A coarse grain model for protein-surface interactions

Journal of Chemical Physics

Volumn 139, Issue 9, 2013, Pages

  Wei, Shuai ^a   Knotts IV, Thomas A ^a  

^a Brigham Young University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORPTION ENERGIES; CHEMICAL SPECIFICITY; COARSE GRAIN MODEL; FREE ENERGY OF ADSORPTION; MOLECULAR SIMULATIONS; PROTEIN STABILITY; PROTEIN-SURFACE INTERACTIONS; SURFACE INTERACTIONS;

ADSORPTION; COMPUTER SIMULATION; MOLECULAR BIOLOGY;

PROTEINS;

PROTEIN; PROTEIN BINDING;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN BINDING; SURFACE PROPERTY;

MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEINS; SURFACE PROPERTIES;

EID: 84884770222     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4819131     Document Type: Article

References (69)

1. P. Jonkheijm, D. Weinrich, H. Schroeder, C. M. Niemeyer, and H. Waldmann, Angew. Chem., Int. Ed. 47, 9618 (2008). 10.1002/anie.200801711
2. U. Bilitewski, Anal. Chim. Acta 568, 232 (2006). 10.1016/j.aca.2005.12. 073
3. H. Zhu and M. Snyder, Curr. Opin. Chem. Biol. 7, 55 (2003). 10.1016/S1367-5931(02)00005-4
4. M. Uttamchandani and S. Q. Yao, Curr. Pharm. Des. 14, 2428 (2008). 10.2174/138161208785777450
5. M. Cretich, F. Damina, G. Pirria, and M. Chiari, Biomol. Eng. 23, 77 (2006). 10.1016/j.bioeng.2006.02.001
6. I. Balboni, S. M. Chan, M. Kattah, J. D. Tenenbaum, A. J. Butte, and P. J. Utz, Annu. Rev. Immunol. 24, 391 (2006). 10.1146/annurev.immunol.24.021605. 090709
7. P. Angenendt, J. Glökler, D. Murphy, H. Lehrach, and D. J. Cahill, Anal. Biochem. 309, 253 (2002). 10.1016/S0003-2697(02)00257-9
8. P. Angenendt, J. Glökler, J. Sobek, H. Lehrach, and D. J. Cahill, J. Chromatogr. A 1009, 97 (2003). 10.1016/S0021-9673(03)00769-6
9. P. Peluso, D. S. Wilson, D. Do, H. Tran, M. Venkatasubbaiah, D. Quincy, B. Heidecker, K. Poindexter, N. Tolani, M. Phelan, K. Witte, L. S. Jung, P. Wagner, and S. Nock, Anal. Biochem. 312, 113 (2003). 10.1016/S0003-2697(02) 00442-6
10. M. Feldmann, Nat. Rev. Immun. 2, 364 (2002). 10.1038/nri802
11. M. Feldmann and L. Steinman, Nature (London) 435, 612 (2005). 10.1038/nature03727
12. J. Vilček and M. Feldmann, Trends Pharmacol. Sci. 25, 201 (2004). 10.1016/j.tips.2004.02.011
13. J. J. Gray, Curr. Opin. Struct. Biol. 14, 110 (2004). 10.1016/j.sbi.2003.12.001
14. R. Wacker, H. Schroder, and C. M. Niemeyer, Anal. Biochem. 330, 281 (2004). 10.1016/j.ab.2004.03.017
15. T. Joos and J. Bachmann, Front. Biosci. 14, 4376 (2009). 10.2741/3534
16. K. Nakanishi, T. Sakiyama, and K. Imamura, J. Biosci. Bioeng. 91, 233 (2001). 10.1016/S1389-1723(01)80127-4
17. M. F. M. Engel, A. J. W. G. Visser, and C. P. M. van Mierlo, Proc. Natl. Acad. Sci. U.S.A. 101, 11316 (2004). 10.1073/pnas.0401603101
