Table of Contents Author Guidelines Submit a Manuscript
The Scientific World Journal
Volume 2014, Article ID 536084, 14 pages
http://dx.doi.org/10.1155/2014/536084
Research Article

Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

1Institute for Computational Science and Technology, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
2Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw, Poland

Received 31 August 2013; Accepted 5 November 2013; Published 2 February 2014

Academic Editors: R. Luo and K. Spiegel

Copyright © 2014 Trang Truc Nguyen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. A. Kollman, I. Massova, C. Reyes et al., “Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models,” Accounts of Chemical Research, vol. 33, no. 12, pp. 889–897, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. J. G. Kirkwood, “Statistical mechanics of fluid mixtures,” The Journal of Chemical Physics, vol. 3, no. 5, pp. 300–313, 1935. View at Google Scholar · View at Scopus
  3. J. Aqvist, C. Medina, and J.-E. Samuelsson, “A new method for predicting binding affinity in computer-aided drug design,” Protein Engineering, vol. 7, no. 3, pp. 385–391, 1994. View at Google Scholar · View at Scopus
  4. R. W. Zwanzig, “High-temperature equation of state by a perturbation method. I. Nonpolar gases,” The Journal of Chemical Physics, vol. 22, no. 12, pp. 1420–1426, 1954. View at Publisher · View at Google Scholar
  5. M. Karplus and J. A. McCammon, “Molecular dynamics simulations of biomolecules,” Nature Structural Biology, vol. 9, no. 9, pp. 646–652, 2002. View at Publisher · View at Google Scholar · View at Scopus
  6. F. S. Lee, Z.-T. Chu, M. B. Bolger, and A. Warshel, “Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603,” Protein Engineering, vol. 5, no. 3, pp. 215–228, 1992. View at Google Scholar · View at Scopus
  7. U. Bren, J. Lah, M. Bren, V. Martnek, and J. Florin, “DNA duplex stability: the role of preorganized electrostatics,” Journal of Physical Chemistry B, vol. 114, no. 8, pp. 2876–2885, 2010. View at Publisher · View at Google Scholar
  8. H. Grubmüller, B. Heymann, and P. Tavan, “Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force,” Science, vol. 271, no. 5251, pp. 997–999, 1996. View at Google Scholar · View at Scopus
  9. B. K. Mai, M. H. Viet, and M. S. Li J, “Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach,” Journal of Chemical Information and Modeling, vol. 50, no. 12, pp. 2236–2247, 2010. View at Publisher · View at Google Scholar
  10. J. H. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, “Interaction models for water in relation to protein hydration,” in Intermolecular Forces, B. Pullmann, Ed., pp. 331–342, 1981. View at Google Scholar
  11. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, “The missing term in effective pair potentials,” Journal of Physical Chemistry, vol. 91, no. 24, pp. 6269–6271, 1987. View at Google Scholar · View at Scopus
  12. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, “Comparison of simple potential functions for simulating liquid water,” The Journal of Chemical Physics, vol. 79, no. 2, pp. 926–935, 1983. View at Google Scholar · View at Scopus
  13. W. L. Jorgensen and J. D. Madura, “Temperature and size dependence for Monte Carlo simulations of TIP4P water,” Molecular Physics, vol. 56, no. 6, pp. 1381–1392, 1985. View at Publisher · View at Google Scholar
  14. B. Hess and N. F. A. van der Vegt, “Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models,” Journal of Physical Chemistry B, vol. 110, no. 35, pp. 17616–17626, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. P. Florova, P. Sklenovsky, P. Banas, and M. Otyepka, “Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact,” Journal of Chemical Theory and Computation, vol. 6, no. 11, pp. 3569–3579, 2010. View at Publisher · View at Google Scholar
  16. Z. Hu and J. Jiang, “Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal,” Journal of Computational Chemistry, vol. 31, no. 2, pp. 371–380, 2009. View at Publisher · View at Google Scholar
  17. M. Almlof, B. O. Brandsdal, and J. Aqvist, “Binding affinity prediction with different force fields: examination of the linear interaction energy method,” Journal of Computational Chemistry, vol. 25, no. 10, pp. 1242–1254, 2004. View at Publisher · View at Google Scholar
  18. T. T. Nguyen, B. K. Mai, and M. S. Li, “Study of tamiflu sensitivity to variants of A/H5N1 virus using different force fields,” Journal of Chemical Information and Modeling, vol. 51, no. 9, pp. 2266–2276, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. P. Cozzini, M. Fornabaio, A. Marabotti, D. J. Abraham, G. E. Kellogs, and A. Mozzarelli, “Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods,” Current Medicinal Chemistry, vol. 11, no. 23, pp. 3093–3118, 2004. View at Google Scholar · View at Scopus
  20. J. Michel, J. Tirado-Rives, and W. L. Jorgensen, “Prediction of the water content in protein binding sites,” Journal of Physical Chemistry B, vol. 113, no. 40, pp. 13337–13346, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. L. Wang, B. J. Berne, and R. A. Friesner, “Ligand binding to protein-binding pockets with wet and dry regions,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 4, pp. 1326–1330, 2011. View at Publisher · View at Google Scholar
