Reference state for the generalized Yvon-Born-Green theory: Application for coarse-grained model of hydrophobic hydration

Journal of Chemical Physics

Volumn 133, Issue 12, 2010, Pages

  Mullinax, J W ^a   Noid, W G ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC SIMULATIONS; COARSE GRAINED MODELS; COARSE-GRAINED; COMPLEX SYSTEMS; COMPUTATIONAL FRAMEWORK; COMPUTATIONALLY EFFICIENT; CORRELATION FUNCTION; DETAILED MODELS; EXPERIMENTAL DATA; HYDROPHOBIC HYDRATION; HYDROPHOBIC SOLUTES; MANY-BODY POTENTIALS; OPTIMAL APPROXIMATION; QUANTITATIVE ACCURACY; REFERENCE STATE; SOLVATION STRUCTURE; STRUCTURAL CORRELATION; STRUCTURAL INFORMATION;

COMPUTATIONAL COMPLEXITY; HYDROPHOBICITY; METHANOL; OPTIMIZATION;

COMPUTER SIMULATION;

METHANOL; SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; MARSILEACEAE; SOLUBILITY; TECHNIQUE; WETTABILITY;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MARSILEACEAE; METHANOL; METHODS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; SOLUBILITY; SOLVENTS; WETTABILITY;

EID: 77957733407     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3481574     Document Type: Article

References (93)

