Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules

Proteins: Structure, Function and Genetics

Volumn 67, Issue 4, 2007, Pages 821-833

  Shirai, Kumiko ^a   Yamazaki, Yoichi ^a   Kamikubo, Hironari ^a   Imamoto, Yasushi ^a   Kataoka, Mikio ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Chimeric protein; Circular dichroism; Information redundancy; Photoreceptor protein; Secondary structure prediction; Trifluoroethanol

Indexed keywords

ASPARTIC ACID; CHIMERIC PROTEIN; CYSTEINE; GLYCINE; LYSINE; METHIONINE; PHENYLALANINE; PHOTOACTIVE YELLOW PROTEIN; PROLINE; SERINE; VALINE;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CIRCULAR DICHROISM; HYDROPHILICITY; HYDROPHOBICITY; INFORMATION SCIENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; WILD TYPE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CIRCULAR DICHROISM; COMPUTATIONAL BIOLOGY; GENE EXPRESSION; MOLECULAR SEQUENCE DATA; MUTATION; PHOTORECEPTORS, MICROBIAL; PROTEIN DENATURATION; RECOMBINANT PROTEINS; SOLUTIONS; THERMODYNAMICS; UREA;

EID: 34248598352     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21331     Document Type: Article

References (46)

1. Dobson CM. Protein folding and misfolding. Nature 2003;426:884-890.
2. Kuroda Y, Kim PS. Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine. J Mol Biol 2000;298:493-501.
3. Brown BM, Sauer RT. Tolerance of arc repressor to multiple-alanine substitutions. Proc Natl Acad Sci USA 1999;96:1983-1988.
4. Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol 1997;4:805-809.
5. Yi Q, Rajagopal P, Klevit RE, Baker D. Structural and kinetic characterization of the simplified SH3 domain FP1. Protein Sci 2003;12:776-783.
6. Akanuma S, Kigawa T, Yokoyama S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc Natl Acad Sci USA 2002;99:13549-13553.
7. Meyer TE. Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. Biochim Biophys Acta 1985;806:175-183.
8. Pellequer J, Wager-Smith KA, Kay SA, Getzoff ED. Photoactive yellow protein: a structural prototypes for the three-dimensional fold of the PAS domain superfamily. Proc Natl Acad Sci USA 1998;95:5884-5890.
9. Ponting CP, Aravind L. PAS: a multifunctional domain family comes to light. Curr Biol 1997;7:R674-R677.
10. Cusanovich MA, Meyer TE. Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism. Biochemistry 2003;42:4759-4770.
11. Crosson S, Moffat K. Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction. Proc Natl Acad Sci USA 2001;98:2995-3000.
12. Borgstahl GE, Williams DR, Getzoff ED. 1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry 1995;34:6278-6287.
13. Baca M, Borgstahl GEO, Boissinot M, Burke PM, Williams DR, Slater KA, Getzoff ED. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry 1994;33:14369-14377.
14. Koh M, van Driessche G, Samyn B, Hoff WD, Meyer TE, Cusanovich MA, van Beeumen JJ. Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens. Biochemistry 1996;35:2526-2534.
15. Jiang Z, Swem LR, Rushing BG, Devanathan S, Tollin G, Bauer CE. Bacterial photoreceptor with similarity to photoactive yellow protein and plant phytochromes. Science 1999;285:406-409.
16. Kort R, Hoff WD, van West M, Kroon AR, Hoffer SM, Vlieg KH, Crielaard W, van Beeumen JJ, Hellingwerf KJ. The xanthopsins: a new family of eubacterial blue-light photoreceptors. EMBO J 1996;15:3209-3218.
17. Jiang Z, Bauer CE. Genetic characterization of photoactive yellow protein from Rhodobacter capsulatus. Direct submission to GenBank; accession no. AF064095; 1998.
18. Prodromou C, Pearl LH. Recursive PCR: a novel technique for total gene synthesis. Protein Eng 1992;5:827-829.
19. Edge MD, Greene AR, Heathcliffe GR, Meacock PA, Schuch W, Scanlon DB, Atkinson TC, Newton CR, Markham AF. Total synthesis of a human leukocyte interferon gene. Nature 1981;292:756-762.
20. Ferretti L, Karnik SS, Khorana HG, Nassal M, Oprian DD. Total synthesis of a gene for bovine rhodopsin. Proc Natl Acad Sci USA 1986;83:599-603.
21. Imamoto Y, Ito T, Kataoka M, Tokunaga F. Reconstitution photoactive yellow protein from apoprotein and p-coumaric acid derivatives. FEBS Lett 1995;374:157-160.
