Synthesis of proteins containing modified arginine residues

Biochemistry

Volumn 46, Issue 13, 2007, Pages 4066-4076

  Choudhury, Ambar K ^a   Golovine, Serguei Y ^a   Dedkova, Larisa M ^a   Hecht, Sidney M ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ENZYMES; LIGHT EMISSION; RNA; SYNTHESIS (CHEMICAL);

ARGININE RESIDUES; ENZYME FUNCTIONS; LUCIFERIN BINDING SITE; STRUCTURAL DOMAINS;

PROTEINS;

ARGININE; CITRULLINE; DIHYDROFOLATE REDUCTASE; HOMOARGININE; LUCIFERASE; N(G) METHYLARGININE; N(G) NITROARGININE; PROLINE; PROTEIN; SYNTHETIC PEPTIDE; TRANSFER RNA;

AMINO ACID COMPOSITION; ARTICLE; BINDING SITE; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; PROTEIN SYNTHESIS; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ARGININE; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; LUCIFERASES, FIREFLY; MODELS, MOLECULAR; RNA, TRANSFER, AMINO ACYL; TETRAHYDROFOLATE DEHYDROGENASE;

PHOTINUS PYRALIS;

EID: 34047198647     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi062042r     Document Type: Article

References (74)

1. Smith, M. (1985) In vitro mutagenesis, Annu. Rev. Genet. 19, 423-462.
2. Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl. Acad. Sci. U.S.A. 82, 488-492.
3. Antikainen, N. M., and Martin, S. F. (2005) Altering protein specificity: Techniques and applications, Bioorg. Med. Chem. 13, 2701-2716.
4. Yuan, L., Kurek, I., English, J., and Keenan, R. (2005) Laboratory-directed protein evolution, Microbiol. Mol. Biol. Rev. 69, 373-392.
5. Hecht, S. M., Alford, B. L., Kuroda, Y., and Kitano, S. (1978) "Chemical aminoacylation" of tRNA's, J. Biol. Chem. 253,4517-4520.
6. phes, J. Biol. Chem. 258, 4492-4495.
7. Heckler, T. G., Chang, L. H., Zama, Y., Naka, T., and Hecht, S. M. (1984) Preparation of 2′(3′)-O-acyl-pCpA derivatives as substrates for T4 RNA ligase-mediated "chemical aminoacylation", Tetrahedron 1984, 40, 87-94.
8. Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C., and Schultz, P. G. (1989) A general method for site-specific incorporation of unnatural amino acids into proteins, Science 244, 182-188.
9. Hecht, S. M. (2007) In Protein Engineering (RajBhandary, U. L., and Koehrer, C., Eds.) in press, Springer, New York.
10. Ellman, J. A., Mendel, D., and Schultz, P. G. (1992) Site-specific incorporation of novel backbone structures into proteins, Science 255, 197-200.
11. Ellman, J. A., Volkman, B. F., Mendel, D., Schultz, P. G., and Wemmer, D. E. (1992) Site-specific isotopic labeling of proteins for NMR studies, J. Am. Chem. Soc. 114, 7959-7961.
12. Mendel, D., Ellman, J. A., Chang, Z., Veenstra, D. L., Kollman, P. A., and Schultz, P. G. (1992) Probing protein stability with unnatural amino acids, Science 256, 1798-1802.
13. Chung, H.-H., Benson, D. R., and Schultz, P. G. (1993) Probing the structure and mechanism of ras protein with an expanded genetic code, Science 259, 806-809.
14. Judice, J. K., Gamble, T. R., Murphy, E. C., deVos, A. M., and Schultz, P. G. (1993) Probing the mechanism of staphylococcal nuclease with unnatural amino acids: Kinetic and structural studies, Science 261, 1578-1581.
15. Mendel, D., Ellman, J. A., and Schultz, P. G. (1993) Protein biosynthesis with conformationally restricted amino acids, J. Am. Chem. Soc. 115, 4359-4360.
16. Cornish, V. W., Benson, D. R., Altenbach, C. A., Hideg, K., Hubbell, W. L., and Schultz, P. G. (1994) Site-specific incorporation of biophysical probes into proteins, Proc. Natl. Acad. Sci. U.S.A. 91, 2910-2914.
17. Thorson, J. S., Chapman, E., Murphy, E. C., Schultz, P. G., and Judice, J. K. (1995) Linear free energy analysis of hydrogen bonding in proteins, J. Am. Chem. Soc. 117, 1157-1158.
