Proteins and peptides at gold surfaces: Insights from atomistic simulations

ACS Symposium Series

Volumn 1120, Issue , 2012, Pages 229-250

  Bellucci, L ^a   Brancolini, G ^a   Calzolari, A ^a   Parramon, O Carrillo ^a   Corni, S ^a   Di Felice, R ^a  

^a CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ELECTRONIC STRUCTURE; HIERARCHICAL SYSTEMS; MOLECULAR DYNAMICS; PEPTIDES;

ATOMISTIC LEVELS; ATOMISTIC MOLECULAR DYNAMICS; ATOMISTIC SIMULATIONS; BROWNIAN DYNAMICS; CLASSICAL METHODS; DOCKING METHODS; HIERARCHICAL STRATEGIES; PROTEIN-SURFACE INTERACTIONS;

BIOINFORMATICS;

EID: 84904972356     PISSN: 00976156     EISSN: 19475918     Source Type: Book Series    
DOI: 10.1021/bk-2012-1120.ch010     Document Type: Conference Paper

References (87)

1. Norde, W; Lyklema, J. J. Biomater. Sci., Polym. Ed. 1991, 2, 183-202.
2. Brash, J. L.; Horbett, T. A. In Proteins at interfaces. II. Fundamentals and applications; Horbett, T. A., Brash, J. L., Eds.; American Chemical Society: Washington, DC, 1995; pp 1-23.
3. Lynch, I.; Dawson, K. A.; Linse, S. Science's STKE 2006, 2006, pe14.
4. Lundqvist, M; Stigler, J.; Elia, G.; Lynch, I.; Cedervall, T; Dawson, K. A. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 14265-14270.
5. Wagner, V; Dullaart, A.; Bock, A. K.; Zweck, A. Nat. Biotechnol. 2006, 24, 1211-1218.
6. Farokhzad, O. C; Langer, R. ACSNano 2009, 3, 16-20.
7. Xia, Y; Lim, B. Nature 2010, 467, 923-924.
8. Sarikaya, M; Tamerler, C; Alex, K. Y. J.; Schulten, K.; Baneyx, F Nat. Mater. 2003, 2, 577-585.
9. Mahmoudi, M; Lynch, I.; Ejtehadi, M; Monopoli, M. P.; Baldelli Bombelli, E; Laurent, S. Chem. Rev. 2011, 777, 5610-5637.
10. Goobes, G.; Goobes, R.; Schueler-Furman, O.; Baker, D.; Stayton, P. S.; Drobny, G. P. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 16083-16088.
11. Wei, Y; Latour, R. A. Langmuir 2009, 25, 5637-5646.
12. Baugh, L.; Weidner, T; Baio, J. E.; Nguyen, P.-C. T; Gamble, L. J.; Stayton, P. S.; Castner, D. G. Langmuir 2010, 26, 16434-16441.
13. Calzolai, L.; Franchini, E; Gilliland, D.; Rossi, F. Nano Lett. 2010, 10, 3101-3105.
14. Liu, Y; Jasensky, J.; Chen, Z. Langmuir 2012, 28, 2113-2121.
15. Gray, J. Curr Opin. Struct. Biol. 2004, 14, 110-115.
16. Cohavi, O.; Corni, S.; De Rienzo, F; Di Felice, R.; Gottschalk, K. E.; Hoefling, M; Kokh, D.; Molinari, E.; Schreiber, G.; Vaskevich, A.; Wade, R. C. J. Mol. Recognit. 2009, 23, 259-262.
17. Cohavi, O.; Reichmann, D.; Abramovich, R.; Tesler, A. B.; Bellapadrona, G.; Kokh, D. B.; Wade, R. C; Vaskevich, A.; Rubinstein, I.; Schreiber, G. Chem. Eur. J. 2011, 17, 1327-1336.
18. Bortolotti, C. A.; Battistuzzi, G.; Borsari, M.; Facci, R; Ranieri, A.; Sola, M. J. Am. Chem. Soc. 2006, 128, 5444-5451.
19. Alessandrini, A.; Salerno, M; Frabboni, S.; Facci, V. Appl. Phys. Lett. 2005, 86, 133902-133903.
20. Chen, Y.-S.; Hong, M.-Y; Huang, G. S. Nat. Nanotech. 2012, 7, 197-203.
21. Zeng, S.; Yong, K.-T.; Roy, I.; Dinh, X.-Q.; Yu, X.; Luan, F. Plasmonics 2011, 491-506.
22. Wetterer, S.; Lavrich, D.; Cummings, T.; Bernasek, S.; Scoles, G. J. Phys. Chem. B 1998, 102, 9266-9275.
