Why the solvation water around proteins is more dense than bulk water

Journal of Physical Chemistry B

Volumn 116, Issue 40, 2012, Pages 12113-12124

  Kuffel, Anna ^a   Zielkiewicz, Jan ^a  

^a GDANSK UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

GEOMETRY; HYDRATION; HYDROGEN BONDS; HYDROPHOBICITY; MOLECULES; NETWORK LAYERS; POTENTIAL ENERGY; PROTEINS; SOLVATION; SURFACE CHEMISTRY;

BRANCHED NETWORK; HYDROGEN BOND NETWORKS; HYDROPHOBIC HYDRATION; HYDROPHOBIC SURFACES; PROTEIN INTERFACES; SOLVATION LAYERS; SPECIAL STRUCTURE; WATER-WATER INTERACTIONS;

PHASE INTERFACES;

EID: 84868145129     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp305172t     Document Type: Article

References (59)

1. Rupley, J. A.; Careri, G. Adv. Protein Chem. 1991, 41, 37.
2. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Parak, F. G. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16047.
3. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Young, R. D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14408.
4. Frauenfelder, H.; Fenimore, P. W.; Chen, G.; McMahon, B. H. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15469.
5. Frauenfelder, H.; Chen, G.; Berendzen, J.; Fenimore, P. W.; Jansson, H.; McMahon, B. H.; Stroe, I. R.; Swenson, J.; Young, R. D. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5129.
6. Shenogina, N.; Keblinski, P.; Garde, S. J. Chem. Phys. 2008, 129, 155105.
7. Vitkup, D.; Ringe, D.; Petsko, G. A.; Karplus, M. Nat. Struct. Biol. 2000, 7, 34.
8. Kuffel, A.; Zielkiewicz, J. Phys. Chem. Chem. Phys. 2012, 14, 5561.
9. Henzler-Wildman, K.; Kern, D. Nature 2007, 450, 964.
10. Ball, P. Chem. Rev. 2008, 108, 74.
11. Ball, P. ChemPhysChem 2008, 9, 2677.
12. Jana, B.; Pal, S.; Maiti, P. K.; Lin, S.-T.; Hynes, J. T.; Bagchi, B. J. Phys. Chem. 2006, 110, 19611.
13. Henchman, R. H. J. Chem. Phys. 2007, 126, 064504.
14. Irudayam, Sh. J.; Henchman, R. H. J. Phys. Condens. Matter 2010, 22, 284108.
15. Czapiewski, D.; Zielkiewicz, J. J. Phys. Chem. B 2010, 114, 4536.
16. Chau, P.-L.; Hardwick, A. J. Mol. Phys. 1998, 93, 511.
17. Ruocco, G.; Sampoli, M.; Vallauri, R. J. Chem. Phys. 1992, 96, 6167.
18. Ruocco, G.; Sampoli, M.; Torcini, A.; Vallauri, R. J. Chem. Phys. 1993, 99, 8095.
19. Shiratani, E.; Sasai, M. J. Chem. Phys. 1996, 104, 7671.
20. Shiratani, E.; Sasai, M. J. Chem. Phys. 1998, 108, 3264.
21. Astley, T.; Birch, G. G.; Drew, M. G. B.; Rodger, P. M.; Wilden, G. R. H. J. Comput. Chem. 1998, 19, 363.
22. Nutt, D. R.; Smith, J. C. J. Am. Chem. Soc. 2008, 130, 13066.
23. Godec, A.; Smith, J. C.; Merzel, F. Phys. Rev. Lett. 2011, 107, 267801.
24. Svergun, D. I.; Richard, S.; Koch, M. H. J.; Sayers, Z.; Kuprin, S.; Zaccai, G. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2267.
25. Smolin, N.; Winter, R. J. Phys. Chem. B 2004, 108, 15928.
26. Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378.
27. Zhou, R.; Huang, X.; Margulis, C. J.; Berne, B. J. Science 2004, 305, 1605.
28. Faraday Discuss. 2009, 141, 309.
29. Huang, D. M.; Chandler, D. J. Phys. Chem. B 2002, 106, 2047.
30. Cheng, Y.-K.; Rossky, P. J. Nature 1998, 392, 696.
