Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies

Journal of Chemical Theory and Computation

Volumn 11, Issue 10, 2015, Pages 4875-4884

  Darre L ^a   Iglesias Fernandez, J ^a   Kohlmeyer, A ^b   Wacklin, H ^c,d   Domene, C ^a,e  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b Temple University   (United States)

^c EUROPEAN SPALLATION SOURCE ERIC   (Sweden)

^d LUND UNIVERSITY   (Sweden)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

1,2-DIHEXADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE; 1,2-OLEOYLPHOSPHATIDYLCHOLINE; DIMYRISTOYLPHOSPHATIDYLCHOLINE; ETHER PHOSPHOLIPID; LIPID BILAYER; MACROMOLECULE; PHOSPHATIDYLCHOLINE;

CHEMISTRY; LIPID BILAYER; MACROMOLECULE; MOLECULAR DYNAMICS; NEUTRON; SYNTHESIS;

DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID BILAYERS; MACROMOLECULAR SUBSTANCES; MOLECULAR DYNAMICS SIMULATION; NEUTRONS; PHOSPHATIDYLCHOLINES; PHOSPHOLIPID ETHERS;

EID: 84944110105     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00635     Document Type: Article

References (31)

1. Hardt, S. L. Rates of Diffusion Controlled Reactions in One, Two and Three Dimensions Biophys. Chem. 1979, 10, 239-243 10.1016/0301-4622(79)85012-7
2. Penfold, J.; Richardson, R. M.; Zarbakhsh, A.; Webster, J. R. P.; Bucknall, D. G.; Rennie, A. R.; Jones, R. A. L.; Cosgrove, T.; Thomas, R. K.; Higgins, J. S.; Fletcher, P. D. I.; Dickinson, E.; Roser, S. J.; McLure, I. A.; Hillman, A. R.; Richards, R. W.; Staples, E. J.; Burgess, A. N.; Simister, E. A.; White, J. W. Recent Advances in the Study of Chemical Surfaces and Interfaces by Specular Neutron Reflection J. Chem. Soc., Faraday Trans. 1997, 93, 3899-3917 10.1039/a702836i
3. Higgins, J. S.; Benoiît, H. Polymers and Neutron Scattering; Oxford Series on Neutron Scattering in Condensed Matter; Clarendon Press: Oxford, U.K., 1994.
4. Heavens, O. S. Optical Properties of Thin Solid Films; Butterworths Scientific Publications: London, U.K., 1955.
5. McGillivray, D. J.; Valincius, G.; Heinrich, F.; Robertson, J. W. F.; Vanderah, D. J.; Febo-Ayala, W.; Ignatjev, I.; Losche, M.; Kasianowicz, J. J. Structure of Functional Staphylococcus aureus Alpha-Hemolysin Channels in Tethered Bilayer Lipid Membranes Biophys. J. 2009, 96, 1547-1553 10.1016/j.bpj.2008.11.020
6. Kucerka, N.; Katsaras, J.; Nagle, J. F. Comparing Membrane Simulations to Scattering Experiments: Introducing the Simtoexp Software J. Membr. Biol. 2010, 235, 43-50 10.1007/s00232-010-9254-5
7. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
8. Rycroft, C. H. Voro++: A Three-Dimensional Voronoi Cell Library in C++ Chaos 2009, 19, 041111 10.1063/1.3215722
9. Nelson, A. Co-Refinement of Multiple-Contrast Neutron/X-ray Reflectivity Data Using Motofit J. Appl. Crystallogr. 2006, 39, 273-276 10.1107/S0021889806005073
10. Nevot, L.; Croce, P. Characterization of Surfaces by Grazing X-ray Reflection-Application to Study of Polishing of Some Silicate-Glasses Rev. Phys. Appl. 1980, 15, 761-779 10.1051/rphysap:01980001503076100
11. Shinoda, W.; DeVane, R.; Klein, M. L. Coarse-Grained Molecular Modeling of Non-Ionic Surfactant Self-Assembly Soft Matter 2008, 4, 2454-2462 10.1039/b808701f
12. Shinoda, W.; DeVane, R.; Klein, M. L. Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field J. Phys. Chem. B 2010, 114, 6836-6849 10.1021/jp9107206
13. Shinoda, W.; DeVane, R.; Klein, M. L. Coarse-Grained Force Field for Ionic Surfactants Soft Matter 2011, 7, 6178-6186 10.1039/c1sm05173c
14. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D., Jr.; Pastor, R. W. Update of the Charmm All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types J. Phys. Chem. B 2010, 114, 7830-7843 10.1021/jp101759q
15. 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, 926-935 10.1063/1.445869
16. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189 10.1063/1.467468
17. Izaguirre, J. A.; Catarello, D. P.; Wozniak, J. M.; Skeel, R. D. Langevin Stabilization of Molecular Dynamics J. Chem. Phys. 2001, 114, 2090-2098 10.1063/1.1332996
18. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593 10.1063/1.470117
19. Andersen, H. C. Rattle-A Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations J. Comput. Phys. 1983, 52, 24-34 10.1016/0021-9991(83)90014-1
20. Tuckerman, M.; Berne, B. J.; Martyna, G. J. Reversible Multiple Time-Scale Molecular-Dynamics-Reply J. Chem. Phys. 1993, 99, 2278-2279 10.1063/1.465242
21. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
22. Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular-Dynamics J. Comput. Phys. 1995, 117, 1-19 10.1006/jcph.1995.1039
23. Hoover, W. G. Constant-Pressure Equations of Motion Phys. Rev. A 1986, 34, 2499-2500 10.1103/PhysRevA.34.2499
24. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, Second Edition; Computational Science Series; Academic Press: San Diego, CA, 2001.
25. Cubitt, R.; Fragneto, G. D17: The New Reflectometer at the ILL Appl. Phys. A: Mater. Sci. Process. 2002, 74, S329-S331 10.1007/s003390201611
26. Guixa-Gonzalez, R.; Rodriguez-Espigares, I.; Ramirez-Anguita, J. M.; Carrio-Gaspar, P.; Martinez-Seara, H.; Giorgino, T.; Selent, J. MEMBPLUGIN: Studying Membrane Complexity in VMD Bioinformatics 2014, 30, 1478-1480 10.1093/bioinformatics/btu037
27. Petrache, H. I.; Feller, S. E.; Nagle, J. F. Determination of Component Volumes of Lipid Bilayers from Simulations Biophys. J. 1997, 72, 2237-2242 10.1016/S0006-3495(97)78867-2
28. Nagle, J. F.; Tristram-Nagle, S. Structure of Lipid Bilayers Biochim. Biophys. Acta, Rev. Biomembr. 2000, 1469, 159-195 10.1016/S0304-4157(00)00016-2
29. Kucerka, N.; Nieh, M. P.; Katsaras, J. Fluid Phase Lipid Areas and Bilayer Thicknesses of Commonly Used Phosphatidylcholines as a Function of Temperature Biochim. Biophys. Acta, Biomembr. 2011, 1808, 2761-2771 10.1016/j.bbamem.2011.07.022
30. Kucerka, N.; Nagle, J. F.; Sachs, J. N.; Feller, S. E.; Pencer, J.; Jackson, A.; Katsaras, J. Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-ray Scattering Data Biophys. J. 2008, 95, 2356-2367 10.1529/biophysj.108.132662
31. Kucerka, N.; Liu, Y. F.; Chu, N. J.; Petrache, H. I.; Tristram-Nagle, S. T.; Nagle, J. F. Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles Biophys. J. 2005, 88, 2626-2637 10.1529/biophysj.104.056606