Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

Journal of Computational Chemistry

Volumn 28, Issue 11, 2007, Pages 1883-1892

  Sun, Y U ^a   Dominy, Brian N ^b   Latour, Robert A ^a  

^a AMRL   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

Hydrophobic surface; Molecular simulation; Peptide adsorption; Potential of mean force; Solvation effects

Indexed keywords

HYDROPHOBIC SURFACE; MEAN FORCE; MOLECULAR SIMULATION; POTENTIAL OF MEAN FORCE; SOLVATION EFFECTS;

ADSORPTION; COMPUTER SIMULATION; ELECTROSTATICS; HYDROPHOBICITY; SOLVATION;

PEPTIDES;

PEPTIDE; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; SURFACE PROPERTY;

MODELS, MOLECULAR; PEPTIDES; SOLVENTS; SURFACE PROPERTIES;

EID: 34547267323     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20716     Document Type: Article

References (38)

1. Robeson, J. L.; Tilton, R. D. Langmuir 1996, 12, 6104.
2. Johnson, C. A.; Yuan, Y.; Lenhoff, A. M. J Colloid Interface Sci 2000, 223, 261.
3. Sharp, J. S.; Forrest, J. A.; Jones, R. A. Biochemistry 2002, 41, 15810.
4. Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R. B.; Ringnalda, M. N.; Sitkoff, D.; Honig, B. J Phys Chem 1996, 100, 11775.
5. Gray, J. J. Curr Opin Struct Biol 2004, 14, 110.
6. Noinville, V.; Vidal-Madjar, C.; Sebille, B. J Phys Chem 1995, 99, 1516.
7. Tobias, D. J.; Mar, W.; Blasie, J. K.; Klein, M. L. Biophys J 1996, 71, 2933.
8. Ravichandran, S.; Madura, J. D.; Talbot, J. J Phys Chem B 2001, 105, 3610.
9. Raffaini, G.; Ganazzoli, F. Langmuir 2004, 20, 3371.
10. Agashe, M.; Raut, V.; Stuart, S. J.; Latour, R. A. Langmuir 2005, 21, 1103.
11. Feig, M.; Brooks, C. L., III. Curr Opin Struct Biol 2004, 14, 217.
12. Steinbach, P. J. Proteins: Struct Funct Genet 2004, 57, 665.
13. Brooks, B. R.; Braccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
14. Sun, Y.; Latour, R. A. J Comput Chem 2006, 27, 1908.
15. Schaefer, M.; Karplus, M. J Phys Chem 1996, 100, 1578.
16. Vernekar, V. N.; Latour, R. A. Mater Res Innovat 2005, 9, 337.
17. Friedman, R. A.; Mezei, M. J Chem Phys 1995, 102, 419.
18. Roux, B. Comput Phys Commun 1995, 91, 275.
19. Masunov, A.; Lazaridis, T. J Am Chem Soc 2003, 125, 1722.
20. Shimizu, S.; Chan, H. S. Proteins: Struct Funct Genet 2002, 48, 15.
21. Southall, N. T.; Dill, K. A. Biophys Chem 2002, 101/102, 295.
22. Raut, V. P.; Agashe, M. A.; Stuart, S. J.; Latour, R. A. Langmuir 2005, 21, 1629.
23. Zheng, J.; Li, L.; Tsao, H. K.; Sheng, Y. J.; Chen, S.; Jiang, S. Biophys J 2005, 89, 158.
24. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606.
25. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
26. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
27. Basalyga, D. M.; Latour, R. A. J Biomed Mater Res A 2003, 64, 120.
28. Latour, R. A.; Hench, L. L. Biomaterials 2002, 23, 4633.
29. Latour, R. A.; Rini, C. J. J Biomed Mater Res 2002, 60, 564.
30. Ulman, A.; Eilers, J. E.; Tillman, N. Langmuir 1989, 5, 1147.
31. Feller, S.; MacKerell, A. D. J Phys Chem B 2000, 104, 7510.
32. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33.
33. Grossfield, A. http://dasher.wustl.edu/alan/.
34. van Gunsteren, W. F.; Liu, H.; Muller-Plathe, F. J Mol Struct (THEOCHEM) 1998, 432, 9.
35. Schaefer, M.; Bartels, C.; Karplus, M. Theor Chem Acc 1999, 101, 194.
36. Jas, G. S.; Kuczera, K. Biophys J 2004, 87, 3786.
37. Czaplewski, G; Rodziewicz-Motowidlo, S.; Dabal, M.; Liwo, A.; Ripoll, D. R.; Scheraga, H. A. Biophys Chem 2003, 105, 339.
38. Baumketner, A.; Shea, J.-E. Biophys J 2005, 89, 1493.