Developing an energy landscape for the novel function of a (β/α)8 barrel: Ammonia conduction through HisF

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

Volumn 100, Issue 13, 2003, Pages 7599-7604

  Amaro, Rommie ^a   Tajkhorshidt, Emad ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; HISF PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CHANNEL GATING; ENERGY; ENZYME ACTIVE SITE; HYDROLYSIS; HYDROPHILICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; AMINOHYDROLASES; AMMONIA; BINDING SITES; BIOPHYSICS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; THERMODYNAMICS; THERMOTOGA MARITIMA;

EID: 0038610896     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1331150100     Document Type: Article

References (42)

1. Jiang, Y., Lee, A., Chen, J., Cadene, M., Chait, B. T. & MacKinnon, R. (2002) Nature 417, 515-522.
2. Jiang, Y., Lee, A., Chen, J., Cadene, M., Chait, B. T. & MacKinnon, R. (2002) Nature 417, 523-526.
3. Tajkhorshid, E., Nollert, P., Jensen, M. O., Miercke, L. J., O'Connell, J., Stroud, R. M. & Schulten, K. (2002) Science 296, 525-530
4. Rhee, S., Parris, K., Ahmed, S. A., Miles, E. W. & Davies, D. R. (1996) Biochemistry 35, 4211-4221.
5. Miles, E. W., Rhee, S. & Davies, D. R. (1999) J. Biol. Chem. 274, 12193-12196.
6. Raushel, F. M., Thoden, J. B. & Holden, H. M. (1999) Biochemistry 38, 7891-7899.
7. O'Donoghue, P., Amaro, R. E. & Luthey-Schulten, Z. (2001)J. Strtici. Biol. 134, 257-268.
8. Beismann-Driemeyer, S. & Sterner, R. (2001)J. Biol. Chem. 276, 20387-20396.
9. Douangamath, A., Walker, M., Beismann-Driemeyer, S., Vega-Fernandez, M. C., Sterner, R. & Wilmanns, M. (2002) Structure (London) 10, 185-193.
10. Chaudhuri, B. N., Lange, S. C., Myers, R. S., Chittur, S. V., Davisson, V. J. & Smith, J. L. (2001) Structure (London) 9, 987-997.
11. Bera, A. K., Smith, J. & Zalkin, H. (2000) J. Biol. Chem. 275, 7975-7979.
12. Huang, X. & Raushel, F. (2000) Biochemistry 39, 3240-3247.
13. Mullins, L. & Raushel, F. (1999) J. Am. Chem. Soc. 121, 3803-3804.
14. Thoden, J., Holden, H., Wesenberg, G., Raushel, F. & Rayment, L. (1997) Biochemistry 36, 6305-6316.
15. Klem, T. J. & Davisson, V. J. (1993) Biochemistry 32, 5177-5186.
16. Raushel, F. M., Mullins, L. & Gibson, G. (1998) Biochemistry 37, 10272-10278.
17. Krahn, J., Kim, J. H., Burns, M., Parry, R., Zalkin, H. & Smith, J. (1997) Biochemistry 36, 11061-11068.
18. Larsen, T., Boehlein, S., Schuster, S., Richards, N., Thoden, J., Holden, H. & Rayment, I. (1999) Biochemistry 38, 16146-16157.
19. Tesmer, J., Klem, T., Deras, M., Davisson, V. J. & Smith, J. (1996) Nat. Struct. Biol 3, 74-86.
20. Zalkin, H. & Smith, J. (1998) Adv. Enzymol. Relat. Areas Mol. Biol. 72, 87-144.
21. Klem, T. J., Chen, Y. & Davisson, V. J. (2001) J. Bacteriol. Bacieriol. 183, 989-996.
22. Thoden, J. B., Huang, X., Raushel, F. M. & Holden, H. M. (1999) Biochemistry 38, 16158-16166.
23. Pomes, R. & Roux, B. (1998) Biophys. J. 75, 33-40.
24. Jarzynski, C. (1997) Phys. Rev. Lett. 78, 2690-2693.
25. Jarzynski, C. (1997) Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top. 56, 5018-5035.
26. Hummer, G. & Szabo, A. (2001) Proc. Natl. Acad. Sci. USA 98, 3658-3661.
27. Jensen, M. O., Park, S., Tajkhorshid, E. & Schulten, K. (2002) Proc. Natl. Acad. Sci. USA 99, 6731-6736.
28. Liphardt, J., Dumont, S., Smith, S. B,., Tinoco, I., Jr., & Bustamante, C. (2002) Science 296, 1832-1835.
29. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K. & Schulten, K. (1999)J. Comp. Phys. 151, 283-312.
30. Grubmuller, H. (1996) SOLVATE (Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich), Version 1.0.
31. Zhang, L. & Hermans, J. (1996) Proteins Struct, Funct. Genet. 24, 433-438.
32. MacKerrell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack R. L., Jr., Evansecl, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) J. Phys. Chem. B 102, 3586-3616.
33. Rizzo, R. C. & Jorgensen, W. L. (1999) J. Am. Chem. Soc. 121, 4827-4836.
34. Jorgensen, W. L., Maxwell, D. S. & Tirado-Rives, J. (1996) J. Am. Chem. Soc. 117, 11225-11236.
35. Maxwell, D. S., Tirado-Rives, J. & Jorgensen, W. L. (1995) J. Comput. Chem. 16, 984-1010.
36. Darden, T., York, D. & Pedersen, L., (1993) J. Chem. Phys. 98, 10089-10092.
37. Chemical Computing Group (2001) MOE (Chemical Computing Group, Montreal).
38. Crooks, G. E. (2000) Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top. 61, 2361-2366.
39. Stone, J., Gullingsrud, J., Schulten, K. & Grayson, P.(2001) in 2001 ACM Symposium on Interactive 3D Graphics, ed. Sequin, J. H. A. C. (Association for Computing Machinery SIGGRAPH, New York), pp. 191-194.
40. Zhou, H., Wlodek, S. & McCammon, J. A. (1998) Proc. Natl. Acad. Sci. USA 95, 9280-9283.
41. Wang, J. & Wolynes, P. (1999) J. Chem. Phys. 110, 4812-4819.
42. Bond, P. J., Faraldo-Gomez, J. D. & Sansom, M. S. (2002) Biophys. J. 83, 763-775.