A challenge for peptide coarse graining: Transferability of fragment-based models

Macromolecular Theory and Simulations

Volumn 20, Issue 7, 2011, Pages 451-465

  Engin, Ozge ^a   Villa, Alessandra ^b   Peter, Christine ^c   Sayar, Mehmet ^a  

^a KOÇ UNIVERSITY   (Turkey)

^b KAROLINSKA INSTITUTE   (Sweden)

^c MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

Author keywords

biomaterials; coarse grained modeling; hydrophobic dipeptide; self assembly; transferable force field

Indexed keywords

ATOMISTIC SYSTEM; BUILDING BLOCKES; COARSE GRAINING; COARSE-GRAINED; COARSE-GRAINED MODELING; COMPLEX MATERIALS; COMPUTATIONAL TECHNIQUE; CONFORMATIONAL BEHAVIOR; DESIGN AND DEVELOPMENT; DEVELOPED MODEL; DI-PEPTIDES; DIPEPTIDE; DRUG DESIGN; IN-LINE; INDISPENSABLE TOOLS; LENGTH SCALE; NOVEL MATERIALS; POTENTIAL APPLICATIONS; SIDE-CHAINS; SOLVENT FREE; TRANSFERABLE FORCE-FIELD;

AMINO ACIDS; ATOMS; BIOMATERIALS; COMPUTER SIMULATION; HYDROPHOBICITY; PEPTIDES; THERMODYNAMIC PROPERTIES;

MATHEMATICAL MODELS;

EID: 80051740011     PISSN: 10221344     EISSN: 15213919     Source Type: Journal    
DOI: 10.1002/mats.201100005     Document Type: Article

References (93)

