Sampling of organic solutes in aqueous and heterogeneous environments using oscillating excess chemical potentials in grand canonical-like Monte Carlo-molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 10, Issue 6, 2014, Pages 2281-2290

  Lakkaraju, Sirish Kaushik ^a   Raman, E Prabhu ^a   Yu, Wenbo ^a   Mackerell, Alexander D ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84902186999     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500201y     Document Type: Article

References (57)

1. Dill, K. A.; Bromberg, S. Molecular driving forces: statistical thermodynamics in chemistry and biology; Taylor & Francis, 2003.
2. Pohorille, A.; Wilson, M. A. Excess chemical potential of small solutes across water-membrane and water-hexane interfaces J. Chem. Phys. 1996, 104, 3760
3. Guarnieri, F.; Mezei, M. Simulated annealing of chemical potential: a general procedure for locating bound waters. Application to the study of the differential hydration propensities of the major and minor grooves of DNA J. Am. Chem. Soc. 1996, 118, 8493-8494
4. Resat, H.; Mezei, M. Grand canonical Monte Carlo simulation of water positions in crystal hydrates J. Am. Chem. Soc. 1994, 116, 7451-7452
5. Jorgensen, W. L.; Ravimohan, C. Monte Carlo simulation of differences in free energies of hydration J. Chem. Phys. 1985, 83, 3050
6. Chang, J. The calculation of chemical potential of organic solutes in dense liquid phases by using expanded ensemble Monte Carlo simulations J. Chem. Phys. 2009, 131, 074103
7. Raman, E. P.; MacKerell, A. D., Jr. Rapid estimation of hydration thermodynamics of macromolecular regions J. Chem. Phys. 2013, 139, 055105
8. Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena Chem. Rev. 1993, 93, 2395-2417
9. Clark, M.; Guarnieri, F.; Shkurko, I.; Wiseman, J. Grand canonical Monte Carlo simulation of ligand-protein binding J. Chem. Info Model 2006, 46, 231-242
10. Woo, H.-J.; Dinner, A. R.; Roux, B. Grand canonical Monte Carlo simulations of water in protein environments J. Chem. Phys. 2004, 121, 6392
11. Kulp, J. L., III; Kulp, J. L., Jr.; Pompliano, D. L.; Guarnieri, F. Diverse fragment clustering and water exclusion identify protein hot spots J. Am. Chem. Soc. 2011, 133, 10740-10743
12. Jayaram, B.; Beveridge, D. Grand canonical Monte Carlo simulations on aqueous solutions of sodium chloride and sodium DNA: excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions J. Phys. Chem. 1991, 95, 2506-2516
13. Mezei, M. A cavity-biased (T, V, μ) Monte Carlo method for the computer simulation of fluids Mol. Phys. 1980, 40, 901-906
14. Small, M. C.; Lopes, P.; Andrade, R. B.; MacKerell, A. D., Jr. Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach PLOS Comput. Biol. 2013, 9, e1003113
15. Bakan, A.; Nevins, N.; Lakdawala, A. S.; Bahar, I. Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules J. Chem. Theory Comput 2012, 8, 2435-2447
16. Lexa, K. W.; Carlson, H. A. Full protein flexibility is essential for proper hot-spot mapping J. Am. Chem. Soc. 2010, 133, 200-202
17. Guvench, O.; MacKerell, A. D., Jr. Computational fragment-based binding site identification by ligand competitive saturation PLOS Comput. Biol. 2009, 5, e1000435
18. Raman, E. P.; Yu, W.; Guvench, O.; MacKerell, A. D., Jr. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations J. Chem. Info Model 2011, 51, 877-896
19. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 2004, 47, 1739-1749
20. Miranker, A.; Karplus, M. Functionality maps of binding sites: a multiple copy simultaneous search method.Proteins Struct, Func, Bioinfo 1991, 11, 29-34
21. Raman, E. P.; Yu, W.; Lakkaraju, S. K.; MacKerell, A. D., Jr. Inclusion of multiple fragment types in the Site Identification by Ligand Competitive Saturation (SILCS) approach J. Chem. Info Model 2013, 53, 3384-3398
22. Torrie, G.; Valleau, J. Electrical double layers. I. Monte Carlo study of a uniformly charged surface J. Chem. Phys. 1980, 73, 5807
23. Caleman, C.; Hub, J. S.; van Maaren, P. J.; van der Spoel, D. Atomistic simulation of ion solvation in water explains surface preference of halides Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 6838-6842
24. Mezei, M. Grand-canonical ensemble Monte Carlo study of dense liquid: Lennard-Jones, soft spheres and water Mol. Phys. 1987, 61, 565-582
25. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 2010, 31, 671-690
26. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926
27. Allen, M. P.; Tildesley, D. J. Computer simulation of liquids; Oxford university press, 1989.
28. Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
29. Nosé, S. A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 1984, 52, 255-268
30. Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695
31. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472
32. Levitt, M.; Lifson, S. Refinement of protein conformations using a macromolecular energy minimization procedure J. Mol. Biol. 1969, 46, 269-279
33. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log (N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089
34. Steinbach, P. J.; Brooks, B. R. New spherical-cutoff methods for long-range forces in macromolecular simulation J. Comput. Chem. 2004, 15, 667-683
35. Speidel, J. A.; Banfelder, J. R.; Mezei, M. Automatic control of solvent density in grand canonical ensemble Monte Carlo simulations J. Chem. Theory Comput. 2006, 2, 1429-1434
36. Deng, Y.; Roux, B. Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant J. Chem. Theory Comput. 2006, 2, 1255-1273
37. Morton, A.; Baase, W. A.; Matthews, B. W. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme Biochemistry 1995, 34, 8564-8575
38. Boyce, S. E.; Mobley, D. L.; Rocklin, G. J.; Graves, A. P.; Dill, K. A.; Shoichet, B. K. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 2009, 394, 747-763
39. Morton, A.; Matthews, B. W. Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity Biochemistry 1995, 34, 8576-8588
40. Mulder, F. A.; Hon, B.; Mittermaier, A.; Dahlquist, F. W.; Kay, L. E. Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme J. Am. Chem. Soc. 2002, 124, 1443-1451
41. Palmer, A. G., III Probing molecular motion by NMR Curr. Opin Struct Biol. 1997, 7, 732-737
42. Eriksson, A.; Baase, W. A.; Zhang, X.; Heinz, D.; Blaber, M.; Baldwin, E. P.; Matthews, B. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect Science 1992, 255, 178-183
43. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations J. Chem. Theory Comput. 2009, 5, 350-358
44. Chalmet, S.; Ruiz-López, M. Molecular dynamics simulation of formamide in water using density functional theory and classical potentials J. Chem. Phys. 1999, 111, 1117
45. Baker, C. M.; Lopes, P. E.; Zhu, X.; Roux, B.; MacKerell, A. D., Jr. Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field J. Chem. Theory Comput. 2010, 6, 1181-1198
46. Harder, E.; Roux, B. On the origin of the electrostatic potential difference at a liquid-vacuum interface J. Chem. Phys. 2008, 129, 234706-234706-234709
47. Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D., Jr. A polarizable model of water for molecular dynamics simulations of biomolecules Chem. Phys. Lett. 2006, 418, 245-249
48. Ben-Shimon, A.; Eisenstein, M. Computational mapping of anchoring spots on protein surfaces J. Mol. Biol. 2010, 402, 259-277
49. Moepps, B.; Fagni, L. Mont Sainte-Odile: a sanctuary for GPCRs EMBO Rep. 2003, 4, 237
50. Mangelsdorf, D. J.; Thummel, C.; Beato, M.; Herrlich, P.; Schütz, G.; Umesono, K.; Blumberg, B.; Kastner, P.; Mark, M.; Chambon, P. The nuclear receptor superfamily: the second decade Cell 1995, 83, 835-839
51. Sharp, K. A. Statistical Thermodynamics of Binding and Molecular Recognition Models Prot.-Lig. Interact. 2012, 3
52. Clark, M.; Meshkat, S.; Wiseman, J. S. Grand Canonical Free-Energy Calculations of Protein- Ligand Binding J. Chem. Inf. Model. 2009, 49, 934-943
53. Foster, T. J.; MacKerell, A. D., Jr.; Guvench, O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery J. Comput. Chem. 2012, 33, 1880-1891
54. Eyrisch, S.; Helms, V. Transient pockets on protein surfaces involved in protein-protein interaction J. Med. Chem. 2007, 50, 3457-3464
55. Pearlman, D. A.; Charifson, P. S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system J. Med. Chem. 2001, 44, 3417-3423
56. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical-thermodynamic basis for computation of binding affinities: a critical review Biophys. J. 1997, 72, 1047-1069
57. Deng, Y.; Roux, B. Hydration of amino acid side chains: nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules J. Phys. Chem. B 2004, 108, 16567-16576