Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

Protein Science

Volumn 19, Issue 4, 2010, Pages 786-795

  Tanaka, Junko ^a   Doi, Nobuhide ^a   Takashima, Hideaki ^a   Yanagawa, Hiroshi ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

In vitro selection; mRNA display; Primitive amino acids; Protein solubility; Random DNA library; Reduced alphabet

Indexed keywords

ALANINE; AMINO ACID; ARGININE; ASPARAGINE; ASPARTIC ACID; GLUTAMIC ACID; GLYCINE; ISOLEUCINE; LYSINE; MESSENGER RNA; METHIONINE; SERINE; THREONINE; VALINE;

AMINO ACID SEQUENCE; ARTICLE; BIOPHYSICS; FRAMESHIFT MUTATION; GENE FUNCTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RANDOM SEQUENCE PROTEIN; RANDOMIZATION; SCREENING; SOLUBILITY; STOP CODON;

AMINO ACID SEQUENCE; AMINO ACIDS; GENE LIBRARY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; RNA, MESSENGER; SOLUBILITY;

EID: 77950226805     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.358     Document Type: Article

References (38)

1. Mandecki W (1998) The game of chess and searches in protein sequence space. Trends Biotechnol 16:200-202.
2. Dryden DTF, Thomson AR, White JH (2008) How much of protein sequence space has been explored by life on earth? J R Soc Interface 5:953-956.
3. Wong JT (2005) Coevolution theory of the genetic code at age thirty. BioEssays 27:416-425.
4. Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22:1-11.
5. Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D (1997) Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol 4:805-809.
6. Silverman JA, Balakrishnan R, Harbury PB (2001) Reverse engineering the (a/b)8 barrel fold. Proc Natl Acad Sci USA 98:3092-3097.
7. Akanuma S, Kigawa T, Yokoyama S (2002) Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc Natl Acad Sci USA 99:13549-13553.
8. Walter KU, Vamvaca K, Hilvert D (2005) An active enzyme constructed from a 9-amino acid alphabet. J Biol Chem 280:37742-37746.
9. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262:1680-1685.
10. Go A, Kim S, Baum J, Hecht MH (2008) Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci 17:821-832.
11. Patel SC, Bradley LH, Jinadasa SP, Hecht MH (2009) Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins. Protein Sci 18:1388-1400.
12. Jumawid MT, Takahashi T, Yamazaki T, Ashigai H, Mihara H (2009) Selection and structural analysis of de novo proteins from an a3b3 genetic library. Protein Sci 18:384-398.
13. Mandecki W (1990) A method for construction of long randomized open reading frames and polypeptides. Protein Eng 3:221-226.
14. Yamauchi A, Yomo T, Tanaka F, Prijambada ID, Ohhashi S, Yamamoto K, Shima Y, Ogasahara K, Yutani K, Kataoka M, Urabe I (1998) Characterization of soluble artificial proteins with random sequences. FEBS Lett 421:147-151.
15. Keefe AD, Szostak JW (2001) Functional proteins from a random-sequence library. Nature 410:715-718.
16. Watters AL, Baker D (2004) Searching for folded proteins in vitro and in silico. Eur J Biochem 271:1615-1622.
17. Davidson AR, Sauer RT (1994) Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci USA 91:2146-2150.
18. Davidson AR, Lumb KJ, Sauer RT (1995) Cooperatively folded proteins in random sequence libraries. Nat Struct Biol 2:856-864.
19. Doi N, Kakukawa K, Oishi Y, Yanagawa H (2005) High solubility of random-sequence proteins consisting of five kinds of primitive amino acids. Protein Eng Des Sel 18:279-284.
20. Miyamoto-Sato E, Takashima H, Fuse S, Ishizaka M, Tateyama S, Horisawa K, Sawasaki T, Endo Y, Yanagawa H (2003) Highly stable and efficient mRNA templates for mRNA-protein fusions and C-terminally labeled proteins. Nucleic Acids Res 31:e78.
21. Cho G, Keefe AD, Liu R, Wilson DS, Szostak JW (2000) Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J Mol Biol 297:309-319.
22. Nemoto N, Miyamoto-Sato E, Husimi Y, Yanagawa H (1997) In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett 414:405-408.
23. Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA 94:12297-12302.
24. Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409.
25. Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255-258.
26. Wilkinson DL, Harrison RG (1991) Predicting the solubility of recombinant proteins in Escherichia coli. Biotechnology 9:443-448.
27. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132.
28. Shiraki K, Nishikawa K, Goto Y (1995) Trifluoroethanol-induced stabilization of the alpha-helical structure of beta-lactoglobulin: implication for non-hierarchical protein folding. J Mol Biol 245:180-194.
29. Stryer L (1965) The interaction of a naphthalene dye with apomyoglobin and apohemoglobin. A fluorescent probe of non-polar binding sites. J Mol Biol 13:482-495.
30. Vamvaca K, Vögeli B, Kast P, Pervushin K, Hilvert D (2004) An enzymatic molten globule: efficient coupling of folding and catalysis. Proc Natl Acad Sci USA 101:12860-12864.
31. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293:321-331.
32. Chaput JC, Szostak JW (2004) Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability. Chem Biol 11:865-874.
33. Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203-207.
34. Seelig B, Szostak JW (2007) Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448:828-831.
35. Taylor SV, Walter KU, Kast P, Hilvert D (2001) Searching sequence space for protein catalysts. Proc Natl Acad Sci USA 98:10596-10601.
36. Reetz MT, Kahakeaw D, Lohmer R (2008) Addressing the numbers problem in directed evolution. Chembiochem 9:1797-1804.
37. Wong JT, Evolution and mutation of the amino acid code. In: Ricard J, Cornish-Bowden A, Eds. (1984) Dynamics of biochemical systems. New York: Plenum Press, pp 247-257.
38. 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.