Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations

  • Kwac, Ki-Jeong (Department of Chemistry and Biochemistry, University of Texas at Austin) ;
  • Wolynes, Peter G. (Department of Chemistry and Biochemistry, University of California San Diego)
  • Published : 2008.11.20
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References

  1. Fersht, A. R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; W. H. Freeman and Co.: New York, 1999
  2. Oleververg, M.; Wolynes, P. G. Quarterly Rev. Biophys. 2005, 38, 405 https://doi.org/10.1017/S0033583505004075
  3. Munoz, V. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 395 https://doi.org/10.1146/annurev.biophys.36.040306.132608
  4. Plotkin, S. S.; Onuchic, J. N. Quarterly Rev. Biophys. 2002, 35, 111
  5. Plotkin, S. S.; Onuchic, J. N. Quarterly Rev. Biophys. 2002, 35, 205
  6. Shea, J.-E.; Brooks III, C. L. Annu. Rev. Phys. Chem. 2001, 52, 499 https://doi.org/10.1146/annurev.physchem.52.1.499
  7. Scheraga, H. A. Biopolymers 2007, 89, 479 https://doi.org/10.1002/bip.20890
  8. Wolynes, P. G. Phil. Trans. R. Soc. A 2005, 363, 453 https://doi.org/10.1098/rsta.2004.1502
  9. Petrey, D.; Honig, B. Mol. Cell 2005, 20, 811 https://doi.org/10.1016/j.molcel.2005.12.005
  10. Floudas, C. A. Biotech. Bioeng. 2007, 97, 207 https://doi.org/10.1002/bit.21411
  11. Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779 https://doi.org/10.1006/jmbi.1993.1626
  12. Fiser, A.; Do, R. K. G.; Sali, A. Prot. Sci. 2000, 9, 1753 https://doi.org/10.1110/ps.9.9.1753
  13. Jones, D. T. J. Mol. Biol. 1999, 287, 797 https://doi.org/10.1006/jmbi.1999.2583
  14. Skolnick, J.; Kihara, D.; Zhang, Y. Proteins 2004, 56, 502 https://doi.org/10.1002/prot.20106
  15. Zhang, Y.; Skolnick, J. Proc. Natl. Acad. Sci. USA 2005, 102, 1029 https://doi.org/10.1073/pnas.0407152101
  16. Boas, F. E.; Harbury, P. B. Curr. Opin. Struct. Biol. 2007, 17, 199 https://doi.org/10.1016/j.sbi.2007.03.006
  17. Quintilla, A.; Starikov, E.; Wenzel, W. J. Chem. Theory Comput. 2007, 3, 1183 https://doi.org/10.1021/ct600274a
  18. Verma, A.; Wenzel, W. BMC Struct. Biol. 2007, 7, 12 https://doi.org/10.1186/1472-6807-7-12
  19. Yang, J. S.; Chen, W. W.; Skolnick, J.; Shakhnovich, E. I. Structure 2007, 15, 53 https://doi.org/10.1016/j.str.2006.11.010
  20. Summa, C. M.; Levitt, M.; Degrado, W. F. J. Mol. Biol. 2005, 352, 986 https://doi.org/10.1016/j.jmb.2005.07.054
  21. Summa, C. M.; Levitt, M. Proc. Natl. Acad. Sci. USA 2007, 104, 3177 https://doi.org/10.1073/pnas.0611593104
  22. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323 https://doi.org/10.1063/1.1383989
  23. Freidrichs, M. S.; Wolynes, P. G. Science 1989, 246, 371 https://doi.org/10.1126/science.246.4928.371
  24. Hardin, C.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14235 https://doi.org/10.1073/pnas.230432197
  25. Hardin, C.; Eastwood, M. P.; Prentiss, M. C.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679 https://doi.org/10.1073/pnas.252753899
  26. Zong, C.; Papoian, G. A.; Ulander, J.; Wolynes, P. G. J. Am. Chem. Soc. 2006, 128, 5168 https://doi.org/10.1021/ja058589v
  27. Prentiss, M. C.; Hardin, C.; Eastwood, M. P.; Zong, C.; Wolynes, P. G. J. Chem. Theory Comput. 2006, 2, 705 https://doi.org/10.1021/ct0600058
  28. Stryer, L. Biochemistry; W. H. Freeman and Company: New York, 1988
  29. Bryngelson, J. D.; Hopfield, J. J.; Southard Jr., S. N. Tetrahedron Computer Methodology 1990, 3, 129 https://doi.org/10.1016/0898-5529(90)90048-D
  30. Krishna, M. M. G.; Maity, H.; Rumbley, J. N.; Lin, Y.; Englander, S. W. J. Mol. Biol. 2006, 359, 1410 https://doi.org/10.1016/j.jmb.2006.04.035
  31. Ptitsyn, O. B. Dokl. Nauk. SSSR 1973, 210, 1213
  32. Baldwin, R. L.; Rose, G. D. Trends Biochem. Sci. 1999, 24, 26 https://doi.org/10.1016/S0968-0004(98)01346-2
