Membrane protein simulations with a united-atom lipid and all-atom protein model: Lipid-protein interactions, side chain transfer free energies and model proteins

Journal of Physics Condensed Matter

Volumn 18, Issue 28, 2006, Pages

  Tieleman, D Peter ^a   MacCallum, Justin L ^a   Ash, Walter L ^a   Kandt, Christian ^a   Xu, Zhitao ^a   Monticelli, Luca ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MEMBRANES; FREE ENERGY; GENE TRANSFER; HYDROCARBONS; HYDROPHOBICITY; LIPIDS;

MODEL PROTEINS; PROTEIN SIMULATIONS; SIDE CHAIN TRANSFER; UNITED-ATOM LIPID;

PROTEINS;

EID: 33745630723     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/18/28/S07     Document Type: Article

References (52)

1. Abraham F F et al 2002 Simulating materials failure by using up to one billion atoms and the world's fastest computer: brittle fracture Proc. Natl Acad. Sci. USA 99 5777-82
2. Alder B J and Wainwright T E 1957 J. Chem. Phys. 27 1208
3. Aliste M P et al 2003 Molecular dynamics simulations of pentapeptides at interfaces: salt bridge and cation-pi interactions. Biochemistry 42 8976-87
4. Aliste M P and Tieleman D P 2005 Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC Biochem. 6 30
5. Allen T W et al 2003 Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J. Am. Chem. Soc. 125 9868-77
6. Andersen O S et al 2005 Gramicidin channels IEEE Trans. Nanobiosci. 4 10-20
7. Anezo C et al 2003 Methodological issues in lipid bilayer simulations J. Phys. Chem. B 107 9424-33
8. Berendsen H J C et al 1981 Interaction models for water in relation to protein hydration Intermolecular Forces ed B Pullman (Dordrecht: Reidel) pp331-42
9. Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A and Haak J R 1984 Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 3684-90
10. Berger O et al 1997 Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 72 2002-13
11. Brooks B R et al 1983 CHARMM-a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217
12. Cornell W D et al 1995 A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 117 5179-97
13. Darden T et al 1993 Particle mesh Ewald-an n.log(n) method for Ewald sums in large systems J. Chem. Phys. 98 10089-92
14. Essmann U et al 1995 A smooth particle mesh Ewald method J. Chem. Phys. 103 8577-93
15. Hess B et al 1997 LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 18 1463-72
16. Jorgensen W L et al 1983 Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 926-35
17. Jorgensen W L and Tirado-Rives J 1988 The OPLS potential functions for proteins-energy minimizations for crystals of cyclic-peptides and crambin J. Am. Chem. Soc. 110 1657-66
18. Jorgensen W L et al 1996 Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 11225-36
19. Kandt C et al 2006 Setting up and running membrane protein simulations Methods at press
20. Karplus M and McCammon J A 2002 Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 646-52
21. Karplus M and Petsko G A 1990 Molecular dynamics simulations in biology Nature 347 631-9
22. Lindahl E et al 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Modeling 7 306-17
23. Lopez C F et al 2002 Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations J. Phys.: Condens. Matter 14 9431-44
24. MacCallum J L and Tieleman D P 2003 Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field J. Comput. Chem. 24 1930-5
25. MacKerell A D 2004 Empirical force fields for biological macromolecules: overview and issues J. Comput. Chem. 25 1584-604
26. MacKerell A D et al 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 3586-616
27. Marrink S J et al 2004 Coarse grained model for semiquantitative lipid simulations J. Phys. Chem. B 108 750-60
28. Marrink S J et al 2005 Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model Chem. Phys. Lipids 135 223-44
29. McCammon J A et al 1977 Dynamics of folded proteins Nature 267 585-90
30. Miyamoto S and Kollman P A 1992 Settle-an analytical version of the shake and rattle algorithm for rigid water models J. Comput. Chem. 13 952-62
31. Nagle J F and Tristram-Nagle S 2000 Structure of lipid bilayers Biochim. Biophys. Acta 1469 159-95
32. Oostenbrink C et al 2004 A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 25 1656-76
33. Petrache H I et al 2002 Hydrophobic matching mechanism investigated by molecular dynamics simulations Langmuir 18 1340-51
34. Ponder J W and Case D A 2003 Force fields for protein simulations Protein Simul. 66 27
35. Radzicka A and Wolfenden R 1988 Comparing the polarities of the amino-acids-side-chain distribution coefficients between the vapour-phase, cyclohexane, 1-octanol, and neutral aqueous-solution Biochemistry 27 1664-70
36. Robertson K M and Tieleman D P 2002 Orientation and interactions of dipolar molecules during transport through OmpF porin FEBS Lett. 528 53-7
37. Schuler L D et al 2001 An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase J. Comput. Chem. 22 1205-18
38. Shirts M R et al 2003 Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 119 5740-61
39. Snow C D et al 2004 Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy Proc. Natl Acad. Sci. USA 101 4077-82
40. Sparr E et al 2005 Self-association of transmembrane alpha-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch J. Biol. Chem. 280 39324-31
41. Stillinger F H and Rahman A 1974 Improved simulation of liquid water by molecular dynamics J. Chem. Phys. 60 1545-57
42. Tieleman D P et al 1999a An alamethicin channel in a lipid bilayer: molecular dynamics simulations Biophys. J. 76 1757-69
43. Tieleman D P et al 1999b Alamethicin helices in a bilayer and in solution: molecular dynamics simulations Biophys. J. 76 40-9
44. Tieleman D P et al 2002 Analysis and evaluation of channel models: simulations of alamethicin Biophys. J. 83 2393-407
45. van der Spoel D et al 1991-2005 GROMACS User Manual
46. van Gunsteren W F 1987 GROMOS. Groningen Molecular Simulation Program Package (Groningen: University of Groningen)
47. van Gunsteren W F and Berendsen H J C 1990 Computer simulation of molecular-dynamics-methodology, applications, and perspectives in chemistry Angew. Chem. Int. Edn Engl. 29 992-1023
48. Villa A and Mark A E 2002 Calculation of the free energy of solvation for neutral analogs of amino acid side chains J. Comput. Chem. 23 548-53
49. Weiner S J et al 1984 A new force-field for molecular mechanical simulation of nucleic-acids and proteins J. Am. Chem. Soc. 106 765-84
50. White S H 2004 The progress of membrane protein structure determination Protein Sci. 13 1948-9
51. Wimley W C and White S H 1996 Experimentally determined hydrophobicity scale for proteins at membrane interfaces Nat. Struct. Biol. 3 842-8
52. Xu Z et al 2006 Improving hydration free energies for OPLS-AA amino acid side chains: new atomic charges and an off-plane charge model for aromatic residues J. Comput. Chem at press