Mutagenesis-based definitions and probes of residue burial in proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 45, 2005, Pages 16221-16226

  Bajaj, Kanika ^a   Chakrabarti, Purbani ^a   Varadarajan, Raghavan ^a,b  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

Author keywords

Accessibility; Aspartate; Phenotype; Scanning mutagenesis

Indexed keywords

ALANINE; ARGININE; ASPARTIC ACID; BACTERIAL TOXIN; GLUTAMIC ACID; LYSINE; MALTOSE BINDING PROTEIN; MUTANT PROTEIN; OLIGONUCLEOTIDE; PROTEIN CCDB; THIOREDOXIN; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; ESCHERICHIA COLI; MUTAGENESIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BACTERIAL TOXINS; CARRIER PROTEINS; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT; SOLUBILITY; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; THIOREDOXIN;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 28044467526     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0505089102     Document Type: Article

References (43)

1. Ponder, J. W. & Richards, F. M. (1987) J. Mol. Biol. 193, 775-791.
2. Lee, B. & Richards, F. M. (1971) J. Mol. Biol. 55, 379-400.
3. Shrake, A. & Rupley, J. A. (1973) J. Mol. Biol. 79, 351-371.
4. Ahmad, S. & Gromiha, M. M. (2002) Bioinformatics 18, 819-824.
5. Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987) J. Mol. Biol. 196, 641-656.
6. Mansoor, S. E., McHaourab, H. S. & Farrens, D. L. (1999) Biochemistry 38, 16383-16393.
7. Chakravarty, S. & Varadarajan, R. (1999) Struct. Folding Des. 7, 723-732.
8. Guan, J. Q., Almo, S. C. & Chance, M. R. (2004) Acc. Chem. Res. 37, 221-229.
9. Bernard, P., Kezdy, K. E., Van Melderen, L., Steyaert, J., Wyns, L., Pato, M. L., Higgins, P. N. & Couturier, M. (1993) J. Mol. Biol. 234, 534-541.
10. Dao-Thi, M. H., Van Melderen, L., De Genst, E., Afif, H., Buts, L., Wyns, L. & Loris, R. (2005) J. Mol. Biol. 348, 1091-1102.
11. Loris, R., Dao-Thi, M. H., Bahassi, E. M., Van Melderen, L., Poortmans, F., Liddington, R., Couturier, M. & Wyns, L. (1999) J. Mol. Biol. 285, 1667-1677.
12. Guzman, L. M., Belin, D., Carson, M. J. & Beckwith, J. (1995) J. Bacteriol. 177, 4121-4130.
13. Chakshusmathi, G., Mondal, K., Lakshmi, G. S., Singh, G., Roy, A., Ch., R. B., Madhusudhanan, S. & Varadarajan, R. (2004) Proc. Natl. Acad. Sci. USA 101, 7925-7930.
14. Johnson, B. H. & Hecht, M. H. (1994) Biotechnology 12, 1357-1360.
15. Ghoshal, A. K., Swaminathan, C. P., Thomas, C. J., Surolia, A. & Varadarajan, R. (1999) Biochem. J. 339, 721-727.
16. Holmgren, A. (1979) J. Biol. Chem. 254, 9627-9632.
17. Sanchez, R. & Sali, A. (1997) Proteins, Suppl. 1, 50-58.
18. Russell, R. B. & Barton, G. J. (1994) J. Mol. Biol. 244, 332-350.
19. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H. & Zehfus, M. H. (1985) Science 229, 834-838.
20. Dickinson, C. D., Kelly, C. R. & Ruf, W. (1996) Proc. Natl. Acad. Sci. USA 93, 14379-14384.
21. Collaborative Computational Project, Number 4 (1994) Acta Crystallogr. D 50, 760-763.
22. Guo, H. H., Choe, J. & Loeb, L. A. (2004) Proc. Natl. Acad. Sci. USA 101, 9205-9210.
23. Bloom, J. D., Silberg, J. J., Wilke, C. O., Drummond, D. A., Adami, C. & Arnold, F. H. (2005) Proc. Natl. Acad. Sci. USA 102, 606-611.
24. Pakula, A. A., Young, V. B. & Sauer, R. T. (1986) Proc. Natl. Acad. Sci. USA 83, 8829-8833.
25. Vershon, A. K., Bowie, J. U., Karplus, T. M. & Sauer, R. T. (1986) Proteins 1, 302-311.
26. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. & Sippl, M. J. (1990) J. Mol. Biol. 216, 167-180.
27. Murray, R. & Spiegel, L. J. S. (2000) Statistics (Tata McGraw-Hill, New York).
28. Bajaj, K., Chakshusmathi, G., Bachhawat-Sikder, K., Surolia, A. & Varadarajan, R. (2004) Biochem. J. 380, 409-417.
29. Chakrabarti, A., Srivastava, S., Swaminathan, C. P., Surolia, A. & Varadarajan, R. (1999) Protein Sci. 8, 2455-2459.
30. Beena, K., Udgaonkar, J. B. & Varadarajan, R. (2004) Biochemistry 43, 3608-3619.
31. Rennell, D., Bouvier, S. E., Hardy, L. W. & Poteete, A. R. (1991) J. Mol. Biol. 222, 67-88.
32. Suckow, J., Markiewicz, P., Kleina, L. G., Miller, J., Kisters-Woike, B. & Muller-Hill, B. (1996) J. Mol. Biol. 261, 509-523.
33. Terwilliger, T. C., Zabin, H. B., Horvath, M. P., Sandberg, W. S. & Schlunk, P. M. (1994) J. Mol. Biol. 236, 556-571.
34. Loeb, D. D., Swanstrom, R., Everitt, L., Manchester, M., Stamper, S. E. & Hutchison, C. A., III (1989) Nature 340, 397-400.
35. Lim, W. A. & Sauer, R. T. (1989) Nature 339, 31-36.
36. Akasako, A., Haruki, M., Oobatake, M. & Kanaya, S. (1997) J. Biol. Chem. 272, 18686-18693.
37. Spudich, G. M., Miller, E. J. & Marqusee, S. (2004) J. Mol. Biol. 335, 609-618.
38. Dao-pin, S., Anderson, D. E., Baase, W. A., Dahlquist, F. W. & Matthews, B. W. (1991) Biochemistry 30, 11521-11529.
39. Shih, P., Holland, D. R. & Kirsch, J. F. (1995) Protein Sci. 4, 2050-2062.
40. Chen, J. & Matthews, K. S. (1994) Biochemistry 33, 8728-8735.
41. Kranz, J. K., Lu, J. & Hall, K. B. (1996) Protein Sci. 5, 1567-1583.
42. Sondek, J. & Shortle, D. (1990) Proteins 7, 299-305.
43. Varadarajan, R., Lambright, D. G. & Boxer, S. G. (1989) Biochemistry 28, 3771-3781.