Redesign of high-affinity nonspecific nucleases with altered sequence preference

Journal of the American Chemical Society

Volumn 131, Issue 47, 2009, Pages 17345-17353

  Wang, Yi Ting ^a,c,d   Wright, Jon D ^b   Doudeva, Lyudmila G ^a   Jhang, Hua Ci ^a   Lim, Carmay ^b,c,d   Yuan, Hanna S ^a,c,e  

^a INSTITUTE OF MOLECULAR BIOLOGY   (Taiwan)

^b INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^c ACADEMIA SINICA   (Taiwan)

^d NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RESIDUES; BACTERIAL TOXIN; BINDING AFFINITIES; COLICIN E7; DNA BINDING AFFINITY; DNA CLEAVAGE; DNA COMPLEX; DNA-BINDING; ELECTROSTATIC REPULSION; ENDONUCLEASES; FLUORESCENCE KINETICS; FOOTPRINT ASSAYS; FREE ENERGY ANALYSIS; HIGH AFFINITY; MODEL SYSTEM; NUCLEASE DOMAIN; PHOSPHATE GROUP; PHOSPHODIESTER BONDS; PROTEIN-DNA INTERACTIONS; PROTEIN-DNA INTERFACE; UNDERLYING PRINCIPLES; WILD TYPES; WILD-TYPE ENZYMES; X-RAY STRUCTURE;

AMINES; AMINO ACIDS; BINDING ENERGY; CARBOXYLATION; DNA; FLUORINE CONTAINING POLYMERS; FREE ENERGY; HYDROGEN BONDS; NUCLEIC ACIDS; ORGANIC ACIDS; PROTEINS; SURFACE CHEMISTRY;

GENES;

COLICIN E1; COLICIN E7; DNA; MUTANT PROTEIN; NUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; DNA CLEAVAGE; DNA FOOTPRINTING; DNA PROTEIN COMPLEX; POINT MUTATION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY ANALYSIS;

BACTERIOCIN PLASMIDS; ENZYMES; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYDROLYSIS; KINETICS; MODELS, MOLECULAR;

EID: 72249088170     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja907160r     Document Type: Article

References (36)

1. Mandel-Gutfreund, Y.; Schueler, O.; Margalit, H. J. Mol. Biol. 1995, 253, 370-382
2. Hsia, K.-C.; Li, C.-L.; Yuan, H. S. Curr. Opin. Struct. Biol. 2005, 15, 126-134.
3. Luscombe, N. M.; Thornton, J. M. J. Mol. Biol. 2002, 320, 991-1009.
4. Sarai, A.; Kono, H. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 379-398
5. Chen, Y. C.; Wu, C. Y.; Lim, C. Proteins: Struct., Funct., Bioinf. 2007, 67, 671-680.
6. Chen, Y. C.; Lim, C. Nucleic Acids Res. 2008, 36, 7078-7087.
7. Lippow, S. M.; Tidor, B. Curr. Opin. Biotechnol. 2007, 18, 305-311
8. Pabo, C. O.; Nekludova, L. J. Mol. Biol. 2000, 301, 597-624.
9. Arnold, F. H.; Wintrode, P. L.; Miyazaki, K.; Gershenson, A. Trends Biochem. Sci. 2001, 26, 100-106
10. Rebar, E. J.; Greisman, H. A.; Pabo, C. O. Methods Enzymol. 1996, 267, 129-149
11. Seligman, L. M.; Chisholm, K. M.; Chevalier, B. S.; Chadsey, M. S.; Edwards, S. T.; Savage, J. H.; Veillet, A. L. Nucleic Acids Res. 2002, 30, 3870-3879
12. Rosen, L. E.; Morrison, H. A.; Masri, S.; Brown, M. J.; Springstubb, B.; Sussman, D.; Stoddard, B. L.; Seligman, L. M. Nucleic Acids Res. 2006, 34, 4791-4800
13. Smith, J.; Bibikova, M.; Whitby, F. G.; Reddy, A. R.; Chandrasegaran, S.; Carroll, D. Nucleic Acids Res. 2000, 28, 3361-3369
14. Chevalier, B. S.; Kortemme, T.; Chadsey, M. S.; Baker, D.; Monnat, R. J.; Stoddard, B. L. Mol. Cell 2002, 10, 895-905.
15. Urnov, F. D.; Miller, J. C.; Lee, Y.-L.; Beausejour, C. M.; Rock, J. M.; Augustus, S.; Jamieson, A. C.; Porteus, M. H.; Gregory, P. D.; Holmes, M. C. Nature 2005, 435, 646-651.
16. Chan, S. H.; Bao, Y.; Ciszak, E.; Laget, S.; Xu, S. Y. Nucleic Acids Res. 2007, 35, 6238-6248
17. Zhang, P. H.; Bao, Y. M.; Higgins, L.; Xu, S. Y. Protein Eng., Des. Sel. 2007, 20, 497-504.
18. Lippow, S. M.; Aha, P. M.; Parker, M. H.; Blake, W. J.; Baynes, B. M.; Lipovsek, D. Nucleic Acids Res. 2009, 37, 3061-3073.
19. Ashworth, J.; Havranek, J. J.; Duarte, C. M.; Sussman, D.; Monnat, R. J., Jr.; Stoddard, B. L.; Baker, D. Nature 2006, 441, 656-659
20. Wang, Y.-T.; Yang, W.-J.; Li, C.-L.; Doudeva, L. G.; Yuan, H. S. Nucleic Acids Res. 2007, 35, 584-594.
21. Cheng, Y. S.; Hsia, K. C.; Doudeva, L. G.; Chak, K. F.; Yuan, H. S. J. Mol. Biol. 2002, 324, 227-236
22. Hsia, K. C.; Chak, K. F.; Liang, P. H.; Cheng, Y. S.; Ku, W. Y.; Yuan, H. S. Structure 2004, 12, 205-214
23. Doudeva, L. G.; Huang, H.; Hsia, K.-C.; Shi, Z.; Li, C.-L.; Shen, Y.; Yuan, H. S. Protein Sci. 2006, 15, 269-280.
24. Koradi, R.; Billeter, M.; Wuthrich, K. J. Mol. Graph. 1996, 14, 51-55.
25. Vriend, G. J. Mol. Graph. 1990, 8, 52-6, 29.
26. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Nucleic Acids Res. 2001, 29, 2860-2874
27. Luscombe, N. M.; Thornton, J. M. J. Mol. Biol. 2002, 320, 991-1009.
28. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
29. Ko, T. P.; Liao, C. C.; Ku, W. Y.; Chak, K. F.; Yuan, H. S. Structure 1999, 7, 91-102.
30. Sano, Y.; Matsui, H.; Kobayashi, M.; Kageyama, M. J. Bacteriol. 1993, 175, 2907-2916.
31. Sano, Y.; Kageyama, M. Mol. Gen. Genet. 1993, 237, 161-170.
32. MacKerell, J. A. D.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
33. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
34. Darden, T.; Perera, L.; Li, L.; Pedersen, L. Structure 1999, 7, 55-60.
35. Lo, C.-H.; Chang, Y.-H.; Wright, J. D.; Chen, S.-H.; Kan, D.; Lim, C.; Liang, P.-H. J. Am. Chem. Soc. 2009, 131, 4051-4062.
36. Otwinowski, Z. Methods Enzymol. 1997, 276, 307-326.