18. P. Billsten, M. Wahlgren, T. Arnebrant, J. McGuire, and H. Elwing, J. Colloid Interface Sci. 175, 77 (1995). 10.1006/jcis.1995.1431
19. C. Czeslik and R. Winter, Phys. Chem. Chem. Phys. 3, 235 (2001). 10.1039/b005900p
20. H. Larsericsdotter, S. Oscarsson, and J. Buijs, J. Colloid Interface Sci. 276, 261 (2004). 10.1016/j.jcis.2004.03.056
21. A. P. L. Brun, S. A. Holt, D. S. Shah, C. F. Majkrzak, and J. H. Lakey, Eur. Biophys. J. 37, 639 (2008). 10.1007/s00249-008-0291-2
22. T. S. Tsapikouni and Y. F. Missirlis, Mater. Sci. Eng., B 152, 2 (2008). 10.1016/j.mseb.2008.06.007
23. V. P. Raut, M. A. Agashe, S. J. Stuart, and R. A. Latour, Langmuir 21, 1629 (2005). 10.1021/la047807f
24. M. Agashe, V. Raut, S. J. Stuart, and R. A. Latour, Langmuir 21, 1103 (2005). 10.1021/la0478346
25. J. Zheng, Y. He, S. Chen, L. Li, M. T. Bernards, and S. Jiang, J. Chem. Phys. 125, 174714 (2006). 10.1063/1.2363978
26. G. Raffaini and F. Ganazzoli, Langmuir 26, 5679 (2010). 10.1021/la903769c
27. S.-W. Hung, P.-Y. Hsiao, M.-C. Lu, and C.-C. Chieng, J. Phys. Chem. B 116, 12661 (2012). 10.1021/jp304695w
28. Y. Sun, W. J. Welsh, and R. A. Latour, Langmuir 21, 5616 (2005). 10.1021/la046932o
29. H.-X. Zhou and K. A. Dill, Biochemistry 40, 11289 (2001). 10.1021/bi0155504
30. J. Zhou, S. Chen, and S. Jiang, Langmuir 19, 3472 (2003). 10.1021/la026871z
31. S. Ravichandran, J. D. Madura, and J. Talbot, J. Phys. Chem. B 105, 3610 (2001). 10.1021/jp010223r
32. F. Carlsson, E. Hyltner, T. Arnebrant, M. Malmsten, and P. Linse, J. Phys. Chem. B 108, 9871 (2004). 10.1021/jp0495186
33. V. Castells and P. R. van Tassel, J. Chem. Phys. 122, 084707 (2005). 10.1063/1.1849772
34. S. Y. Victoria Castells and P. R. V. Tassel, Phys. Rev. E 65, 031912 (2002). 10.1103/PhysRevE.65.031912
35. T. A. Knotts IV, N. Rathore, and J. J. de Pablo, Biophys. J. 94, 4473 (2008). 10.1529/biophysj.107.123158
36. Z. Zhuang, A. I. Jewett, P. Soto, and J.-E. Shea, Phys. Biol. 6, 015004 (2009). 10.1088/1478-3975/6/1/015004
37. Y. Xie, J. Zhou, and S. Jiang, J. Chem. Phys. 132, 065101 (2010). 10.1063/1.3305244
38. M. Friedel, A. Baumketner, and J. Shea, Proc. Natl. Acad. Sci. U.S.A. 103, 8396 (2006). 10.1073/pnas.0601210103
39. T. A. Knotts IV, N. Rathore, and J. J. de Pablo, Proteins 61, 385 (2005). 10.1002/prot.20581
40. S. Wei and T. A. Knotts IV, J. Chem. Phys. 133, 115102 (2010). 10.1063/1.3479039
41. Y. Wei and R. A. Latour, Langmuir 25, 5637 (2009). 10.1021/la8042186
42. A. Morriss-Andrews, G. Bellesia, and J.-E. Shea, J. Chem. Phys. 135, 085102 (2011). 10.1063/1.3624929
43. R. B. Pandey, Z. Kuang, B. L. Farmer, S. S. Kim, and R. R. Naik, Soft Matter 8, 9101 (2012). 10.1039/c2sm25870f
