Computational alanine scanning mutagenesis - An improved methodological approach

Journal of Computational Chemistry

Volumn 28, Issue 3, 2007, Pages 644-654

  Moreira, Irina S ^a   Fernandes, Pedro A ^a   Ramos, Maria J ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

Alanine scanning mutagenesis; Binding free energy; Computational mutagenesis; Generalized Born model; Hot spot; MM PBSA; Molecular mechanics; Poisson Boltzmann; Protein protein interfaces

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COMPUTATIONAL METHODS; FREE ENERGY; MOLECULAR DYNAMICS; POISSON EQUATION; PROTEINS;

ALANINE SCANNING MUTAGENESIS; BINDING FREE ENERGY; COMPUTATIONAL MUTAGENESIS; FREE ENERGY PERTURBATION (FEP); GENERALIZED BORN MODEL; MOLECULAR MECHANICS/POISSON-BOLTZMANN SURFACE AREA (MM-PBSA); THERMODYNAMIC INTEGRATION (TI);

MUTAGENESIS;

ALANINE; PROTEIN; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS; MUTAGENESIS; THERMODYNAMICS;

ALANINE; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 33847650393     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20566     Document Type: Article

References (53)

1. Kortemme, T.; Baker, D. Curr Opin Chem Biol 2004, 8, 91.
2. Russel, R. B.; Alber, F.; Aloy, P.; Davis, F. P.; Korkin, D.; Pichaud, M.; Topf, M.; Sali, A. Curr Opin Struct Biol 2004, 14, 313.
3. Clackson, T.; Wells, J. A. Science 1995, 267, 383.
4. Lo Conte, L.; Chothia, C.; Janin, J. J Mol Biol 1999, 285, 2177.
5. Arkin, R.; Randal, M.; DeLano, W. L.; Hyde, J.; Luong, T. H.; Oslob, J. D.; Raphael, D. R.; Taylor, L.; Wang, J.; McDowell, R. S.; Wells, J. A.; Braisted, A. C. Proc Natl Acad Sci USA 2003, 100, 1603.
6. Bogan, A. A.; Thorn, K. S. J Mol Biol 1998, 280, 1.
7. Pons, J.; Rajpal, A.; Kirsch, J. Protein Sci 1999, 8, 958.
8. Hu, Z.; Ma, B.; Nussinov, R. Proteins 2000, 39, 331.
9. Keskin, O.; Ma, B.; Nussinov, R. J Mol Biol 2005, 345, 1281.
10. Verkhivker, G. M.; Bouzida, D.; Gehlhaar, D. K.; Rejto, P. A.; Freer, S. T.; Rose, P. M. Proteins 2003, 53, 201.
11. Gao, Y.; Wang, R.; Lia, L. J Mol Model 2004, 10, 44.
12. Lopez, M. A.; Kollman, P. A. Protein Sci 1993, 2, 1975.
13. Kortemme, T.; Baker, D. Proc Natl Acad Sci USA 2002, 99, 14116.
14. Kortemme, T.; Kim, D. E.; Baker, D. Sci STKE 2004, 219, 12.
15. Schapira, M.; Totrov, M.; Abagyan, R. J Mol Recognit 1999, 12, 177.
16. Aqvist, J.; Medina, C.; Samuelsson, J. E. Protein Eng 1994, 7, 385.
17. Verkhivker, G. M.; Bouzida, D.; Gehlhaar, D. K.; Rejto, P. A.; Freer, S. T.; Rose, P. M. Proteins 2002, 48, 539.
18. Guerois, R.; Nielsen, J. E.; Serrano, L. J Mol Biol 2002, 320, 369.
19. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Accounts Chem Res 2002, 33, 889.
20. Wang, W.; Donini, O.; Reyes, C. M.; Kollman, P. A. Annu Rev Biophys Biomol Struct 2001, 30, 211.
21. Massova, I.; Kollman, P. A. J Am Chem Soc 1999, 121, 8133.
22. Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. J Am Chem Soc 2001, 123, 5221.
23. Wang, W.; Kollman, P. A. J Mol Biol 2000, 303, 567.
24. Reyes, C. M.; Kollman, P. A. J Mol Biol 2000, 295, 1.
25. Huo, S.; Massova, I.; Kollman, P. A. J Comput Chem 2002, 23, 15.
26. Wagoner, J.; Baker, N. A. J Comput Chem 2004, 25, 1623.
27. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L., III. J Comput Chem 2004, 25, 265.
28. Juffer, A.; Argos, P.; Vogel, H. J Phys Chem B 1997, 101, 7664.
29. Mosyak, L.; Zhang, Y.; Glasfeld, E.; Haney, S.; Stahl, M.; Seehra, J.; Somers, W. S. EMBO J 2002, 19, 3179.
30. Sauer-Eriksson, A. E.; Kleywegt, G. J.; Uhlen, M.; Jones, T. A. Structure 1995, 3, 265.
31. Bhat, T. N.; Bentley, G. A.; Boulot, G.; Greene, M. I.; Tello, D.; Dall'Acqua, W.; Souchon, H.; Schwarz, F. P.; Mariuzza, R. A.; Poljak, R. J. Proc Natl Acad Sci USA 1994, 9, 1089.
32. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A.AMBER 8; University of California, San Francisco, 2004. The Amber biomolecular simulation program.
33. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T., Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
34. Tsui, V.; Case, D. A. Biopolymers (Nucleic Acid Sci) 2001, 56, 275.
35. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. J Comput Phys 1997, 23 327.
36. Pastor, I. W.; Brooks, B. R.; Szabo, A. Mol Phys 1998, 65, 1409.
37. Loncharich, R. J.; Brooks, B. R.; Pastor, R. W. Biopolymers 1992, 32, 523.
38. Izaguirre, J. A.; Catarello, D. P.; Wozniak, J. M.; Skeel, R. D. J Chem Phys 2001, 114, 2090.
39. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. J Comput Chem 2002, 23, 128.
40. Rocchia, W.; Alexov, E.; Honig, B. J Phys Chem B 2001, 105, 6507.
41. Sitkoff, D.; Sharp, K. A.; Honig, B. J Phys Chem 1994, 98, 1978.
42. Moreira, I. S.; Fernandas, P. A.; Ramos, M. J. J Mol Struct (Theochem) 2005, 729, 11.
43. Connolly, M. L. J AppI Crystallogr 1983, 16, 548.
44. Hinke, S. A.; Manhart, S.; Speck, M.; Pederson, R. A.; Demuth, H. U.; McIntosh, C. H. Life Sci 2004, 75, 1857.
45. Arkin, M. R.; Wells, J. A. Nat Rev Drug Discov 2004, 3, 301.
46. Cohlke, H.; Case, D. A. J Comput Chem 2004, 25, 238.
47. Xia, B.; Tsui, V.; Case, D. A.; Dyson, J.; Wright, P. E. J Biomol NMR 2002, 22, 317.
48. Sheinerman, F. B.; Norel, R.; Honig, B. Curr Opin Struct Biol 2002, 10, 153.
49. Schutz, C. N.; Warshel, A. Proteins 2001, 44, 400.
50. Luo, R.; Hsieh, M. J. Proteins 2004, 56, 475.
51. Gilson, M. K.; Honig, B. Biopolymers 1986, 25, 2097.
52. Simonson, T. J Am Chem Soc 1998, 120, 4875.
53. Wisz, M. S.; Hellinga, H. W. Proteins 2003, 51, 360.