1. M. P. Allen and D. P. Tildesley, Computer Simulation of Liquids (Oxford, New York, 1987).
2. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic, San Diego, 2002).
3. G. Brannigan, L. C.-L. Lin, and F. L. H. Brown, Eur. Biophys. J. EBJOE8 0175-7571 35, 104 (2006). 10.1007/s00249-005-0013-y (Pubitemid 43042770)
4. M. Levitt, J. Mol. Biol. JMOBAK 0022-2836 104, 59 (1976). 10.1016/0022-2836(76)90004-8
5. Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by, G. A. Voth, (CRC, Boca Raton, FL, 2009).
6. V. Tozzini, Curr. Opin. Struct. Biol. COSBEF 0959-440X 15, 144 (2005). 10.1016/j.sbi.2005.02.005
7. C. Clementi, Curr. Opin. Struct. Biol. COSBEF 0959-440X 18, 10 (2008).
8. A. T. Hagler and B. Honig, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 75, 554 (1978). 10.1073/pnas.75.2.554
9. G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. COSBEF 0959-440X 17, 192 (2007). 10.1016/j.sbi.2007.03.004 (Pubitemid 46584804)
10. T. Murtola, A. Bunker, I. Vattulainen, M. Deserno, and M. Karttunen, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 11, 1869 (2009). 10.1039/b818051b
11. Y. Mu, D. S. Kosov, and G. Stock, J. Phys. Chem. B JPCBFK 1089-5647 107, 5064 (2003). 10.1021/jp022445a
12. T. Yoda, Y. Sugita, and Y. Okamoto, Chem. Phys. CMPHC2 0301-0104 307, 269 (2004). 10.1016/j.chemphys.2004.08.002
13. C. Maciel, E. E. Fileti, and R. Rivelino, J. Phys. Chem. B JPCBFK 1089-5647 113, 7045 (2009). 10.1021/jp902265a
14. R. DeVane, M. L. Klein, C. C. Chiu, S. O. Nielsen, W. Shinoda, and P. B. Moore, J. Phys. Chem. B JPCBFK 1089-5647 114, 6386 (2010). 10.1021/jp9117369
15. C. C. Chiu, R. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, and S. O. Nielsen, J. Phys. Chem. B JPCBFK 1089-5647 114, 6394 (2010). 10.1021/jp9117375
16. J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, and M. L. Klein, J. Phys. Chem. B JPCBFK 1089-5647 105, 4464 (2001). 10.1021/jp010238p (Pubitemid 35381588)
17. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Chem. Phys. JCPSA6 0021-9606 119, 7043 (2003). 10.1063/1.1607955
18. W. Shinoda, R. Devane, and M. L. Klein, Mol. Simul. MOSIEA 0892-7022 33, 27 (2007). 10.1080/08927020601054050 (Pubitemid 46446368)
19. S. J. Marrink, A. H. de Vries, and A. E. Mark, J. Phys. Chem. B JPCBFK 1089-5647 108, 750 (2004). 10.1021/jp036508g
20. S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries, J. Phys. Chem. B JPCBFK 1089-5647 111, 7812 (2007). 10.1021/jp071097f (Pubitemid 47169693)
21. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S. -J. Marrink, J. Chem. Theory Comput. JCTCCE 1549-9618 4, 819 (2008). 10.1021/ct700324x
22. R. DeVane, W. Shinoda, P. B. Moore, and M. L. Klein, J. Chem. Theory Comput. JCTCCE 1549-9618 5, 2115 (2009). 10.1021/ct800441u
23. A. Liwo, S. Oldziej, M. R. Pincus, R. J. Wawak, S. Rackovsky, and H. A. Scheraga, J. Comput. Chem. JCCHDD 0192-8651 18, 849 (1997). 10.1002/(SICI)1096- 987X(199705)18:7<849::AID-JCC1>3.0.CO;2-R
24. W. Tschöp, K. Kremer, J. Batoulis, T. Burger, and O. Hahn, Acta Polym. ACPODY 0323-7648 49, 61 (1998). 10.1002/(SICI)1521-4044(199802)49:2/ 3<61::AID-APOL61>3.0.CO;2-V
25. J. Baschnagel, K. Binder, P. Doruker, A. A. Gusev, O. Hahn, K. Kremer, W. L. Mattice, F. Muller-Plathe, M. Murat, W. Paul, S. Santos, U. W. Suter, and V. Tries, Adv. Polym. Sci. APSIDK 0065-3195 152, 41 (2000). 10.1007/3-540-46778-5- 2
26. V. A. Harmandaris, N. P. Adhikari, N. F. A. van der Vegt, and K. Kremer, Macromolecules MAMOBX 0024-9297 39, 6708 (2006). 10.1021/ma0606399 (Pubitemid 44555117)
27. W. Schommers, Phys. Rev. A PLRAAN 1050-2947 28, 3599 (1983). 10.1103/PhysRevA.28.3599
28. F. Müller-Plathe, ChemPhysChem CPCHFT 1439-4235 3, 754 (2002). 10.1002/1439-7641(20020916)3:9<754::AID-CPHC754>3.0.CO;2-U
29. D. Reith, M. Pütz, and F. Müller-Plathe, J. Comput. Chem. JCCHDD 0192-8651 24, 1624 (2003). 10.1002/jcc.10307