44. J. Karanicolas and C. L. Brooks III, J. Mol. Biol. 334, 309 (2003). 10.1016/j.jmb.2003.09.047
45. J. Karanicolas and C. L. Brooks III, Proc. Natl. Acad. Sci. U.S.A. 100, 3954 (2003). 10.1073/pnas.0731771100
46. J. Karanicolas and C. L. Brooks III, Proc. Natl. Acad. Sci. U.S.A. 101, 3432 (2004). 10.1073/pnas.0304825101
47. R. D. Hills, Jr. and C. L. Brooks III, Int. J. Mol. Sci. 10, 889 (2009). 10.3390/ijms10030889
48. Y. Wei and R. A. Latour, Langmuir 26, 18852 (2010). 10.1021/la103685d
49. A. Lehninger, D. L. Nelson, and M. M. Cox, Lehninger Principles of Biochemistry, 5th ed. (W. H. Freeman, 2008).
50. J. Kyte and R. F. Doolittle, J. Mol. Biol. 157, 105 (1982). 10.1016/0022-2836(82)90515-0
51. M. Hanson, K. Unger, R. Denoyel, and J. Rouquerol, J. Biochem. Biophys. Methods 29, 283 (1994). 10.1016/0165-022X(94)90039-6
52. G. Wildegger and T. Kiefhaber, J. Mol. Biol. 270, 294 (1997). 10.1006/jmbi.1997.1030
53. W. Chen, H. Huang, C. Lin, F. Lin, and Y. Chan, Langmuir 19, 9395-9403 (2003). 10.1021/la034783o
54. M. Iafisco, B. Palazzo, G. Falini, M. Di Foggia, S. Bonora, S. Nicolis, L. Casella, and N. Roveri, Langmuir 24, 4924 (2008). 10.1021/la703381h
55. J. Lee and S. Saavedra, Langmuir 12, 4025 (1996). 10.1021/la960253z
56. J. Santos, N. Matsuda, Z. Qi, T. Yoshida, A. Takatsu, and K. Kato, Surf. Interface Anal. 35, 432 (2003). 10.1002/sia.1551
57. J. Salafsky and K. Eisenthal, J. Phys. Chem. B 104, 7752 (2000). 10.1021/jp001294d
58. T. J. Schmitt, J. E. Clark, and T. A. Knotts IV, J. Chem. Phys. 131, 235101 (2009). 10.1063/1.3270167
59. J. I. Lewis, D. J. Moss, and T. A. Knotts IV, J. Chem. Phys. 136, 245101 (2012). 10.1063/1.4729604
60. B. Brooks, R. Bruccoleri, D. Olafson, D. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983). 10.1002/jcc.540040211
61. A. MacKerell, Jr., B. Brooks, C. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus, CHARMM: The Energy Function and Its Parameterization with an Overview of the Program (John Wiley Sons, Chichester, 1998), pp. 271-277.
62. B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus, J. Comput. Chem. 30, 1545 (2009). 10.1002/jcc.21287
63. S. Wei and T. A. Knotts IV, J. Chem. Phys. 134, 185101 (2011). 10.1063/1.3589863
64. T. Beutler and W. Vangunsteren, J. Chem. Phys. 100, 1492 (1994). 10.1063/1.466628
65. S. Nosé, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
66. W. G. Hoover, Phys. Rev. A 31, 1695 (1985). 10.1103/PhysRevA.31.1695
67. S. Nosé, J. Phys.: Condens. Matter 2, SA115 (1990). 10.1088/0953-8984/2/S/013
68. N. A. Vellore, J. A. Yancey, G. Collier, R. A. Latour, and S. J. Stuart, Langmuir 26, 7396 (2010). 10.1021/la904415d
69. X. P. Geng, M. R. Zheng, B. H. Wang, Z. M. Lei, and X. D. Geng, J. Therm. Anal. Calorim. 93, 503 (2008). 10.1007/s10973-007-8676-5