Volumetric properties of hydrated peptides: Voronoi-delaunay analysis of molecular simulation runs

Journal of Physical Chemistry B

Volumn 115, Issue 48, 2011, Pages 14217-14228

  Voloshin, Vladimir P ^a   Medvedev, Nikolai N ^a,b   Andrews, Maximilian N ^c   Burri, R Reddy ^c   Winter, Roland ^c   Geiger, Alfons ^c  

^a INSTITUTE OF CHEMICAL KINETICS AND COMBUSTION   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^c TU DORTMUND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; MOLECULES; NUMERICAL MODELS; PROTEINS; SOLUTIONS; VAN DER WAALS FORCES; VOLUMETRIC ANALYSIS;

DELAUNAY TESSELLATIONS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; PARTIAL MOLAR VOLUME; SIDE CHAIN CONTRIBUTION; STRUCTURAL INFORMATION; VOLUMETRIC MEASUREMENT; VOLUMETRIC PROPERTIES;

HYDRATION;

EID: 80052614322     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2050788     Document Type: Article

References (69)

1. Royer, C. A. Biochim. Biophys. Acta 2002, 1595, 201-209
2. Chalikian, T. V. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 207-235
3. Seemann, H.; Winter, R.; Royer, C. A. J. Mol. Biol. 2001, 307, 1091-1102
4. Rösgen, J.; Hinz, H.-J. Biophys. Chem. 2000, 83, 61-71
5. Ravindra, R.; Winter, R. ChemPhysChem 2003, 4, 359-365
6. Mitra, L.; Rouget, J. B.; Garcia-Moreno, B.; Royer, C. A.; Winter, R. ChemPhysChem 2008, 9, 2715-2721
7. Lin, L. N.; Brandts, J. F.; Brandts, J. M.; Plotnikov, V. Anal. Biochem. 2002, 302, 144-160
8. Ravindra, R.; Winter, R. ChemPhysChem 2004, 5, 566-571
9. Mitra, L.; Smolin, N.; Ravindra, R.; Royer, C.; Winter, R. Phys. Chem. Chem. Phys. 2006, 8, 1249-1265
10. Schweiker, K. L.; Fitz, V. W.; Makhatadze, G. I. Biochemistry 2009, 48, 10846-10851
11. Ravindra, R.; Royer, C.; Winter, R. Chem. Phys. Phys. Chem. 2004, 6, 1952-1961
12. Sirotkin, V. A.; Winter, R. J. Phys. Chem. B 2010, 114, 16881-16886
13. Zhai, Y.; Okoro, L.; Cooper, A.; Winter, R. Biophys. Chem. 2011, 156, 13-23
14. Lounnas, V.; Pettitt, B. M. Proteins: Struct., Funct., Genet. 1994, 18, 133-147
15. Vaisman, I. I.; Brown, F. K.; Tropsha, A. J. Phys. Chem. 1994, 98, 5559-5564
16. Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 537853-83
17. Henchman, R. H.; McCammon, A. M. Protein Sci. 2002, 11, 2080-2090
18. Paschek, D. J. Chem. Phys. 2004, 10605-10617
19. Schröder, C.; Rudas, T.; Boresch, S.; Steinhausera, O. J. Chem. Phys. 2006, 124, 234907
20. Smolin, N.; Daggett, V. J. Phys. Chem. B 2008, 112, 61936202
21. Brovchenko, I.; Burri, R. R.; Krukau, A.; Oleinikova, A.; Winter, R. J. Chem. Phys. 2008, 129, 195101
22. Okabe, A.; Boots, B.; Sugihara, K.; Chiu, S. N. Spatial Tessellations: Concepts and Applications of Voronoi Diagrams; Wiley: Chichester, U.K., 2000.
23. Medvedev, N. N. The Voronoi-Delaunay Method in the Structural Investigation of Non-crystalline Systems; SB RAS: Novosibirsk, Russia, 2000, (in Russian).
24. Edelsbrunner, H. Discrete Comput. Geom. 1995, 13, 415-440
25. Alinchenko, M. G.; Anikeenko, A. V.; Medvedev, N. N.; Voloshin, V. P.; Mezei, M.; Jedlovszky, P. J. Phys. Chem. B 2004, 108, 19056-19067
26. Poupon, A. Curr. Opin. Struct. Biol. 2004, 14, 233
27. Kim, D.-S.; Seo, J.; Kim, D; Ryu, L.; Cho, C.-H. Comput.-Aided Des. 2006, 38, 1179-1191
28. David, E. E.; David, C. W. J. Chem. Phys. 1982, 76, 4611-4614
29. Voronoi, G. F. J. Reine Angew. Math. 1909, 136, 67-179
30. Delaunay, B. N. Proc. Math. Congr. Toronto, Aug 11-16, 1924, 1928, 695-700.
31. Mezei, M. Mol. Simul. 1988, 1, 327-332
32. Gellatly, B. J.; Finney, J. L. J. Mol. Biol. 1982, 161, 305-322