18. Cornish, V. W., Mendel, D., and Schultz, P. G. (1995) Probing protein structure and function with an expanded genetic code, Angew. Chem., Int. Ed. Engl. 34, 621-633.
19. Nowak, M. W., Kearney, P. C., Sampson, J. R., Saks, M. E., Labarca, C. G., Silverman, S. K., Zhong, W., Thorson, J., Abelson, J. N., Davidson, N., Schultz, P. G., Dougherty, D. A., and Lester, H. A. (1995) Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells, Science 268, 439-442.
20. Mamaev, S. V., Laikhter, A. L., Arslan, T., and Hecht, S. M. (1996) Firefly luciferase: Alteration of the color of emitted light resulting from substitutions at position 286, J. Am. Chem. Soc. 118, 7243-7244.
21. Gln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression, J. Biol. Chem. 271, 23169-23175.
22. Steward, L. E., Collins, C. S., Gilmore, M. A., Carlson, J. E., Ross, J. B. A., and Chamberlin, A. R. (1997) In vitro site-specific incorporation of fluorescent probes into β-galactosidase, J. Am. Chem. Soc. 119, 6-11.
23. Arslan, T., Mamaev, S. V., Mamaeva, N. V., and Hecht, S. M. (1997) Structurally modified firefly luciferase. Effects of amino acid substitution at position 286, J. Am. Chem. Soc. 119, 10877-10887.
24. England, P. M., Lester, H. A., Davidson, N., and Dougherty, D. A. (1997) Site-specific, photochemical proteolysis applied to ion channels in vivo, Proc. Natl. Acad. Sci. U.S.A. 94, 11025-11030.
25. Hohsaka, T., Ashizuka, Y., Taira, H., Murakami, H., and Sisido, M. (2001) Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system, Biochemistry 40, 11060-11064.
26. + channel with backbone mutations in the selectivity filter, Nature Neurosci. 4, 239-246.
27. Wang, B., Brown, K. C., Lodder, M., Craik, C. S., and Hecht, S. M. (2002) Chemically mediated site-specific proteolysis. Alteration of protein-protein interaction, Biochemistry 41, 2805-2813.
28. Gao, R., Zhang, Y., Choudhury, A. K., Dedkova, L. M., and Hecht, S. M. (2005) Analogues of vaccinia virus DNA topoisomerase I modified at the active site tyrosine, J. Am. Chem. Soc. 127, 3321-3331.
29. Gao, R., Zhang, Y., Dedkova, L., Choudhury, A. K., Rahier, N. J., and Hecht, S. M. (2006) Effects of modification of the active site tyrosine of human DNA topoisomerase I, Biochemistry 45, 8402-8410.
30. Karginov, V. A., Mamaev, S. V., An, A., Van Cleve, M. D., Hecht, S. M., Komatsoulis, G. A., and Abelson, J. N. (1997) Probing the role of an active site aspartic acid in dihydrofolate reductase, J. Am. Chem. Soc. 119, 8166-8176.
31. Graveley, B. R., and Maniatis, T. (1998) Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA, Mol. Cell 1, 765-771.
32. Zapp, M. L., Hope, T. J., Parslow, T. G., and Green, M. R. (1991) Oligomerization and RNA binding domains of the type 1 human immunodeficiency virus rev protein: A dual function for an arginine-rich binding motif, Proc. Natl. Acad. Sci. U.S.A. 88, 7734-7738.
33. Truant, R., and Cullen, B. R. (1999) The arginine-rich domains present in human immunodeficiency virus type 1 tat and rev function as direct importin β-dependent nuclear localization signals, Mol. Cell. Biol. 19, 1210-1217.
34. Ruoslahti, E., and Pierschbacher, M. D. (1987) New perspectives in cell-adhesion-RGD and integrins, Science 238, 491-497.
35. Xuan, J. W., Hota, C., Shigeyama, Y., D'Errico, J. A., Somerman, M. J., and Chambers, A. F. (1995) Site-directed mutagenesis of the arginine-glycine- aspartic acid sequence in osteopontin destroys cell-adhesion and migration functions, J. Cell. Biochem. 57, 680-690.