30. A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E PLEEE8 1063-651X 52, 3730 (1995). 10.1103/PhysRevE.52.3730
31. A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E PLEEE8 1063-651X 55, 5689 (1997). 10.1103/PhysRevE.55.5689
32. M. S. Shell, J. Chem. Phys. JCPSA6 0021-9606 129, 144108 (2008). 10.1063/1.2992060
33. A. Savelyev and G. A. Papoian, J. Phys. Chem. B JPCBFK 1089-5647 113, 7785 (2009). 10.1021/jp9005058
34. A. Savelyev and G. A. Papoian, Biophys. J. BIOJAU 0006-3495 96, 4044 (2009). 10.1016/j.bpj.2009.02.067
35. R. L. McGreevy and L. Pusztai, Mol. Simul. MOSIEA 0892-7022 1, 359 (1988). 10.1080/08927028808080958
36. D. A. Keen and R. L. McGreevy, Nature (London) NATUAS 0028-0836 344, 423 (1990). 10.1038/344423a0
37. T. Murtola, M. Karttunen, and I. Vattulainen, J. Chem. Phys. JCPSA6 0021-9606 131, 055101 (2009). 10.1063/1.3167405
38. E. C. Allen and G. C. Rutledge, J. Chem. Phys. JCPSA6 0021-9606 130, 034904 (2009). 10.1063/1.3055594
39. E. C. Allen and G. C. Rutledge, J. Chem. Phys. JCPSA6 0021-9606 130, 204903 (2009). 10.1063/1.3139025
40. R. L. Henderson, Phys. Lett. A PYLAAG 0375-9601 49, 197 (1974). 10.1016/0375-9601(74)90847-0
41. J. T. Chayes, L. Chayes, and E. H. Lieb, Commun. Math. Phys. CMPHAY 0010-3616 93, 57 (1984). 10.1007/BF01218639
42. J. T. Chayes and L. Chayes, J. Stat. Phys. JSTPBS 0022-4715 36, 471 (1984). 10.1007/BF01010992
43. G. Megariotis, A. Vyrkou, A. Leygue, and D. N. Theodorou, " Systematic coarse graining of 4-cyano-4-pentylbiphenyl.," Ind. Eng. Chem. Res. IECRED 0888-5885 10.1021/ie901957r (in press).
44. S. Izvekov and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 109, 2469 (2005). 10.1021/jp044629q (Pubitemid 40304419)
45. S. Izvekov and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 123, 134105 (2005). 10.1063/1.2038787 (Pubitemid 41434694)
46. W. G. Noid, J. -W. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 128, 244114 (2008). 10.1063/1.2938860
47. W. G. Noid, P. Liu, Y. T. Wang, J. -W. Chu, G. S. Ayton, S. Izvekov, H. C. Andersen, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 128, 244115 (2008). 10.1063/1.2938857
48. W. G. Noid, J. -W. Chu, G. S. Ayton, and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 111, 4116 (2007). 10.1021/jp068549t (Pubitemid 46732961)
49. L. Larini, L. Y. Lu, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 132, 164107 (2010). 10.1063/1.3394863
50. A. Das and H. C. Andersen, J. Chem. Phys. JCPSA6 0021-9606 132, 164106 (2010). 10.1063/1.3394862
51. V. Krishna, W. G. Noid, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 131, 024103 (2009). 10.1063/1.3167797
52. J. W. Mullinax and W. G. Noid, J. Chem. Phys. JCPSA6 0021-9606 131, 104110 (2009). 10.1063/1.3220627
53. J. W. Mullinax and W. G. Noid, Phys. Rev. Lett. PRLTAO 0031-9007 103, 198104 (2009). 10.1103/PhysRevLett.103.198104
54. J. W. Mullinax and W. G. Noid, J. Phys. Chem. C JPCCCK 1932-7447 114, 5661 (2010). 10.1021/jp9073976
55. J. -P. Hansen and I. R. McDonald, Theory of Simple Liquids, 2nd ed. (Academic, San Diego, CA, 1990).
56. M. Praprotnik, L. Delle Site, and K. Kremer, J. Chem. Phys. JCPSA6 0021-9606 126, 134902 (2007). 10.1063/1.2714540 (Pubitemid 46550269)
57. M. Praprotnik, L. Delle Site, and K. Kremer, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 59, 545 (2008). 10.1146/annurev.physchem.59.032607.093707 (Pubitemid 351703397)
58. J. W. Mullinax and W. G. Noid, " Recovering physical potentials from a model protein databank.," Proc. Natl. Acad. Sci. USA (to be published).
59. A. J. Chorin, O. H. Hald, and R. Kupferman, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 97, 2968 (2000). 10.1073/pnas.97.7.2968 (Pubitemid 30183238)
60. A. J. Chorin, Multiscale Model. Simul. MMSUBT 1540-3459 1, 105 (2003). 10.1137/S1540345902405556
61. A. J. Chorin and O. H. Hald, Stochastic Tools in Mathematics and Science (Springer, New York, 2006).
62. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. JMMOFK 0948-5023 7, 306 (2001).
63. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. JCCHDD 0192-8651 26, 1701 (2005). 10.1002/jcc.20291 (Pubitemid 43076182)
64. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. JACSAT 0002-7863 118, 11225 (1996). 10.1021/ja9621760 (Pubitemid 26399746)
65. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 99, 8345 (1993). 10.1063/1.465608
66. S. Noś, Mol. Phys. MOPHAM 0026-8976 52, 255 (1984). 10.1080/00268978400101201
67. W. G. Hoover, Phys. Rev. A PLRAAN 1050-2947 31, 1695 (1985). 10.1103/PhysRevA.31.1695
68. M. Parrinello and A. Rahman, J. Chem. Phys. JCPSA6 0021-9606 76, 2662 (1982). 10.1063/1.443248
69. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in FORTRAN: The Art of Scientific Computing (Cambridge University Press, New York, 1992).
70. J. W. Demmel, Applied Numerical Linear Algebra (SIAM, Philadelphia, PA, 1997).
71. E. Anderson, Z. Bai, C. Bischof, S. Blackford, J. Demmel, J. Dongarra, J. D. Croz, A. Greenbaum, S. Hammarling, A. McKenney, and D. Sorensen, LAPACK Users' Guide (SIAM, Philadelphia, PA, 1999).
72. J. G. Speight, Lange's Handbook of Chemistry, 16th ed. (McGraw-Hill, New York, 2005).
73. D. van der Spoel, E. Lindahl, B. Hess, A. R. van Buuren, E. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, K. A. Feenstra, R. van Drunen, and H. J. C. Berendsen, GROMACS user manual version 3.3 (2005).
74. H. C. Andersen, D. Chandler, and J. D. Weeks, Adv. Chem. Phys. ADCPAA 0065-2385 34, 105 (1976). 10.1002/9780470142530.ch2
75. C. Oostenbrink, A. Villa, A. E. Mark, and W. F. Van Gunsteren, J. Comput. Chem. JCCHDD 0192-8651 25, 1656 (2004). 10.1002/jcc.20090
76. A. A. Louis, J. Phys.: Condens. Matter JCOMEL 0953-8984 14, 9187 (2002). 10.1088/0953-8984/14/40/311 (Pubitemid 35275047)
77. M. E. Johnson, T. Head-Gordon, and A. A. Louis, J. Chem. Phys. JCPSA6 0021-9606 126, 144509 (2007). 10.1063/1.2715953 (Pubitemid 46610010)
78. S. Tanaka and H. A. Scheraga, Macromolecules MAMOBX 0024-9297 9, 945 (1976). 10.1021/ma60054a013
79. S. Miyazawa and R. L. Jernigan, Macromolecules MAMOBX 0024-9297 18, 534 (1985). 10.1021/ma00145a039
80. M. J. Sippl, J. Mol. Biol. JMOBAK 0022-2836 213, 859 (1990). 10.1016/S0022-2836(05)80269-4
81. M. J. Sippl, Curr. Opin. Struct. Biol. COSBEF 0959-440X 5, 229 (1995). 10.1016/0959-440X(95)80081-6
82. R. L. Jernigan and I. Bahar, Curr. Opin. Struct. Biol. COSBEF 0959-440X 6, 195 (1996). 10.1016/S0959-440X(96)80075-3 (Pubitemid 26128823)
83. J. Moult, Curr. Opin. Struct. Biol. COSBEF 0959-440X 7, 194 (1997). 10.1016/S0959-440X(97)80025-5 (Pubitemid 27156717)
84. F. E. Boas and P. B. Harbury, Curr. Opin. Struct. Biol. COSBEF 0959-440X 17, 199 (2007). 10.1016/j.sbi.2007.03.006 (Pubitemid 46575252)
85. C. Wilson and S. Doniach, Proteins: Struct., Funct., Genet. PSFGEY 0087-3585 6, 193 (1989). 10.1002/prot.340060208
86. J. Skolnick, Curr. Opin. Struct. Biol. COSBEF 0959-440X 16, 166 (2006). 10.1016/j.sbi.2006.02.004
87. P. D. Thomas and K. A. Dill, J. Mol. Biol. JMOBAK 0022-2836 257, 457 (1996). 10.1006/jmbi.1996.0175 (Pubitemid 26114046)
88. A. Ben-Naim, J. Chem. Phys. JCPSA6 0021-9606 107, 3698 (1997). 10.1063/1.474725
89. J. Shimada, A. V. Ishchenko, and E. I. Shakhnovich, Protein Sci. PRCIEI 0961-8368 9, 765 (2000).
90. J. Skolnick, L. Jaroszewski, A. Kolinski, and A. Godzik, Protein Sci. PRCIEI 0961-8368 6, 676 (1997). 10.1002/pro.5560060317
91. M. R. Betancourt and D. Thirumalai, Protein Sci. PRCIEI 0961-8368 8, 361 (1999).
92. S. Liu, C. Zhang, H. Y. Zhou, and Y. Q. Zhou, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 56, 93 (2004). 10.1002/prot.20019 (Pubitemid 38720841)
93. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics JMGRDV 0263-7855 14, 33 (1996). 10.1016/0263-7855(96)00018-5 (Pubitemid 26152973)