1. S. Verma, K. Joshi, S. Ghosh, J. Med. Chem. 2007, 3, 605.
2. B. Law, R. Weissleder, C. Tung, Biomacromolecules 2006, 7, 1261.
3. T. Holmes, Trends Biotechnol. 2002, 20, 16.
4. D. Harrington, E. Cheng, M. Guler, L. Lee, J. Donovan, R. Claussen, S. Stupp, J. Biomed. Mater. Res. Part A 2006, 78a, 157.
5. S. Segman-Magidovich, H. Grisaru, T. Gitli, Y. Levi-Kalisman, H. Rapaport, Adv. Mater. 2008, 20, 2156.
6. K. Enander, L. Choulier, A. Olsson, D. Yushchenko, D. Kanmert, A. Klymchenko, A. Demchenko, Y. Mly, D. Altschuh, Bioconjugate Chem. 2008, 19, 1864.
7. J. Dovera, G. Hwang, E. Mullen, B. Prorok, S. Suh, J. Microbiol. Methods 2009, 78, 10.
8. J. Hartgerink, T. Clark, M. Ghadiri, Chem. Eur. J. 1998, 4, 1367.
9. X. Gao, H. Matsui, Adv. Mater. 2005, 17, 2037.
10. C. Clementi, Curr. Opin. Struct. Biol. 2008, 18, 10.
11. A. Khalfa, W. Treptow, B. Maigret, M. Tarek, J. Chem. Phys. 2009, 358, 161.
12. M. McCullagh, T. Prytkova, S. Tonzani, N. Winter, G. Schatz, J. Phys. Chem. B 2008, 112, 10388.
13. G. Whitesides, M. Boncheva, PNAS 2002, 99, 4769.
14. G. Colombo, P. Soto, E. Gazit, Trends Biotechnol. 2007, 25, 211.
15. R. J. Hills, L. Lanyuan, G. Voth, PLoS Comput. Biol. 2010, 6, 1.
16. Coarse-Graining of Condensed Phase and Biomolecular Systems, G. A. Voth, Ed., Chapman and Hall, London / CRC Press, Boca Raton, FL / Taylor & Francis, London 2008.
17. G. Bellesia, J. E. Shea, J. Chem. Phys. 2007, 126, 245104.
18. J. Maupetit, P. Tuffery, P. Derreumaux, Proteins Struct. Funct. Bioinf. 2007, 69, 394.
19. W. Tschop, K. Kremer, J. Batoulis, T. Burger, O. Hahn, Acta Polym. 1998, 49, 61.
20. C. Abrams, K. Kremer, Macromolecules 2003, 36, 260.
21. V. A. Harmandaris, D. Reith, N. F. A. van der Vegt, K. Kremer, Macromol. Chem. Phys. 2007, 208, 2109.
22. D. Fritz, V. A. Harmandaris, K. Kremer, N. F. A. van der Vegt, Macromolecules 2009, 42, 7579.
23. A. Villa, C. Peter, N. F. A. van der Vegt, Phys. Chem. Chem. Phys. 2009, 11, 2068.
24. C. Goerbitz, Chem. -Eur. J. 2007, 13, 1022.
25. V. Tozzini, W. Rocchia, A. McCammon, J. Chem. Theory Comput. 2006, 2, 667.
26. C. Abrams, K. Kremer, J. Chem. Phys. 2002, 116, 3162.
27. W. Noid, J. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, A. Andersen, J. Chem. Phys. 2008, 128, 244114.
28. Z. Zhang, L. Lu, W. Noid, J. Krishna, V. Pfaendtner, G. A. Voth, Biophys. J. 2008, 95, 5073.
29. A. Irback, F. Sjunnesson, S. Wallin, PNAS 2000, 97, 13614.
30. H. Nguyen, C. Hall, Biophys. J. 2004, 87, 4122.
31. T. Bereau, M. Deserno, J. Chem. Phys. 2009, 130, 235106.
32. J. Honeycutt, D. Thirumalai, Biopolymers 1992, 32, 695.
33. S. Brown, N. J. Fawzi, T. Head-Gordon, PNAS 2003, 100, 10712.
34. L. Monticelli, S. Kandasamy, X. Periole, R. Larson, P. Tieleman, S. Marrink, J. Chem. Theory Comput. 2008, 4, 819.
35. P. Das, S. Matsiyak, C. Clementi, PNAS 2005, 102, 10141.
36. A. Liwo, S. Oldziej, M. Pincus, R. Wawak, S. Rackovsky, H. Scheraga, J. Comput. Chem. 1997, 18, 849.
37. H. D. Nguyen, C. K. Hall, PNAS 2004, 101, 16180.
38. P. Derreumaux, N. Mousseau, J. Chem. Phys. 2007, 126, 025101.
39. A. Villa, N. F. A. van der Vegt, C. Peter, Phys. Chem. Chem. Phys. 2009, 11, 2077.
40. W. Han, Y. Wu, J. Chem. Theory Comput. 2007, 3, 2146.
41. H. Nguyen, A. Marchut, C. Hall, Protein Sci. 2004, 13, 2909.
42. G. Milano, S. Goudeau, F. Muller-Plathe, J. Polym. Sci., Part B: Polym. Phys. 2005, 43, 871.
43. C. Peter, L. Delle Site, K. Kremer, Soft Matter 2008, 4, 859.
44. G. S. Ayton, W. G. Noid, G. A. Voth, Curr. Opin. Struct. Biol. 2007, 17, 192.
45. S. Miyazawa, R. Jernigan, Macromolecules 1985, 18, 534.
46. S. Miyazawa, R. L. Jernigan, J. Mol. Biol. 1996, 256, 623.
47. S. Marrink, H. Risselada, S. Yefimov, P. Tieleman, A. Vries, J. Phys. Chem. B 2007, 111, 7812.
