Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach

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

Volumn 100, Issue 9, 2003, Pages 5091-5096

  Moore, Gregory L ^a   Maranas, Costas D ^a  

^a The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DIHYDROFOLATE REDUCTASE; HYBRID PROTEIN; PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE;

AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; CALCULATION; COMBINATORIAL LIBRARY; ENERGY; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

PROTEIN CONFORMATION; PROTEINS; TETRAHYDROFOLATE DEHYDROGENASE;

ESCHERICHIA COLI;

EID: 0037627753     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0831190100     Document Type: Article

References (42)

1. Petrounia, I. P. & Arnold, F. H. (2000) Curr. Opin. Biotechnol. 11, 325-330.
2. Brakmann, S. (2001) Chembiochem 2, 865-871.
3. Schmidt-Dannert, C. (2001) Biochemistry 40, 13125-13136.
4. Ostermeier, M., Nixon, A. E. & Benkovic, S. J. (1999) Bioorg. Med. Chem. 7, 2139-2144.
5. Lutz, S., Ostermeier, M., Moore, G. L., Maranas, C. D. & Benkovic, S. J. (2001) Proc. Natl. Acad. Sci. USA 98, 11248-11253.
6. Sieber, V., Martinez, C. A. & Arnold, F. A. (2001) Nat. Biotechnol. 19, 456-460.
7. Short, J. M. (1999) U.S. Patent 5,965,408.
8. Bogarad, L. D. & Deem, M. W. (1999) Proc Natl. Acad. Sci. USA 96, 2591-2595.
9. Voigt, C. A., Martinez, C., Wang, Z.-G., Mayo, S. L. & Arnold, F. H. (2002) Nat. Struct. Biol. 9, 553-558.
10. Moore, G. L., Maranas, C. D., Lutz, S. & Benkovic. S. J. (2001) Proc. Natl. Acad. Sci. USA 98, 3226-3231.
11. Moore, G. L. & Maranas, C. D. (2000) J. Theor. Biol. 205, 483-503.
12. Ostermeier, M., Shim, J. H. & Benkovic, S. J. (1999) Nat. Biotechnol. 17, 1205-1209.
13. Lutz, S., Ostermeier, M. & Benkovic, S. J. (2001) Nucleic Acids Res. 29, e16.
14. Voigt, C. A., Mayo, S. L., Arnold, F. H. & Wang, Z.-G. (2001) Proc. Natl. Acad. Sci. USA 98, 3778-3783.
15. Dahiyat, B. I. & Mayo, S. L. (1997) Science 278, 82-87.
16. Koehl, P. & Levitt, M. (1999) J. Mol. Biol. 293, 1161-1181.
17. Raha, K., Wollacott, A. M., Italia, M. J. & Desjarlais, J. R. (2000) Protein Sci. 9, 1106-1119.
18. Wernisch, L., Hery, S. & Wodak, S. J. (2000) J. Mol. Biol. 301, 713-736.
19. Kono, H. & Saven, J. G. (2001) J. Mol. Biol. 306, 607-628.
20. Dunbrack, R. L., Jr., & Cohen, F. E. (1997) Protein Sci. 6, 1661-1681.
21. Brooks, B., Bruccoleri, R., Olafson. B., States. D., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
22. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) J. Phys. Chem. B 102, 3586-3616.
23. Wesson, L. & Eisenberg, D. (1992) Protein Sci. 1, 227-235.
24. Street, A. G. & Mayo, S. L. (1998) Folding Des 3, 253-258.
25. Elcock, A. H. (1999) J. Mol. Biol. 294, 1051-1062.
26. Koehl, P. & Delarue, M. (1994) J. Mol. Biol. 239, 249-275.
27. Lee, C. (1994) J. Mol. Biol. 236, 918-939.
28. Koehl, P. & Delarue, M. (1995) Nat. Struct. Biol. 2, 163-170.
29. Vasquez, M. (1995) Biopolymers 36, 53-70.
30. Zou, J. & Saven, J. G. (2000) J. Mol. Biol. 296, 281-294.
31. Bethe, H. A. (1935) Proc. R. Soc. London Ser. A 150, 552-575.
32. Pathria, R. K. (1996) Statistical Mechanics (Butterworth-Heinemann, Boston).
33. Freeman, W. T., Pasztor, E. C. & Carmichael, O. T. (2000) Int. J. Comput. Vis. 40, 25-47.
34. Pearl, J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Kaufmann, San Francisco).
35. Yedidia, J. S. (2001) in Advanced Mean Field Methods: Theory and Practice, eds. Opper, M. & Saad, D. (MIT Press, Cambridge, MA).
36. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., Griffiths-Jones, S., Howe, K. L., Marshall, M. & Sonnhammer, E. L. (2002) Nucleic Acids Res. 20, 276-280.
37. Sawaya, M. R. & Kraut, J. (1997) Biochemistry 36, 586-603.
38. Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C. & Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662.
39. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
40. Radkiewicz, J. L. & Brooks, C. L., III (2000) J. Am. Chem. Soc. 122, 225-231.
41. Klein, C., Chen, P., Arevalo, J. H., Stura, E. A., Marolewski, A., Warren, M. S., Benkovic, S. J. & Wilson, I. A. (1995) J. Mol. Biol. 249, 153-175.
42. Agarwal, P. K., Billeter, S. R., Rajagopalan, P. T., Benkovic, S. J. & Hammes-Schiffer, S. (2002) Proc. Natl. Acad. Sci. USA 99, 2794-2799.