36. Savage, B., Marzec, U. M., Chao, B. H., Harker, L. A., Maraganore, J. M., and Ruggeri, Z. M. (1990) Binding of the snake venom-derived proteins applaggin and echistatin to the arginine-glycine-aspartic acid recognition site(s) on platelet glycoprotein IIb-IIIa complex inhibits receptor function, J. Biol. Chem. 265, 11766-11772.
37. Shen, E. C., Henry, M. F., Weiss, V. H., Valentini, S. R., Silver, P. A., and Lee, M. S. (1998) Arginine methylation facilitates the nuclear export of hnRNP proteins, Genes Devel. 12, 679-691.
38. Yun, C. Y., and Fu, X.-D. (2000) Conserved Sr protein kinase functions in nuclear import and its action, is counteracted by arginine methylation in Saccharomyces cerevisiae, J. Cell Biol. 150, 707-717.
39. Strahl, B. D., and Allis, C. D. (2000) The language of covalent histone modifications, Nature 403, 41-45.
40. Lee, Y. H., Coonrod, S. A., Kraus, W. L., Jelinek, M. A., and Stallcup, M. R. (2005) Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination, Proc. Natl. Acad. Sci. U.S.A. 102, 3611-3616.
41. Rothnagel, J. A., and Rogers, G. E. (1984) Citrulline in proteins from the enzymatic determination of arginine residues, Methods Enzymol. 107, 624-631.
42. Asaga, H., and Ishigami, A. (2001) Protein determination in the rat brain after kainate administration: Citrulline-containing proteins as a novel marker of neurodegeneration, Neurosci. Lett. 299, 5-8.
43. Asaga, H., Akiyama, K., Ohsawa, T., and Ishigami, A. (2002) Increased and type II-specific expression of peptidylarginine deiminase in activated microglia but not hyperplastic astrocytes following kainic acid-evoked neurodegeneration in the rat brain, Neurosci. Lett. 326, 129-132.
44. Ishigami, A., Ohsawa, T., Hiratsuka, M., Taguchi, H., Kobayashi, S., Saito, Y., Murayama, S., Asaga, H., Toda, T., Kimura, N., and Maruyama, N. (2005) Abnormal accumulation of citrullinated proteins catalyzed by peptidylarginine deiminase in hippocampal extracts from patients with Alzheimer's disease, J. Neurosci. Res. 80, 120-128.
45. Siddiqui, K. S., Poljak, A., Guilhaus, M., De Francisci, D., Curmi, P. M. G., Feller, G., D'Amico, S., Gerday, C., Uversky, V. N., and Cavicchioli, R. (2006) Role of lysine versus arginine in enzyme cold-adaptation: Modifying lysine to homo-arginine stabilizes the cold-adapted α-amylase from Pseudoalteramonas haloplanktis, Proteins 64, 486-501.
46. Lodder, M. (2000) Ph.D. Thesis, University of Virginia, Charlottesville, Virginia.
47. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature 227, 680-685.
48. Robertson, S. A., Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C., and Schultz, P. G. (1989) The use of 5′-phospho-2-deoxyri- bocytidylylriboadenosine as a facile route to chemical aminoacylation of transfer RNA, Nucleic Acids Res. 17, 9649-9660.
49. Webb, T. R., and Eigenbrot, C. (1991) Conformationally restricted arginine analogs, J. Org. Chem. 56, 3009-3016.
50. Kim, K., Lin, Y.-T., and Mosher, H. S. (1988) Monosubstituted guanidines from primary amines and aminoirninomethanesulfonic acid, Tetrahedron Lett. 29, 3183-3186.
51. phe are not essential for ternary complex formation and peptide elongation, EMBO J. 13, 2464-2471.
52. Varshney, U., Lee, C. P., and RajBhandary, U. L. (1991) Direct analysis of aminoacylation levels of tRNAs in vivo application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase, J Biol. Chem. 266, 24712-24718.
53. Dedkova, L. M., Fahmi, N. E., Golovine, S. Y., and Hecht, S. M. (2003) Enhanced D-amino acid incorporation into protein by modified ribosomes, J. Am. Chem. Soc. 125, 6616-6617.