22. Mihara K, Hisatomi O, Imamoto Y, Kataoka M, Tokunaga F. Functional expression and site-directed mutagenesis of photoactive yellow protein. J Biochem 1997;121:876-880.
23. Sreerama N, Woody RW. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 2000;287:252-260.
24. Frishman D, Argos P. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 1996;9:133-142.
25. Ohishi S, Shimizu N, Mihara K, Imamoto Y, Kataoka M. Light induced destabilization of photoactive yellow protein. Biochemistry 2001;40:2854-2859.
26. Shiraki K, Nishikawa K, Goto Y. Trifluoroethanol-induced stabilization of the α-helical structure of β-lactoglobulin: implication for non-hierarchical protein folding. J Mol Biol 1995;245:180-194.
27. Hirota N, Mizuno K, Goto Y. Cooperative α-helix formation of β-lactoglobulin and melittin induced by hexafluoroisopropanol. Protein Sci 1997;6:416-421.
28. Hamada D, Chiti F, Guijarro JI, Kataoka M, Taddei N, Dobson CM. Evidence concerning rate-limiting steps in protein folding from the effects of trifluoroethanol. Nat Struct Biol 2000;7:58-61.
29. Imamoto Y, Koshimizu H, Mihara K, Hisatomi O, Mizukami T, Tsuijimoto K, Kataoka M, Tokunaga F. Roles of amino acid residues near the chromophore of photoactive yellow protein. Biochemistry 2001;40:4679-4685.
30. Meyer TE, Devanathan S, Woo T, Getzoff ED, Tollin G, Cusanovich MA. Site-specific mutations provide new insights into the origin of pH effects and alternative spectral forms in the photoactive yellow protein. Biochemistry 2003;42:3319-3325.
31. Kyndt JA, Vanrobaeys FV, Fitch JC, Devreese BV, Meyer TE, Cusanovich MA, van Beeumen JJ. Heterologous production of Halorhodospira halophila holo-photoactive yellow protein through tandem expression of the postulated biosynthetic genes. Biochemistry 2003;42:965-970.
32. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometric features. Biopolymers 1983;22:2577-2637.
33. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM. Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc Natl Acad Sci USA 1999;96:3590-3594.
34. Taylor SV, Walter KU, Kast P, Hilvert D. Searching sequence space for protein catalysts. Proc Natl Acad Sci USA 2001;98:10596-10601.
35. Walter KU, Vamvaca K, Hilvert D. An active enzyme constructed from a 9-amino acid alphabet. J Biol Chem 2005;280:37742-37746.
36. Yamauchi A, Yomo T, Tanaka F, Prijambada ID, Ohhashi S, Yamamoto K, Shima Y, Ogasahara K, Yutani K, Kataoka M, Urabe I. Characterization of soluble artificial proteins with random sequence. FEBS Lett 1998;421:147-151.
37. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH. Protein design by binary patterning of polar and nonpolar amino acids. Science 1993;262:1680-1685.
38. Beasley JR, Hecht MH. Protein design: the choice of the de novo sequences. J Biol Chem 1997;272:2031-2034.
39. Hecht MH, Das A, Go A, Bradley LH, Wei Y. De novo proteins from designed combinatorial libraries, Protein Sci 2004;13:1711-1723.
40. 8 barrel fold. Proc Natl Acad Sci USA 2001;98:3092-3097.
41. Harigai M, Yasuda S, Imamoto Y, Yoshihisa K, Tokunaga F, Kataoka M. Amino acids in the N-terminal region regulate the photocycle of photoactive yellow protein. J Biochem 2001;130:51-56.
42. Vreede J, van der Horst MA, Hellingwerf KJ, Crielaard W, van Aalten MF. PAS domains: common structure and common flexibility. J Biol Chem 2003;278:18434-18439.
43. Bernard C, Houben K, Derix NM, Marks D, van der Horst MA, Hellingwerf KJ, Boelens R, Kaptein R, van Nuland NAJ. The solution structure of transient photoreceptor intermediate: Δ25 photoactive yellow protein. Structure 2005;13:953-962.
44. Getzoff ED, Gutwin KN, Genick UK. Anticipatory active-site motions and chromophore distortions prime photoreceptor PYP for light activation. Nat Struct Biol 2003;10:663-668.
45. Harigai M, Imamoto Y, Kamikubo H, Yamazaki Y, Kataoka M. Role of an N-terminal loop in the secondary structural change of photoactive yellow protein. Biochemistry 2003;42:13893-13900.
46. Rose GD, Creamer TP. Protein folding: predicting predicting. Proteins: Struct Funct Genet 1994;19:1-3.