31. Ashbaugh, H. E.; Paulaitis, M. E. J. Am. Chem. Soc. 2001, 123, 10721.
32. Raschke, T. M.; Levitt, M. J. Phys. Chem. B 2004, 108, 13492.
33. Stanley, H. E.; Kumar, P.; Franzese, G.; Xu, L.; Yan, Z.; Mazza, M. G.; Buldyrev, S. V.; Chen, S.-H.; Mallamace, F. Eur. Phys. J. Special Topics 2008, 161, 1.
34. Nilsson, A.; Pettersson, L. G. M. Chem. Phys. 2011, 389, 1.
35. Xu, L. M.; Mallamace, F.; Yan, Z. Y.; Starr, F. W.; Buldyrev, S. V.; Stanley, H. E. Nat. Phys. 2009, 5, 565.
36. Appignanesi, G. A.; Rodriguez Fris, J. A.; Sciortino, F. Eur. Phys. J. E 2009, 29, 305.
37. Accordino, S. R.; Rodriguez Fris, J. A.; Sciortino, F.; Appignanesi, G. A. Eur. Phys. J. E 2011, 34, 48.
38. Limmer, D. T.; Chandler, D. J. Chem. Phys. 2011, 135, 134503.
39. Tanaka, H. Phys. Rev. Lett. 1998, 80, 5750.
40. Tanaka, H. J. Chem. Phys. 2000, 112, 799.
41. Tanaka, H. J. Phys.: Condens. Matter 1999, 11, L159.
42. Strässler, S.; Kittel, C. Phys. Rev. A 1965, 139, 758.
43. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, 2008.
44. 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.
45. Sindelar, C. V.; Budny, M. J.; Rice, S.; Naber, N.; Fletterick, R.; Cooke, R. Nature Struct. Mol. Biol. 2002, 9, 844.
46. Meagher, K. L.; Redman, L. T.; Carlson, H. A. J. Comput. Chem. 2003, 24, 1016.
47. Bernal, J. D.; Finney, J. L. Discuss. Faraday Soc. 1967, 43, 62.
48. Chang, S. L.; Wu, T.-M.; Mou, C.-Y. J. Chem. Phys. 2004, 121, 3605.
49. Richards, F. M. J. Mol. Biol. 1974, 82, 1.
50. Procacci, P.; Scateni, R. Int. J. Quantum Chem. 1992, 42, 1515.
51. Voloshin, V. P.; Medvedev, N. N.; Andrews, M. N.; Burri, R. R.; Winter, R.; Geiger, A. J. Phys. Chem. B 2011, 115, 14217.
52. Sterpone, F.; Ceccarelli, M.; Marchi, M. J. Mol. Biol. 2001, 311, 409.
53. Gellatly, B. J.; Finney, J. L. Mol. Biol. 1982, 161, 305.
54. Mezei, M. Mol.Simul. 1988, 1, 327.
55. Wernet, Ph.; Nordlund, D.; Bergmann, U.; Cavalleri, M.; Odelius, M.; Ogasawara, H.; Näslund, L. A.; Hirsch, T. K.; Ojamäe, L.; Glatzel, P.; Pettersson, L. G. M.; Nilsson, A. Science 2004, 304, 995.
56. Local corrugation coefficient γ introduced in our previous paper8 was defined as a ratio of volume of monomolecular layer of solvation water to the area of water-protein contact surface. This value was divided by the van der Waals radius of oxygen atom of water molecule (to make the parameter dimensionless). The volume and the surface area were calculated by Voronoi tessellation, taking into account all atoms surrounding given water molecule (all atoms of protein and all atoms of other water molecules). Herein, we use a weighted method of tessellation, and the weights are van der Waals radiuses of neighboring atoms (see Methods section). This is why the values of γ parameters are different from the previous ones.8
57. Matysiak, S.; Debenedetti, P. G.; Rossky, P. J. J. Phys. Chem. B 2011, 115, 14859.
58. Raiteri, P.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2004, 93, 087801.
59. Perera, P. N.; Fega, K. R.; Lawrence, C.; Sundstrom, E. J.; Tomlinson-Phillips, J.; Ben-Amotz, D. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 12230.