Acceleration of lateral equilibration in mixed lipid bilayers using replica exchange with solute tempering

Journal of Chemical Theory and Computation

Volumn 10, Issue 10, 2014, Pages 4264-4272

  Huang, Kun ^a   García, Angel E ^a  

^a Research Rensselaer Polytechnic Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84908013724     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500305u     Document Type: Article

References (47)

1. Wu, E.; Jacobson, K.; Papahadjopoulos, D. Lateral diffusion in phospholipid multibilayers measured by fluorescence recovery after photobleaching Biochemistry 1977, 16, 3936-3941
2. 31P two-dimensional exchange solid-state NMR study Biophys. J. 1998, 74, 857-868
3. Scomparin, C.; Lecuyer, S.; Ferreira, M.; Charitat, T.; Tinland, B. Diffusion in supported lipid bilayers: Influence of substrate and preparation technique on the internal dynamics Eur. Phys. J. E 2009, 28, 211-220
4. Poger, D.; Mark, A. E. Lipid bilayers: The effect of force field on ordering and dynamics J. Chem. Theory Comput. 2012, 8, 4807-4817
5. Falck, E.; Róg, T.; Karttunen, M.; Vattulainen, I. Lateral diffusion in lipid membranes through collective flows J. Am. Chem. Soc. 2008, 130, 44-45
6. Roark, M.; Feller, S. E. Molecular dynamics simulation study of correlated motions in phospholipid bilayer membranes J. Phys. Chem. B 2009, 113, 13229-13234
7. Sodt, A. J.; Sandar, M. L.; Gawrisch, K.; Pastor, R. W.; Lyman, E. The molecular structure of the liquid-ordered phase of lipid bilayers J. Am. Chem. Soc. 2014, 136, 725-732
8. Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314, 141-151
9. García, A. E.; Sanbonmatsu, K. Y. Exploring the energy landscape of a β hairpin in explicit solvent Proteins Struct. Funct. Bioinfomatics 2001, 42, 345-354
10. Paschek, D.; Hempel, S.; García, A. E. Computing the stability diagram of the Trp-cage miniprotein Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 17754-17759
11. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. Replica exchange with solute tempering: A method for sampling biological systems in explicit water Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749-13754
12. Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction J. Chem. Phys. 2002, 116, 9058
13. Huang, X.; Hagen, M.; Kim, B.; Friesner, R. A.; Zhou, R.; Berne, B. Replica exchange with solute tempering: Efficiency in large scale systems J. Phys. Chem. B 2007, 111, 5405-5410
14. Wang, L.; Friesner, R. A.; Berne, B. Replica exchange with solute scaling: A more efficient version of replica exchange with solute tempering (REST2) J. Phys. Chem. B 2011, 115, 9431-9438
15. Terakawa, T.; Kameda, T.; Takada, S. On easy implementation of a variant of the replica exchange with solute tempering in GROMACS J. Comput. Chem. 2011, 32, 1228-1234
16. Berendsen, H.; van der Spoel, D.; Van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 1995, 91, 43-56
17. 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
18. Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 014101-014101
19. Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182
20. Berendsen, H.; Grigera, J.; Straatsma, T. The missing term in effective pair potentials J. Chem. Phys. 1987, 91, 6269-6271
21. Chiu, S.; Pandit, S.; Scott, H.; Jakobsson, E. An improved united atom force field for simulation of mixed lipid bilayers J. Phys. Chem. B 2009, 113, 2748-2763
22. Miyamoto, S.; Kollman, P. SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
23. Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472
24. 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, 10089-10093
25. Neale, C.; Madill, C.; Rauscher, S.; Pomès, R. Accelerating convergence in Molecular Dynamics simulations of solutes in lipid membranes by conducting a random walk along the bilayer normal J. Chem. Theory Comput. 2013, 9, 3686-3703
