Emergence of polyproline II-like structure at early stages of experimental evolution from random polypeptides

Molecular Biology and Evolution

Volumn 25, Issue 6, 2008, Pages 1113-1119

  Toyota, Hitoshi ^a   Hosokawa, Masato ^a   Urabe, Itaru ^a   Yomo, Tetsuya ^a,b  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

DNA binding; Early evolution; Experimental evolution; Polyproline II; Random polypeptide

Indexed keywords

POLYPROLINE 2; PROLINE; PROLINE DERIVATIVE; UNCLASSIFIED DRUG; DNA; DNA BINDING PROTEIN; PEPTIDE; POLYPROLINE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; BACTERIOPHAGE; BINDING AFFINITY; DNA BINDING; GENE MUTATION; GENE SEQUENCE; MOLECULAR CLONING; NONHUMAN; PHYLOGENETIC TREE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; CATALYSIS; CHEMISTRY; CIRCULAR DICHROISM; CLASSIFICATION; DIRECTED MOLECULAR EVOLUTION; GENETICS; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; SURFACE PLASMON RESONANCE;

CATALYSIS; CIRCULAR DICHROISM; DIRECTED MOLECULAR EVOLUTION; DNA; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MUTATION; PEPTIDES; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; SURFACE PLASMON RESONANCE;

EID: 44649113997     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn063     Document Type: Article

References (30)

1. Adzhubei AA, Sternberg MJ. 1993. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol. 229:472-493.
2. Arakawa T, Jongsareejit B, Tatsumi Y, et al. (14 co-authors). 1996. Application of N-terminally truncated DNA polymerase from Thermus thermophilus (ΔTth polymerase) to DNA sequencing and polymerase chain reactions: comparative study of ΔTth and wild-type Tth polymerases. DNA Res. 3:87-92.
3. Bochicchio B, Tamburro AM. 2002. Polyproline II structure in proteins: identification by chiroptical spectroscopies, stability, and functions. Chirality. 14:782-792.
4. Cadwell RC, Joyce GF. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:28-33.
5. Choo Y, Castellanos A, Garcia-Hernandez B, Sanchez-Garcia I, Klug A. 1997. Promoter-specific activation of gene expression directed by bacteriophage-selected zinc fingers. J Mol Biol. 273:525-532.
6. Cubellis MV, Caillez F, Blundell TL, Lovell SC. 2005. Properties of polyproline II, a secondary structure element implicated in protein-protein interactions. Proteins. 58:880-892.
7. Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T. 2003. Can an arbitrary sequence evolve towards acquiring a biological function? J Mol Evol. 56:162-168.
8. Henry ER, Hofrichter J. 1992. Singular value decomposition: application to analysis of experimental data. Methods Enzymol. 210:129-192.
9. Hicks JM, Hsu VL. 2004. The extended left-handed helix: a simple nucleic acid-binding motif. Proteins. 55:330-338.
10. Hirel PH, Schmitter MJ, Dessen P, Fayat G, Blanquet S. 1989. Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. Proc Natl Acad Sci U S A. 86:8245-8251.
11. Ito Y, Kawama T, Urabe I, Yomo T. 2004. Evolution of an arbitrary sequence in solubility. J Mol Evol. 58:196-202.
12. James LC, Tawfik DS. 2003. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem Sci. 28:361-368.
13. Johnson CW. 1992. Analysis of circular dichroism spectra. Methods Enzymol. 210:426-447.
14. Keefe AD, Szostak JW. 2001. Functional proteins from a random-sequence library. Nature. 410:715-718.
15. Makarov AA, Lobachov VM, Adzhubei IA, Esipova NG. 1992. Natural polypeptides in left-handed helical conformation. A circular dichroism study of the linker histones' C-terminal fragments and β-endorphin. FEBS Lett. 306:63-65.
16. Marks JD, Hoogenboom HR, Bonnert TP, McCafferty J, Griffiths AD, Winter G. 1991. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J Mol Biol. 222:581-597.
17. McGhee JD, von Hippel PH. 1974. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 86:469-489.
18. Nakashima T, Ishiguro N, Yamaguchi M, Yamauchi A, Shima Y, Nozaki C, Urabe I, Yomo T. 2000. Construction and characterization of phage libraries displaying artificial proteins with random sequences. J Biosci Bioeng. 90:253-259.
19. Nakashima T, Toyota H, Urabe I, Yomo T. 2007. Effective selection system for experimental evolution of random polypeptides towards DNA-binding protein. J Biosci Bioeng. 103:155-160.
20. Nilsson P, Persson B, Uhlen M, Nygren PA. 1995. Real-time monitoring of DNA manipulations using biosensor technology. Anal Biochem. 224:400-408.
21. Prijambada ID, Yomo T, Tanaka F, Kawama T, Yamamoto K, Hasegawa A, Shima Y, Negoro S, Urabe I. 1996. Solubility of artificial proteins with random sequences. FEBS Lett. 382:21-25.
22. Saito S, Sasai M, Yomo T. 1997. Evolution of the folding ability of proteins through functional selection. Proc Natl Acad Sci USA. 94:11324-11328.
23. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
24. Sreerama N, Woody RW. 1994. Poly(pro)II helices in globular proteins: identification and circular dichroic analysis. Biochemistry. 33:10022-10025.
25. Suga Y, Yomo T, Urabe I. 1996. Heme content of catalase I from Bacillus stearothermophilus. J Ferment Bioeng. 81:259-261.
26. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599.
27. Uversky VN. 1993. Use of fast protein size-exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule. Biochemistry. 32:13288-13298.
28. Yamauchi A, Nakashima T, Tokuriki N, Hosokawa M, Nogami H, Arioka S, Urabe I, Yomo T. 2002. Evolvability of random polypeptides through functional selection within a small library. Protein Eng. 15:619-626.
29. Yamauchi A, Yomo T, Tanaka F, et al. (11 co-authors). 1998. Characterization of soluble artificial proteins with random sequences. FEBS Lett. 421:147-151.
30. Yomo T, Saito S, Sasai M. 1999. Gradual development of protein-like global structures through functional selection. Nat Struct Biol. 6:743-746.