23. Syomin, D.; Koel, B. E. Surf. Sci. 2002, 498, 61-73.
24. Corradini, V; Menozzi, C; Cavallini, M.; Biscarini, K; Betti, M. G. Surf. Sci. 2003, 532, 249-254.
25. Ayton, G. S.; Noid, W. G.; Voth, G. A. Curr Opin. Struct. Biol. 2007, 17, 192-198.
26. Tozzini, V. Acc. Chem. Res. 2010, 43, 220-230.
27. Enhanced sampling can effectively extend the time frame for both ab initio and classical simulations. The interpretation of results, however, rely on statistical mechanics theories of chemical kinetics. Here we limit ourselves to the time-span accessible to straight simulations.
28. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M; Ferguson, D. M; Spellmeyer, D. C; Fox, T.; Caldwell, J.; Kollman, R A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
29. MacKerell, A. D., Jr.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
30. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
31. Hess, B.; Kutzner, C; Van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-147.
32. Phillips, J. C; Braun, R.; Wang, W; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802.
33. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M; Salmon, J. K.; Shan, Y; Wriggers, W Science 2010, 330, 341-346.
34. Di Felice, R.; Selloni, A. J. Chem. Phys. 2004, 120, 4906-4914.
35. Di Felice, R.; Selloni, A.; Molinari, E. J. Phys. Chem. B 2003, 107, 1151-1156.
36. Iori, E; Corni, S.; Di Felice, R. J. Phys. Chem. C 2008, 112, 13540-13545.
37. Calzolari, A.; Cicero, G.; Cavazzoni, C; Di Felice, R.; Catellani, A.; Corni, S. J. Am. Chem. Soc. 2010, 132, 4790-1795.
38. Iori, E; Di Felice, R.; Molinari, E.; Corni, S. J. Comput. Chem. 2009, 30, 1465-1476.
39. Kokh, D. B.; Corni, S.; Winn, P. J.; Hoefling, M.; Gottschalk, K. E.; Wade, R. C. J. Chem. Theory Comput. 2010, 6, 1753-1768.
40. Tozzini, V Curr. Opin. Struct. Biol. 2005, 15, 144-150.
41. Tkatchenko, A.; Romaner, L.; Hofmann, O.; Zojer, E.; Ambrosch-Draxl, C.; Scheffler, M. MRS Bull. 2010, 35, 435-142.
42. Gross, E. K. U.; Dreizler, R. M. Density Functional Theory; Springer-Verlag, 1995.
43. De Renzi, V; Di Felice, R.; Marchetto, D.; Biagi, R.; Del Pennino, U.; Selloni, A. J. Phys. Chem. B 2004, 108, 16-20.
44. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
45. Vargas, M. C; Giannozzi, P.; Selloni, A.; Scoles, G. J. Phys. Chem. B 2001, 105, 9509-9513.
46. Hammer, B.; Norskov, J. K. Theory of Adorption and Surface Reactions. In Chemisorption and Reactivity of Supported Clusters and Thin Films; Lambert, R. M, Pacchioni, G., Eds.; Kluwer Academic Publishers: The Netherlands, 1997.
47. Kleiman, G. G.; Landman, U. Phys. Rev. Lett. 1973, 31, 707-710.
48. Hoefling, M; Monti, S.; Corni, S.; Gottschalk, K. E. PLoS One 2011, 6, e20925.
49. Cicero, G.; Calzolari, A.; Corni, S.; Catellani, A. J. Phys. Chem. Lett. 2011, 2582-2586.
50. Frenkel, D.; Smit, B. Understanding molecular simulation: from algorithms to applications; Academic Press Inc.: 1996.
51. Marx, D.; Hutter, J. Ab initio molecular dynamics: basic theory and advanced methods; Cambridge University Press: 2009.
52. Schlick, T. Molecular modeling and simulation: an interdisciplinary guide; Springer Verlag: 2010; Vol. 21.
53. Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Curr Opin. Struct. Biol. 2009, 19, 120-127.
54. Van der Kamp, M. W.; Shaw, K. E.; Woods, C. J.; Mulholland, A. J. J. R. Soc, Interface 2008, 5, 173-190.
55. Adcock, S. A.; McCammon, J. A. Chem. Rev. 2006, 106, 1589-1615.
56. Vellore, N. A.; Yancey, J. A.; Collier, G.; Latour, R. A.; Stuart, S. J. Langmuir 2010, 26, 7396-7404.
57. Puleo, D. A.; Bizios, R. Biological Interactions on Materials Surfaces: Understanding and Controlling Protein, Cell, and Tissue Responses; Springer Verlag: 2009.
58. Iori, E; Corni, S. J. Comput. Chem. 2008, 29, 1656-1666.
59. Hoefling, M.; Iori, E; Corni, S.; Gottschalk, K.-E. Langmuir 2010, 26, 8347-8351.
60. Hoefling, M.; Iori, E; Corni, S.; Gottschalk, K. E. ChemPhysChem 2010, 11, 1763-1767.
61. Trzesniak, D.; Kunz, A. P. E.; van Gunsteren, W. F. ChemPhysChem 2007, 8, 162-169.
62. Kastner, J. Wiley lnterdiscip. Rev: Comput. Mol. Sci. 2011, 1, 932-942.
63. Crescenzi, O.; Tomaselli, S.; Guerrini, R.; Salvadori, S.; D'Ursi, A. M.; Temussi, P. A.; Picone, D. Fur. J. Biochem. 2002, 269, 5642-5648.
64. Schlick, T F Biol. Rep. 2009, 1, 1-9.
65. Sugita, Y; Okamoto, Y Chem. Phys. Lett. 1999, 314, 141-151.
66. Li, X.; Latour, R. A.; Stuart, S. J. J. Chem. Phys. 2009, 130, 174106-174109.
67. Laio, A.; Gervasio, F. L. Rep. Prog. Phys. 2008, 71, 126601-126622.
68. Schneider, J.; Colombi Ciacchi, L. J. Am. Chem. Soc. 2012, 134, 2407-2413.
69. Isralewitz, B.; Gao, M; Schulten, K. Curr. Opin. Struct. Biol. 2001, 11, 224-230.
70. Madura, J. D.; Briggs, J. M; Wade, R. C; et al. Comput. Phys. Commun. 1995, 91, 57-95.
71. Gabdoulline, R. R.; Wade, R. C. Biophys. J. 1997, 72, 1917-1929.
72. Northrup, S. H. Macrodox v. 2.0.2: Software for Prediction of Macromolecular Interaction; Tennesse Technological University: Cookeville, TN, 1995.
73. Gabdoulline, R. R.; Wade, R. C. Methods 1998, 14, 329-341.
74. http://projects.villa-bosch.de/mcmsoft/sda/6.00/.
75. Tomasio, S. M; Walsh, T. R. J. Phys. Chem. C 2009, 113, 8778-8785.
76. Mitternacht, S.; Schnabel, S.; Bachmann, M; Janke, W.; Irback, A. J. Phys. Chem. B 2007, 777, 4355-4360.
77. Skelton, A. A.; Liang, T; Walsh, T. R. ACSAppl. Mater. Interfaces 2009, 1, 1482-1491.
78. Horinek, D.; Mamatkulov, S. I.; Netz, R. R. J. Chem. Phys. 2009, 130, 124507.
79. Latour, R. A. Biointerphases 2008, 3, FC2-FC9.
80. Gabdoulline, R. R.; Wade, R. C. J. Phys. Chem. 1996, 100, 3868-3878.
81. Elcock, A. H.; Gabdoulline, R. R.; Wade, R. C; McCammon, J. A. J. Mol. Biol. 1999, 291, 149-162.
82. Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E., III. J. Chem. Theory Comput. 2007, 3, 2312-2334.
83. Brancolini, G.; Kokh, D. B.; Calzolai, L.; Wade, R. C; Corni, S. Docking of ubiquitin on gold nanoparticles. Unpublished
84. Reith, D.; Piitz, M.; Mtiller-Plathe, F. J. Comput. Chem. 2003, 24, 1624-1636.
85. Rueda, M; Chacon, P.; Orozco, M. Structure 2007, 15, 565-575.
86. Emperador, A.; Carrillo, O.; Rueda, M; Orozco, M. Biophys. J. 2008, 95, 2127-2138.
87. Carrillo, O.; Laughton, C. A.; Orozco, M. J. Chem. Theory Comput. 2012, 8, 792-799.