  33. Cuff, J. A.; Clamp, M. E.; Siddiqui, A. S.; Finlay, M.; Barton, G. J. Bioinformatics 1998, 14, 892 https://doi.org/10.1093/bioinformatics/14.10.892
  34. Pollastri, G.; McLysaght, A. Bioinformatics 2005, 21, 1719 https://doi.org/10.1093/bioinformatics/bti203
  35. Rost, B.; Sander, C. J. Mol. Biol. 1993, 232, 584 https://doi.org/10.1006/jmbi.1993.1413
  36. Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A. Proteins 2004, 55, 351 https://doi.org/10.1002/prot.10613
  37. Papoian, G. A.; Ulander, J.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352 https://doi.org/10.1073/pnas.0307851100
  38. Goldstein, R. A.; Luthey-Schulten, Z. A.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4918, 9029
  39. Aurora, R.; Creamer, T. P.; Srinivasan, R.; Rose, G. D. J. Biol. Chem. 1997, 272, 1413 https://doi.org/10.1074/jbc.272.3.1413
  40. Scott, K. A.; Alonso, D. O. V.; Sato, S.; Fersht, A. R.; Daggett, V. Proc. Natl. Acad. Sci. USA 2007, 104, 2661 https://doi.org/10.1073/pnas.0611182104
  41. Sharpe, T.; Jonsson, A. L.; Rutherford, T. J.; Daggett, V.; Fersht, A. R. Prot. Sci. 2007, 16, 2233 https://doi.org/10.1110/ps.073004907
  42. Jayachandran, G.; Vishal, V.; Garcia, A. E.; Pande, V. S. J. Struct. Biol. 2007, 157, 491 https://doi.org/10.1016/j.jsb.2006.10.001
  43. Kim, D. E.; Yi, Q.; Gladwin, S. T.; Goldberg, J. M.; Baker, D. J. Mol. Biol. 1998, 284, 807 https://doi.org/10.1006/jmbi.1998.2200
  44. Charkrabarty, A.; Baldwin, R. L. Adv. Protein Chem. 1995, 46, 141 https://doi.org/10.1016/S0065-3233(08)60334-4
  45. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Proc. Natl. Acad. Sci. USA 1997, 94, 2833 https://doi.org/10.1073/pnas.94.7.2833
  46. Dyson, H. J.; Merutka, G.; Waltho, J. P.; Lerner, R. A.; Wright, P. E. J. Mol. Biol. 1992, 226, 795 https://doi.org/10.1016/0022-2836(92)90633-U
  47. Dyson, H. J.; Sayre, J. R.; Meruka, G.; Shin, H.-C.; Lerner, R. A.; Wright, P. E. J. Mol. Biol. 1992, 226, 819 https://doi.org/10.1016/0022-2836(92)90634-V
  48. Jimenez, M. A.; Munoz, V.; Rico, M.; Serrano, L. J. Mol. Biol. 1994, 242, 487
  49. Saven, J. G.; Wolynes, P. G. J. Mol. Biol. 1996, 257, 199 https://doi.org/10.1006/jmbi.1996.0156
  50. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, Jr., K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179 https://doi.org/10.1021/ja00124a002
  51. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. J. Comput. Chem. 2003, 24, 1999
  52. Onufriev, A.; Bashford, D.; Case, D. A. Proteins 2004, 55, 383 https://doi.org/10.1002/prot.20033
  53. Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev. A. J. Chem. Theory Comput. 2007, 3, 156 https://doi.org/10.1021/ct600085e
  54. Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.; Wolynes, P. G. IBM J. Res. Dev. 2001, 45, 475 https://doi.org/10.1147/rd.453.0475
  55. Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G. Prot. Sci. 1996, 5, 1043
  56. Andersen, C. A. F.; Palmer, A. G.; Brunak, S.; Rost, B. Structure 2002, 10, 175 https://doi.org/10.1016/S0969-2126(02)00700-1
  57. Case, D A.; Darden, T. A.; Cheatham III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, Jr., K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006
  58. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684 https://doi.org/10.1063/1.448118
  59. Garcia, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782 https://doi.org/10.1073/pnas.042496899
  60. The definitions of the ${\alpha}R$, $\beta$, $P_{II}$, and ${\alpha}$L regions in the Ramachandran plot are the same as in the following paper: Kwac, K.; Lee, K.-K.; Han, J. B.; Oh, K.-I.; Cho, M. J. Chem. Phys. 2008, 128, 105106 https://doi.org/10.1063/1.2837461

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