  22. M. Chaplin, “Water structure and science,” 2000, http://www.lsbu.ac.uk/water/.
  23. P. J. Collins, L. F. Haire, Y. P. Lin et al., “Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants,” Nature, vol. 453, no. 7199, pp. 1258–1261, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, “Comparison of multiple amber force fields and development of improved protein backbone parameters,” Proteins, vol. 65, no. 3, pp. 712–725, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. B. R. Brooks, C. L. Brooks, A. D. Mackerell et al., “CHARMM: the biomolecular simulation program,” Journal of Computational Chemistry, vol. 30, no. 10, pp. 1545–1614, 2009. View at Publisher · View at Google Scholar
  26. W. L. Jorgensen and J. Tirado-Rives, “The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin,” Journal of the American Chemical Society, vol. 110, no. 6, pp. 1657–1666, 1988. View at Google Scholar · View at Scopus
  27. W. F. van Gunsteren, S. R. Billeter, A. A. Eising et al., Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Zurich, Zurich, Switzerland, 1996.
  28. R. G. Webster and E. A. Govorkova, “H5N1 influenza—continuing evolution and spread,” The New England Journal of Medicine, vol. 355, no. 21, pp. 2174–2177, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. The Writing Committee of the World Health Organization (WHO) Consultation on Human Influenza A/H5, “Avian influenza A (H5N1) infection in humans,” The New England Journal of Medicine, vol. 353, no. 13, pp. 1374–1385, 2005. View at Publisher · View at Google Scholar
  30. Schrödinger, PyMOL: The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, 2010.
  31. D. M. F. van Aalten, R. Bywater, J. B. C. Findlay, M. Hendlich, R. W. W. Hooft, and G. Vriend, “PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules,” Journal of Computer-Aided Molecular Design, vol. 10, no. 3, pp. 255–262, 1996. View at Publisher · View at Google Scholar
  32. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian 03, Revision C.02, Gaussian, Wallingford, Conn, USA, 2004.
  33. A. W. S. D. Silva, W. F. Vranken, and E. D. Laue, “ACPYPE—AnteChamber PYthon Parser interfacE,” submitted.
  34. A. S. T. R. Andre, A. C. H. Bruno, and B. A. Ricardo, “MKTOP: a program for automatic construction of molecular topologies,” Journal of the Brazilian Chemical Society, vol. 19, no. 7, pp. 1433–1435, 2008. View at Publisher · View at Google Scholar
  35. V. Zoete, M. A. Cuendet, A. Grosdidier, and O. Michielin, “SwissParam: a fast force field generation tool for small organic molecules,” Journal of Computational Chemistry, vol. 32, no. 11, pp. 2359–2368, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. B. Guillot, “A reappraisal of what we have learnt during three decades of computer simulations on water,” Journal of Molecular Liquids, vol. 101, no. 1-3, pp. 219–260, 2002. View at Publisher · View at Google Scholar
  37. J. D. Bernal and R. H. Fowler, “A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions,” The Journal of Chemical Physics, vol. 1, no. 8, pp. 515–548, 1933. View at Google Scholar · View at Scopus
  38. T. Darden, D. York, and L. Pedersen, “Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems,” The Journal of Chemical Physics, vol. 98, no. 12, pp. 10089–10092, 1993. View at Google Scholar · View at Scopus
  39. R. W. Hockney, S. P. Goel, and J. W. Eastwood, “Quiet high-resolution computer models of a plasma,” Journal of Computational Physics, vol. 14, no. 2, pp. 148–158, 1974. View at Google Scholar · View at Scopus
  40. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984. View at Google Scholar · View at Scopus
  41. M. Parrinello and A. Rahman, “Polymorphic transitions in single crystals: a new molecular dynamics method,” Journal of Applied Physics, vol. 52, no. 12, pp. 7182–7190, 1981. View at Publisher · View at Google Scholar · View at Scopus
  42. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GRGMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation,” Journal of Chemical Theory and Computation, vol. 4, no. 3, pp. 435–447, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. L. S. Cheng, R. E. Amaro, D. Xu, W. W. Li, P. W. Arzberger, and J. A. McCammon, “Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase,” Journal of Medicinal Chemistry, vol. 51, no. 13, pp. 3878–3894, 2008. View at Publisher · View at Google Scholar · View at Scopus
  44. C. B. Barber, D. P. Dobkin, and H. Huhdanpaa, “The quickhull algorithm for convex hulls,” ACM Transactions on Mathematical Software, vol. 22, no. 4, pp. 469–483, 1996. View at Google Scholar · View at Scopus
  45. K. L. Clarkson, K. Menlhorn, and R. Seidel, “Four results on randomized incremental constructions,” Computational Geometry, vol. 3, no. 4, pp. 185–212, 1993. View at Publisher · View at Google Scholar
  46. P. L. Chau, “Water movement during Ligand Unbinding from receptor site,” Biophysical Journal, vol. 87, no. 1, pp. 121–128, 2004. View at Publisher · View at Google Scholar
  47. MATLAB Version 7.0.1 (R2007a), The MathWorks Inc., Natick, Mass, USA, 2007.
  48. O. Aruksakunwong, M. Malaisree, P. Decha et al., “On the lower susceptibility of oseltamivir to influenza neuraminidase subtype N1 than those in N2 and N9,” Biophysical Journal, vol. 92, no. 3, pp. 798–807, 2007. View at Publisher · View at Google Scholar · View at Scopus