48. E. Gazit, Febs J. 2005, 272, 5971.
49. J. Shelley, M. Shelley, R. Reeder, S. Bandyopadhyay, M. Klein, J. Phys. Chem. B 2001, 105, 4464.
50. S. O. Nielsen, C. F. Lopez, G. Srinivas, M. L. Klein, J. Chem. Phys. 2003, 119, 7043.
51. S. J. Marrink, A. H. de Vries, A. E. Mark, J. Phys. Chem. B 2004, 108, 750.
52. W. Shinoda, R. Devane, M. Klein, Mol. Simul. 2007, 33, 27.
53. R. Baron, D. Trzesniak, A. de Vries, A. Elsener, S. Marrink, F. van Gunsteren, Chem. Phys. Chem. 2007, 8, 452.
54. A. J. Rzepiela, M. Louhivuori, C. Peter, S. J. Marrink, Phys. Chem. Chem. Phys. 2011, 13, 10437.
55. A. P. Lyubartsev, A. Laaksonen, Phys. Rev. E 1995, 52, 3730.
56. F. Muller-Plathe, Chem. Phys. Chem. 2002, 3, 754.
57. T. Murtola, A. Bunker, I. Vattulainen, M. Deserno, M. Karttunen, Phys. Chem. Chem. Phys. 2009, 11, 1869.
58. C. Peter, K. Kremer, Soft Matter 2009, 5, 4357.
59. V. Rühle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theory Comput. 2009, 5, 3211.
60. S. Izvekov, G. A. Voth, J. Phys. Chem. B 2005, 109, 2469.
61. J. Zhou, I. F. Thorpe, S. Izvekov, G. A. Voth, Biophys. J. 2007, 92, 4289.
62. J. Mullinax, W. Noid, J. Chem. Phys. 2009, 131, 104110.
63. W. Noid, J. Chu, G. Ayton, G. Voth, J. Phys. Chem. B 2007, 111, 4116.
64. M. E. Johnson, T. Head-Gordon, A. A. Louis, J. Chem. Phys. 2007, 126, 144509.
65. A. Villa, C. Peter, N. F. A. van der Vegt, J. Chem. Theory Comput. 2010, 6, 2434.
66. I. R. Cooke, K. Kremer, M. Deserno, Phys. Rev. E 2005, 72, 011506.
67. C. F. Lopez, S. O. Nielsen, P. B. Moore, M. L. Klein, Proc. Natl. Acad. Sci. USA 2004, 101, 4431.
68. P. J. Bond, M. S. P. Sansom, J. Am. Chem. Soc. 2006, 128, 2697.
69. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, S. J. Marrink, J. Chem. Theor. Comput. 2008, 4, 819.
70. J. Michel, M. Orsi, J. W. Essex, J. Phys. Chem. B 2008, 112, 657.
71. B. Hess, C. Holm, N. F. A. van der vegt, J. Chem. Phys. 2006, 124, 164509.
72. B. Hess, C. Holm, N. F. A. van der Vegt, J. Phys. Rev. Lett. 2006, 96, 147801.
73. N. Basdevant, D. Borgis, T. Ha-Duong, J. Phys. Chem. B 2007, 111, 9390.
74. S. Takada, Z. Schulten, P. Wolynes, J. Chem. Phys. 1999, 110, 11616.
75. D. Alemani, F. Collu, M. Cascella, M. Dal Peraro, J. Chem. Theory Comput. 2009, 6, 315.
76. T. Ha-Duong, J. Chem. Theory Comput. 2010, 6, 761.
77. J. Cheung, T. Truskett, Biophys. J. 2005, 89, 2372.
78. J. Silbermann, S. H. L. Klapp, M. Schoen, N. Chennamsetty, H. Bock, K. Gubbins, J. Chem. Phys. 2006, 124, 074105.
79. J. Fischer, D. Paschek, A. Geiger, G. Sadowski, J. Phys. Chem. B 2008, 112, 13561.
80. E. C. Allen, G. C. Rutledge, J. Chem. Phys. 2009, 130, 034904.
81. T. Murtola, M. Karttunen, I. Vattulainen, J. Chem. Phys. 2009, 131, 055101.
82. E. C. Allen, G. C. Rutledge, J. Chem. Phys. 2008, 128, 154115.
83. B. M. Mognetti, P. Virnau, L. Yelash, W. Paul, K. Binder, M. Mueller, L. G. MacDowell, J. Chem. Phys. 2009, 130, 044101.
84. V. Krishna, V. Noid, G. Voth, J. Chem. Phys. 2009, 131, 024103.
85. R. DeVane, M. Klein, C. Chiu, S. O. Nielsen, W. Shinoda, P. Moore, J. Phys. Chem. B 2010, 114, 6386.
86. R. DeVane, W. Shinoda, P. Moore, M. Klein, J. Chem. Theory Comput. 2009, 5, 2115.
87. J. D. McCoy, J. C. Curro, Macromolecules 1998, 31, 9362.
88. A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H. A. Scheraga, PNAS 2002, 99, 1937.
89. D. Curco, R. Nussinov, C. Aleman, J. Phys. Chem. B 2007, 111, 10538.
90. R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein, J. Chem. Theory Comput. 2009, 5, 2115.
91. V. A. Harmandaris, N. P. Adhikari, N. F. A. van der Vegt, K. Kremer, Macromolecules 2006, 39, 6708.
92. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089.
93. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, L. G. Pedersen, J. Chem. Phys. 1995, 103, 8577.