54. Short, G. F., III, Golovine, S. Y., and Hecht, S. M. (1999) Effects of release factor 1 on in vitro protein translation and the elaboration of proteins containing unnatural amino acids, Biochemistry 38, 8808-8819.
55. Bodanszky, M., and Bodanszky, A. (1994) In The Practice of Peptide Synthesis, 2nd ed., p 96, Springer-Verlag, New York.
56. Noren, C. J., Anthony-Cahill, S. J., Suich, D. J., Noren, K. A., Griffith, M. C., and Schultz, P. G. (1990) In vitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription, Nucleic Acids Res. 18, 83-88.
57. Lodder, M., Golovine, S., and Hecht, S. M. (1997) Chemical deprotection strategy for the elaboration of misacylated transfer RNA's, J. Org. Chem. 62, 778-779.
58. Lodder, M., Golovine, S., Laikhter, A. L., Karginov, V. A., and Hecht, S. M. (1998) Misacylated transfer RNAs having a chemically removable protecting group, J. Org. Chem. 63, 794-803.
59. 13C]tryptophan, Biochemistry 20, 6169-6178.
60. 19F]tryptophan-labeled Escherichia coli dihydrofolate reductase: Equilibrium folding and ligand binding studies, Biochemistry 33, 5502-5509.
61. Basran, J., Casarotto, M. G., Basran, A., and Roberts, G. C. K. (1997) Effects of single-residue substitutions on negative cooperativity in ligand binding to dihydrofolate reductase, Protein Eng. 10, 815-826.
62. Ohmae, E., Sasaki, Y., and Gekko, K. (2001) Effects of five tryptophan mutations on structure, stability and, function of Escherichia coli dihydrofolate reductase, J. Biochem. 130, 439-447.
63. Xu, Y., Feller, G., Gerday, C., and Glansdorff, N. (2003) Moritella cold-active dihydrofolate reductase: Are there natural limits to optimization of catalytic efficiency at low temperature? J. Bacterial 185, 5519-5526.
64. Gould, S. J., and Subramani, S. (1988) Firefly luciferase as a tool in molecular and cell biology, Anal. Biochem. 175, 5-13.
65. Kricka, L. J. (1995) Chemiluminescence and bioluminescence, Anal. Chem. 67, 499R-502R.
66. Price, R. L., Squirrell, D. J., and Murphy, M. J. (1998) Luciferase and recombinant luciferase labels, J. Clin. Ligand Assay 21, 349-357.
67. Kricka, L. J. (2000) Application of bioluminescence and chemiluminescence in biomedical sciences, Methods Enzymol. 305, 333-345.
68. Conti, E., Franks, N. P., and Brick, P. (1996) Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes, Structure 4, 287-298.
69. Franks, N. P., Jenkins, A., Conti, E., Lieb, W. R., and Brick, P. (1998) Structural basis for the inhibition of firefly luciferase by a general anesthetic, Biophys. J. 75, 2205-2211.
70. Branchini, B. R., Magyar, R. A., Murtiashaw, M. H., Anderson, S. M., and Zimmer, M. (1998) Site-directed mutagenesis of histidine 245 in firefly luciferase: A proposed model of the active site, Biochemistry 37, 15311-15319.
71. Sandalova, T. P., and Ugarova, N. N. (1999) Model of the active site of firefly luciferase, Biochemistry (Moscow) 64, 962-967.
72. Branchini, B. R., Magyar, R. A., Murtiashaw, M. H., Anderson, S. M., Helgerson, L. C., and Zimmer, M. (1999) Site-directed mutagenesis of firefly luciferase active site amino acids: A proposed model for bioluminescence color, Biochemistry 38, 13223-13230.
73. Branchini, B. R., Murtiashaw, M. H., Magyar, R. A., and Anderson, S. M. (2000) The role of lysine 529, a conserved residue of the acyl-adenylate-forming enzyme superfamily, in firefly luciferase, Biochemistry 39, 5433-5440.
74. Branchini, B. R., Magyar, R. A., Murtiashaw, M. H., and Portier, N. G. (2001) The role of active site residue arginine 218 in firefly luciferase bioluminescence, Biochemistry 40, 2410-2418.