Rational design of aminoacyl-tRNA synthetase specific for p-acetyl-l-phenylalanine

Biochemical and Biophysical Research Communications

Volumn 391, Issue 1, 2010, Pages 709-715

  Sun, Renhua ^a   Zheng, Heng ^a   Fang, Zhengzhi ^a   Yao, Wenbing ^a  

^a CHINA PHARMACEUTICAL UNIVERSITY   (China)

Author keywords

Aminoacyl tRNA synthetase; Binding affinity; Homology modeling; Molecular docking; Unnatural amino acid

Indexed keywords

ALANINE; AMINO ACID TRANSFER RNA LIGASE; ASPARTIC ACID; GLYCINE; ISOLEUCINE; LEUCINE; P ACETYL LEVO PHENYLALANINE; PHENYLALANINE DERIVATIVE; TYROSINE; UNCLASSIFIED DRUG; VALINE;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; ENZYME BINDING; ESCHERICHIA COLI; GENE MUTATION; HYDROPHOBICITY; METHANOCOCCUS JANNASCHII; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; METHANOCOCCUS; MUTATION; PHENYLALANINE; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; PROTEIN ENGINEERING; TYROSINE; TYROSINE-TRNA LIGASE;

ESCHERICHIA COLI; METHANOCALDOCOCCUS JANNASCHII;

EID: 72949108449     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.11.125     Document Type: Article

References (27)

1. Wang L., Brock A., Herberich B., and Schultz P.G. Expanding the genetic code of Escherichia coli. Science 292 (2001) 498-500
2. Zhang Z., Gildersleeve J., Yang Y.Y., Xu R., Loo J.A., Uryu S., Wong C.H., and Schultz P.G. A new strategy for the synthesis of glycoproteins. Science 303 (2004) 371-373
3. Wang L., Zhang Z., Brock A., and Schultz P.G. Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 100 (2003) 56-61
4. Chin J.W., Martin A.B., King D.S., Wang L., and Schultz P.G. Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 99 (2002) 11020-11024
5. Zhang Z., Gildersleeve J., Yang Y.Y., Xu R., Loo J.A., Uryu S., Wong C.H., and Schultz P.G. A new strategy for the synthesis of glycoproteins. Science 303 (2004) 371-373
6. Chin J.W., and Schultz P.G. In vivo photocrosslinking with unnatural amino acid mutagenesis. Chembiochem 3 (2002) 1135-1137
7. Zhang Z., Wang L., Brock A., and Schultz P.G. The selective incorporation of alkenes into proteins in Escherichia coli. Angew. Chem. Int. Ed. Engl. 41 (2002) 2840-2842
8. Alfonta L., Zhang Z., Uryu S., Loo J.A., and Schultz P.G. Site-specific incorporation of a redox-active amino acid into proteins. J. Am. Chem. Soc. 125 (2003) 14662-14663
9. Cornish V.W., Hahn K.M., and Schultz P.G. Site-specific protein modification using a ketone handle. J. Am. Chem. Soc. 118 (1996) 8150-8151
10. Geoghegan K.F., and Stroh J.G. Site-directed conjugation of nonpeptide groups to peptides and proteins via periodate oxidation of a 2-amino alcohol. Bioconjug. Chem. 3 (1992) 138-146
11. Mahal L.K., Yarema K.J., and Bertozzi C.R. Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis. Science 276 (1997) 1125-1128
12. Kobayashi T., Nureki O., Ishitani R., Yaremchuk A., Tukalo M., Cusack S., Sakamoto K., and Yokoyama S. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat. Struct. Biol. 10 (2003) 425-432
13. Zhang Y., Wang L., and Schultz P.G. Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-l-tyrosine. Protein Sci. 14 (2005) 1340-1349
14. Bissantz C., Folkers G., and Rognan D. Protein-based virtual screening of chemical databases. J. Med. Chem. 43 (2000) 4759-4767
15. Wang R., Lu Y., and Wang S. Comparative evaluation of 11 scoring functions for molecular dockings. J. Med. Chem. 46 (2003) 2287-2303
16. Wang R., Lu Y., Fang X., and Wang X. An extensive test of 14 scoring functions using the PDB bind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 44 (2004) 2114-2125
17. Warren G.L., Andrews C.W., Capelli A.M., Clarke B., Laonde J., Lambert M.H., Lindvall M., Nevins N., Semus S.F., Senger S., Tedesco G., Wall I.D., Woolven J.M., Peishoff C.E., and Head M.S. A critical assessment of docking programs and scoring functions. J. Med. Chem. 49 (2006) 5912-5931
18. Lovell S.C., Davis I.W., Arendall I.I.I.W.B., Bakker P.I., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50 (2003) 437-450
19. Dunbrack J.R.L., and Cohen F.E. Bayesian statistical analysis of protein sidechain rotamer preferences. Protein Sci. 6 (1997) 1661-1681
20. Laskowski R.A., Rullmannn J.A., Macarthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 477-486
21. Colovos C., and Yeates T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 2 (1993) 1511-1519
22. Ibba M., and Soll D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650
23. Labute P. The Generalized Born/Volume Integral (GB/VI) implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area. J. Comp. Chem. 29 (2008) 1693-1698
24. D. Labute, The London dG Scoring Function for Binding Affinity Estimation, Unpublished.
25. Wojciechowski M., and Lesyng B. Generalized born model: analysis, refinement and applications to proteins. J. Phys. Chem. B 108 (2004) 18368-18376
26. Kleywegt G.J. Validation of protein crystal structures. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 249-265
27. Wang L., Zhang Z., Brock A., and Schultz P.G. Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 100 (2002) 56-61