26. Garcia, A. E.; Herce, H.; Paschek, D. Simulations of temperature and pressure unfolding of peptides and proteins with replica exchange molecular dynamics Annu. Rep. Comput. Chem. 2006, 2, 83-95
27. Zuckerman, D. M.; Lyman, E. A second look at canonical sampling of biomolecules using replica exchange simulation J. Chem. Theory Comput. 2006, 2, 1200-1202
28. Nymeyer, H. How efficient is replica exchange molecular dynamics? An analytic approach J. Chem. Theory Comput. 2008, 4, 626-636
29. Falck, E.; Patra, M.; Karttunen, M.; Hyvönen, M. T.; Vattulainen, I. Lessons of slicing membranes: Interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers Biophys. J. 2004, 87, 1076-1091
30. Pan, J.; Mills, T. T.; Tristram-Nagle, S.; Nagle, J. F. Cholesterol perturbs lipid bilayers nonuniversally Phys. Rev. Lett. 2008, 100, 198103
31. Pan, J.; Tristram-Nagle, S.; Nagle, J. F. Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation Phys. Rev. E 2009, 80, 021931
32. McMullen, T. P.; McElhaney, R. N. Physical studies of cholesterol-phospholipid interactions Curr. Opin. Colloid Interface Sci. 1996, 1, 83-90
33. Andoh, Y.; Oono, K.; Okazaki, S.; Hatta, I. A molecular dynamics study of the lateral free energy profile of a pair of cholesterol molecules as a function of their distance in phospholipid bilayers J. Chem. Phys. 2012, 136, 155104
34. Chong, P. Evidence for regular distribution of sterols in liquid crystalline phosphatidylcholine bilayers Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 10069-10073
35. Liu, F.; Sugar, I. P.; Chong, P. Cholesterol and ergosterol superlattices in three-component liquid crystalline lipid bilayers as revealed by dehydroergosterol fluorescence Biophys. J. 1997, 72, 2243-2254
36. Huang, J.; Feigenson, G. W. A microscopic interaction model of maximum solubility of cholesterol in lipid bilayers Biophys. J. 1999, 76, 2142-2157
37. Huang, J. Exploration of molecular interactions in cholesterol superlattices: Effect of multibody interactions Biophys. J. 2002, 83, 1014-1025
38. Ali, M. R.; Cheng, K. H.; Huang, J. Assess the nature of cholesterol-lipid interactions through the chemical potential of cholesterol in phosphatidylcholine bilayers Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 5372-5377
39. Murtola, T.; Falck, E.; Karttunen, M.; Vattulainen, I. Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints J. Chem. Phys. 2007, 126, 075101
40. Izvekov, S.; Voth, G. A. A multiscale coarse-graining method for biomolecular systems J. Phys. Chem. B 2005, 109, 2469-2473
41. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: Coarse grained model for biomolecular simulations J. Phys. Chem. B 2007, 111, 7812-7824
42. Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S.-J. The MARTINI coarse-grained force field: Extension to proteins J. Chem. Theory Comput. 2008, 4, 819-834
43. Arcario, M. J.; Ohkubo, Y. Z.; Tajkhorshid, E. Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane mimetic model J. Phys. Chem. B 2011, 115, 7029-7037
44. Ohkubo, Y. Z.; Pogorelov, T. V.; Arcario, M. J.; Christensen, G. A.; Tajkhorshid, E. Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model Biophys. J. 2012, 102, 2130-2139
45. Wang, Y.; Markwick, P. R.; de Oliveira, C. A. F.; McCammon, J. A. Enhanced lipid diffusion and mixing in accelerated molecular dynamics J. Chem. Theory Comput. 2011, 7, 3199-3207
46. Neale, C.; Bennett, W. F. D.; Tieleman, D. P.; Pomès, R. Statistical convergence of equilibrium properties in simulations of molecular solutes embedded in lipid bilayers J. Chem. Theory Comput. 2011, 7, 4175-4188
47. Huang, K.; García, A. E. Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation Biophys. J. 2013, 104, 412-420