All-atom level direct folding simulation of a ΒΒα miniprotein

Journal of Chemical Physics

Volumn 128, Issue 10, 2008, Pages

  Jang, Soonmin ^a   Kim, Eunae ^b   Pak, Youngshang ^b,c  

^a Sejong University   (South Korea)

^b Pusan National University   (South Korea)

^c NONE   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; PROTEIN FOLDING; SOLVATION;

BALANCED FORCE FIELDS; CONFORMATIONAL SAMPLING;

PEPTIDES;

PROTEIN; SOLVENT;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; TEMPERATURE;

ALGORITHMS; COMPUTER SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOLVENTS; TEMPERATURE;

EID: 40849124251     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2837655     Document Type: Article

References (38)

1. D. J. Osguthorpe, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00067-1 10, 146 (2000); R. Bonneau and D. Baker, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.30.1.173 30, 173 (2001); C. Hardin, T. V. Pogorelov, and Z. Luthey-Schulten, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(02)00306-8 12, 176 (2002).
2. P. Derreumaux, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.479501 111, 2301 (1999); J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D. R. Ripoll, R. Kamierkiewicz, S. Odziej, W. J. Wedemeyer, K. D. Gibson, Y. A. Arnautova, J. Saunders, Y.-J. Ye, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.041609598 98, 2329 (2001); G. Wei, N. Mousseau, and P. Derreumaux, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1522373 117, 11379 (2002); S.-Y. Kim, J. Lee, and J. Lee, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1689643 120, 8271 (2004).
3. Y. Duan and P. A. Kollman, Science SCIEAS 0036-8075 10.1126/science.282. 5389.740 282, 740 (1998); F. Rao and A. Caflisch, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1591721 119, 4035 (2003).
4. J. Juraszek and P. G. Bolhuis, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0606692103 103, 15859 (2006).
5. N. A. Baker, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2005.02.001 15, 137 (2005).
6. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00172a038 112, 6127 (1990).
7. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.51.1.129 51, 129 (2000); S. Jang, S. Shin, and Y. Pak, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja025675b 124, 4976 (2002); W. L. Jorgensen, J. P. Ulmschneider, and J. Tirado-Rives, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0484579 108, 16264 (2004); H. Fan, A. E. Mark, J. Zhu, and B. Honig, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0408857102 102, 6760 (2005).
8. H. Nymeyer and A. E. Garcia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2232868100 100, 13934 (2003).
9. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0307898101 101, 6456 (2004).
10. R. Zhou, Proteins: Struct., Funct., Genet. PSFGEY 0087-3585 10.1002/prot.10483 53, 148 (2003).
11. T. Yoda, Y. Sugita, and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2004.01.078 386, 460 (2004).
12. Y. Pak, E. Kim, and S. Jang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1804159 121, 9184 (2004).
13. A. Okur, L. Wickstrom, M. Layten, R. Geney, K. Song, V. Hornak, and C. Simmerling, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct050196z 2, 420 (2006).
14. R. Geney, M. Layten, R. Gomperts, V. Hornak, and C. Simmerling, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct050183l 2, 115 (2006).
15. S. Jang, E. Kim, and Y. Pak, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 62, 663 (2006).
16. J. Chen, W. Im, and C. L. Brooks III, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja057216r 128, 3728 (2006).
17. C. B. Anfinsen, Science SCIEAS 0036-8075 10.1126/science.181.4096.223 181, 223 (1973).
18. S. Jang, E. Kim, and Y. Pak, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 66, 53 (2007).
19. E. Kim, S. Jang, and Y. Pak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2775450 127, 145104 (2007).
20. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999).
21. M. Shirts and V. S. Pande, Science SCIEAS 0036-8075 10.1126/science.290. 5498.1903 290, 1903 (2000).
22. Y. M. Rhee and V. S. Pande, Biophys. J. BIOJAU 0006-3495 84, 775 (2003).
23. X. Periole and A. E. Mark, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2404954 126, 014903 (2007).
24. S. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003).
25. W.-J. Son, S. Jang, Y. Pak, and S. Shin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2538966 126, 104906 (2007).
26. C. M. Santiveri, D. Pantoja-Uceda, M. Rico, and M. A. Jiḿnez, Biopolymers BIPMAA 0006-3525 10.1002/bip.20345 79, 150 (2005).
27. Y. Xu, R. Oyola, and F. Gai, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja037053b 125, 15388 (2003).
28. M. Struthers, J. J. Ottesen, and B. Imperiali, Folding Des. FODEFH 1359-0278 10.1016/S1359-0278(98)00015-7 3, 95 (1998).
29. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00124a002 117, 5179 (1995).
30. A. E. García and K. Y. Sanbonmatsu, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.042496899 99, 2782 (2002).
31. J. G. Kim, Y. Fukunishi, A. Kidera, and H. Nakamura, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1786578 121, 5590 (2004).
32. A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Odziej, K. Wachucik, and H. A. Scheraga, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp065380a 111, 260 (2007).
33. J. W. Ponder, TINKER 4.1, software tools for molecular design, Washington University, 2003.
34. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. di Nola, and J. R. Haak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.448118 81, 3684 (1984).
35. M. G. Paterlini and D. M. Ferguson, Chem. Phys. CMPHC2 0301-0104 10.1016/S0301-0104(98)00214-6 236, 243 (1998).
36. B. J. Palmer, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1993.1045 104, 470 (1993).
37. X. Daura, K. Gademann, B. Jaun, D. Seebach, W. F. van Gunsteren, and A. E. Mark, Angew. Chem., Int. Ed. 38, 236 (1999).
38. W. L. DeLano, The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, CA, 2002); http://pymol.sourceforge.net/.