2001) Proc. Natl Acad. Sci. USA, 98, 4825-4826.
13. Grossman,H.L., Myers,W.R., Vreeland,V.J., Bruehl,R., Alper,M.D., Bertozzi,C.R. and Clarke,J. (2004) Proc. Natl Acad. Sci. USA, 101, 129-134.
14. Gupta,V., Earl,D.J. and Deem,M.W. (2006) Vaccine, 24, 3881-3888.
15. Hanes,J. and Plückthun,A. (1997) Proc. Natl Acad. Sci. USA, 94, 4937-4942.
16. Hoogenboom,H.R. (2005) Nat. Biotechol., 23, 1105-1116.
17. Jung,S.T., Jeong,K.J., Iverson,B.L. and Georgiou,G. (2007) Biotechnol. Bioeng., 98, 39-47.
18. Kabat,E.A., Wu,T.T. and Bilofsky,H. (1977) J. Biol. Chem., 252, 6609-6616.
19. Kawarasaki,Y., Griswold,K., Stevenson,J.D., Selzer,T., Benkovic,S.J., Iverson,B.L. and Georgiou,G. (2003) Nucleic Acids Res., 31, E126.
20. Kozel,T.R., Murphy,W.J., Brandt,S., Blazar,B.R., Lovchik,J.A., Thorkildson,P., Percival,A. and Lyons,C.R. (2004) Proc. Natl Acad. Sci. USA, 101, 5042-5047.
21. Layzer,D. (1990) Cosmogenesis: the Growth of Order in the Universe. Oxford University Press, New York.
22. Link,A.J., Jeong,J.K. and Georgiou,G. (2007) Nat. Rev. Microbiol., 5, 680-688.
23. Marshall,A., DeFrancesco,L., Aschheim,K., Taroncher-Oldenburg,G., Francisco,M., Hare,P., Louët,S. and Theunissen,J.W. (2005) Nat. Biotechol., 23, 1025.
24. Park,J.M. and Deem,M.W. (2004) Phys. A, 341, 455-470.
25. Ptitsyn,O.B. and Volkenstein,M.V. (1986) J. Biomol. Struct. Dynamics, 4, 137-156.
26. Saleh,O.A. and Sohn,L.L. (2003) Proc. Natl Acad. Sci. USA, 100, 820-824.
27. Schweitzer,B., Wiltshire,S., Lambert,J., O'Malley,S., Kukanskis,K., Zhu,Z., Kingsmore,S.F., Lizardi,P.M. and Ward,D.C. (2000) Proc. Natl Acad. Sci. USA, 97, 10113-10119.
28. Shakhnovich,E. (2006) Chem. Rev., 106, 1559-1588.
29. Shannon,C.E. (1948) Bell Syst. Tech., 27, 623-656.
30. Stȧhl,S. and Uhlén,M. (1997) Trends Biotechnol., 15, 185-192.
31. Tan,T., Bogarad,L.D. and Deem,M.W. (2004) J. Mol. Evol., 59, 385-399.
32. Tian,F., Tsao,M.L. and Schultz,P.G. (2004) J. Am. Chem. Soc., 126, 15962-15963.
33. van Hest,J.C.M., Kiick,K.L. and Tirrell,D.A. (2000) J. Am. Chem. Soc., 122, 1282-1288.
34. Wilson,D.S., Keefe,A.D. and Szostak,J.W. (2001) Proc. Natl Acad. Sci. USA, 98, 3750-3755.
35. Winter,G., Griffiths,A.D., Hawkins,R.E. and Hoogenboom,H.R. (1994) Ann. Rev. Immunol., 12, 433-455.
36. Yang,C.Y., Brooks,E., Li,Y., Denny,P., Ho,C.M., Qi,F., Shi,W., Wolinsky,L., Wu,B.,Wong,D.T.W. and Montemagno,C.D. (2005) Lab Chip, 5, 1017-1023.
37. Zemlin,M., Klinger,M., Link,J., Zemlin,C., Bauer,K., Engler,J.A., Schroeder,H.W.J. and Kirkham,P.M. (2003a) J. Mol. Biol., 334, 733-749.
38. Zemlin,M., Klinger,M., Link,J., Zemlin,C., Bauer,K., Engler,J.A., Schroeder,H.W.J. and Kirkham,P.M. (2003b) J. Mol. Biol., 334, 733-749, data available at doi: 10.1016/j.jmb.2003.10.007.
39. Zhou,H. and Deem,M.W. (2006) Vaccine, 24, 2451-2459.