A redesigned genetic code for selective labeling in protein NMR

BioEssays

Volumn 30, Issue 8, 2008, Pages 772-780

  Gáspári, Zoltán ^a   Pál, Gábor ^a   Perczel, András ^a,b  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b MTA ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; MESSENGER RNA; PROTEIN; TRANSFER RNA;

AMINO ACID SEQUENCE; AMINOACYLATION; ARTICLE; BINDING SITE; CODON; GENE MUTATION; GENETIC CODE; GENETIC ENGINEERING; GENOMICS; IN VITRO STUDY; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; RNA TRANSLATION;

AMINO ACIDS; CELL-FREE SYSTEM; CODON; GENETIC CODE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BIOSYNTHESIS; RNA, TRANSFER; SEQUENCE ANALYSIS, PROTEIN;

EID: 48949100383     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20786     Document Type: Article

References (39)

1. 15N-Labelled proteins by cell-free protein synthesis: Strategies for high-throughput NMR studies of proteins and protein-ligand complexes. FEBS. 273:4154-4159.
2. Staunton D, Schlinkert R, Zanetti G, Coelbrook SA, Campbell ID. 2006. Cell-free expression and selective isotope labelling for protein NMR. Magn Reson Chem 44:S2-S9.
3. Yabuki T, Kigawa T, Dohmae N, Takio K, Terada T, et al. 1998. Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis. J Biomol NMR 11:295-306.
4. Shekhtman A. 2005. Protein chemical ligation as an invaluable tool for structural NMR. Protein Pept Lett 12:765-768.
5. Goto NK, Kay LE. 2000. New developments in isotope labeling strategies for protein solution NMR spectroscopy. Curr Opin Struct Biol 10:585-592.
6. Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R, et al. 2004. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics 5:63-68.
7. Vinarov DA, Loushin Newman CL, Markley JL. 2006. Wheat germ cell-free platform for eukaryotic protein production. FEBS J 273:4160-4169.
8. Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, et al. 2006. Optimal isotope labelling for NMR protein structure determinations. Nature 440:52-57.
9. Takeda M, Ikeya T, Güntert P, Kainosho M. 2007. Automated structure determination of proteins with the SAIL-FLYA NMR method. Nat. Protoc 2:2896-2902.
10. Xie J, Schultz PG. 2005. Adding amino acids to the genetic repertoire. Curr Opin Chem Biol 9:548-554.
11. 19F-phenylalanine-labeled intestinal fatty acid binding protein: evidence for conformational heterogeneity in the native state. Biochemistry 44:2369-2377.
12. 19F-amino acid into proteins as an NMR probe for characterizing protein structure and reactivity. J Am Chem Soc 129:1160-1166.
13. Rajagopal S, Kent SBH. 2007. Total chemical synthesis and biophysical characterization of the minimal isoform of the KChlP2 potassium channel regulatory subunit. Protein Science 16:2054-2064.
14. Pál G, Santamaria F, Kossiakoff AA, Lu W. 2003. The first semi-synthetic serine protease made by native chemical ligation. Protein Expr Purif 29:185-192.
15. Torizawa T, Shimizu M, Taoka M, Miyano H, Kainosho M. 2004. Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol. J Biomol NMR 30:311-325.
16. Ohtsuki T, Manabe T, Sisido M. 2005. Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures. FEBS Lett 579:6769-6774.
17. Rodriguez EA, Lester HA, Dougherty DA. 2006. In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression. Proc Natl Acad Sci USA 103:8650-8655.
18. Santoro SW, Anderson JC, Lakshman V, Schultz PG. 2003. An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res 31:6700-6709.
19. Liu DR, Schultz PG. 1999. Progress toward the evolution of an organism with an expanded genetic code. Proc Natl Acad Sci USA 96:4780-4785.
20. Pastrnak M, Magliery TJ, Schultz PG. 2000. A new orthogonal suppressor tRNA/aminoacyl-tRNA synthetase pair for evolving an organism with an expanded genetic code. Helv Chim Acta 83:2277-2286.
21. Kowal AK, Köhrer C, RajBhandary UL. 2001. Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria. Proc Natl Acad Sci USA 98:2268-2273.
22. Wang L, Magliery TJ, Liu DR, Schultz PG. 2000. A new functional suppressor tRNA/aminoacyl-tRNA synthetase pair for the in vivo incorporation of unnatural amino acids into proteins. J Am Chem Soc 122:5010-5011.
23. Anderson JC, Schultz PG. 2003. Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber and opal suppression. Biochemistry 42:9598-9608.
24. Tyr and tyrosyl-tRNA synthetase in Escherichia coli: possibility to expand the genetic code. J Biochem 124:1065-1068.
25. Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, et al. 2003. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol 10:425-432.
26. Shimizu Y, Kanamori T, Ueda T. 2005. Protein synthesis by pure translation systems. Methods 35:299-304.
27. Heim M. 2006. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res 34:721-733.
28. Agris PF. 2004. Decoding the genome: a modified view. Nucleic Acids Res 32:223-238.
29. 2 modifications of U34. Eur J Biochem 266:1128-1135.
30. Glu is a positive determinant for amino-acylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 32:3836-3841.
31. Rodnina MV, Gromadski KB, Kothe U, Wieden H-J. 2005. Recognition and selection of tRNA in translation. FEBS Lett 579:938-942.
32. Crick FH. 1966. Codon - anticodon pairing: the wobble hypothesis. J Mol Biol 19:548-555.
33. Agris PF, Vendeix FAP, Graham WD. 2007. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol 366:1-13.
34. Ser. Biochem Biophys Res Commun 257:662-667.
35. Zahnd C, Amstutz P, Plückthun A. 2007. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 4:269-279.
36. McTigue MA, Davies JF, Kaufman BT, Xoung N-H, Kraut J. 1992. 2.2 Ångströms crystal structure of chicken liver dihydrofolate reductase compelexd with NADP+ and biopterin. Biochemistry 31:7264-7273.
37. Vulpetti A, Casale E, Roletto F, Amici R, Villa M, et al. 2006. Structure-based drug design to the discovery of new 2-aminothiazole CDK2 inhibitors. J Mol Graph Model 24:341-348.
38. Bunney TD, Harris R, Gandarillas NL, Josephs MB, Roe SM, et al. 2006. Structural and mechanistic insights into Ras asscociation with phospholipase C epsilon. Mol Cell 21:495-507.
39. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. 2004. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612.