33. Procacci, P.; Scateni, R. Int. J. Quantum Chem. 1992, 42, 1515-1528
34. Raschke, T. M.; Levitt, M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6777-6782
35. Sterpone, F.; Marchetti, G.; Pierleoni, C.; Marchi, M. J. Phys. Chem. B 2006, 110, 11504-11510
36. Schröder, C.; Neumayr, G.; Steinhauser, O. J. Chem. Phys. 2009, 130, 194503
37. Bouvier, B.; Gruberg, R.; Nilges, M.; Cazals, F. Proteins: Struct., Funct., Bioinf. 2009, 76, 677-692
38. Neumayr, G.; Rudas, T.; Steinhauser, O. J. Chem. Phys. 2010, 133, 084108
39. Paci, E.; Marchi, M. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 11609-11614
40. Paci, E. Biochim. Biophys. Acta 2002, 1595, 185-200
41. Marchi, M. J. Phys. Chem. B 2003, 107, 6598-6602
42. Voloshin, V. P.; Anikeenko, A. V.; Medvedev, N. N.; Geiger, A.; Stoyan, D. Proc.7-th Int. Symp. on Voronoi Diagrams in Science and Engineering, Quebec, 28-30 June 2010; Quebec, Canada, 2010, 254-259.
43. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701
44. Voet, D.; Voet, J. G. Biochemistry, 3 rd ed.; John Wiley & Sons: Hoboken, N.J., 2004.
45. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
46. Kaminski, G.; Friesner, R.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487
47. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Chem. Phys. 1987, 91, 6269
48. Andrews, M. N.; Winter, R. Biophys. Chem. 2011, 156, 43-50
49. Oleinikova, A.; Smolin, N.; Brovchenko, I.; Geiger, A.; Winter, R. J. Phys. Chem. B 2005, 109, 1988-1998
50. Brovchenko, I.; Paschek, D.; Geiger, A. J. Chem. Phys. 2000, 113, 5026-5036
51. Anishchik, S. V.; Medvedev, N. N. Phys. Rev. Lett. 1995, 75, 4314-4317
52. Medvedev, N. N.; Voloshin, V. P.; Luchnikov, V. A.; Gavrilova, M. L. J. Comput. Chem. 2006, 27, 1676-1692
53. Aurenhammer, F. SIAM J. Comput. 1987, 16, 78-96
54. Oleinikova, A.; Brovchenko, I.; Winter, R. J. Phys. Chem. C 2009, 113, 11110-11118
55. Harrington, S.; Poole, P. H.; Stanley, H. E. J. Chem. Phys. 1997, 107, 7443
56. Weiss, V. Stochast. Stochast. Rep. 1995, 55, 295
57. Sastry, S; Corti, D. S.; Debenedetti, P. G.; Stillinger, F. H. Phys. Rev. E 1997, 56, 5524-5532
58. Liang, J.; Edelsbrunner, H.; Fu, P.; Sudhakar, P. V.; Subramaniam, S. Proteins: Struct., Funct., Genet. 1998, 33, 1-17
59. Ryua, J.; Parka, R.; Kim, D.-S. Comput.-Aided Des. 2007, 39, 1042-1057
60. Cazals, F.; Kanhere, H.; Loriot, S. ACM Trans. Math. Software 2011, 38, in press.
61. Edelsbrunner, H.; Koehl, P. In MSRI Publications-Vol. 52: Combinatorial and Computational Geometry; Goodman, J. E.; Pach, J.; Welzl, E., Eds.; Cambridge University Press: Cambridge, U.K., 2007; pp 243 - 275.
62. Till, M.; Ullmann, G. J. Mol. Model. 2010, 16, 419
63. Voloshin, V. P.; Anikeenko, A. V.; Medvedev, N. N.; Geiger, A. Proc. of 8-th Int. Symp. on Voronoi Diagrams in Science and Engineering, 28-30 June 2011, China; Quingdao, China, 2011, (in press).
64. Haeckel, D.; Hinz, H.-J.; Hedwig, G. R. Biophys. Chem. 1999, 82, 35
65. Brovchenko, I.; Andrews, M. N.; Oleinikova, A. Phys. Chem. Chem. Phys. 2010, 12, 4233-4238
66. Geiger, A.; Mausbach, P.; Schnitker, J. In Water and Aqueous Solutions; Neilson, G. W.,; Enderby, J. E., Eds.; Adam Hilger: Bristol, U.K., 1986; pp 15-30.
67. Voloshin, V. P.; Medvedev, N. N.; Naberukhin, Yu.I.; Geiger, A.; Klene, M. J. Struct. Chem. 2005, 46, 451-458
68. Mishra, R.; Winter, R. Angew. Chem., Int. Ed. 2008, 47, 6518-6521
69. Sarupria, S.; Ghosh, T.; Garcia, A. E.; Garde, S. Proteins: Struct., Funct., Bioinf. 2010, 78, 1641-1651