Atomically detailed lipid bilayer models for the interpretation of small angle neutron and X-ray scattering data

Biochimica et Biophysica Acta - Biomembranes

Volumn 1848, Issue 2, 2015, Pages 662-672

  Fogarty, Joseph C ^a   Arjunwadkar, Mihir ^b   Pandit, Sagar A ^a   Pan, Jianjun ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b UNIVERSITY OF PUNE   (India)

Author keywords

Model membrane; SANS; SAXS; Simplex based optimization

Indexed keywords

1,2-DIPHYTANOYLPHOSPHATIDYLCHOLINE; 1,2-OLEOYLPHOSPHATIDYLCHOLINE; 1-PALMITOYL-2-OLEOYLGLYCERO-3-PHOSPHOGLYCEROL; 1-PALMITOYL-2-OLEOYLGLYCERO-3-PHOSPHOSERINE; 1-PALMITOYL-2-OLEOYLPHOSPHATIDYLCHOLINE; LIPID BILAYER; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLGLYCEROL; PHOSPHATIDYLSERINE;

CHEMICAL MODEL; CHEMISTRY; LIPID BILAYER; NEUTRON DIFFRACTION; QUANTUM THEORY; RADIATION SCATTERING; X RAY DIFFRACTION;

LIPID BILAYERS; MODELS, CHEMICAL; NEUTRON DIFFRACTION; PHOSPHATIDYLCHOLINES; PHOSPHATIDYLGLYCEROLS; PHOSPHATIDYLSERINES; QUANTUM THEORY; SCATTERING, RADIATION; X-RAY DIFFRACTION;

EID: 84919935015     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2014.10.041     Document Type: Article

References (29)

1. Richard C. Aster, Brian Borchers, and Clifford H. Thurber Parameter Estimation and Inverse Problems 2004 Elsevier San Diego
2. O. Berger, O. Edholm, and F. Jähnig Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 72 5 1997 2002 2013
3. K.P. Burnham, and D.R. Anderson Model Selection and Multimodel Inference 2002 Springer New York
4. See-Wing Chiu, Sagar A. Pandit, H.L. Scott, and Eric Jakobsson An improved united atom force field for simulation of mixed lipid bilayers J. Phys. Chem. B 113 9 2009 2748 2763 (PMID: 19708111)
5. Jhuma Das, Elijah Flenner, and Ioan Kosztin Anomalous diffusion of water molecules in hydrated lipid bilayers J. Chem. Phys. 139 6 2013 065102
6. Joseph C. Fogarty, See-Wing Chiu, Peter Kirby, Eric Jakobsson, and Sagar A. Pandit Automated optimization of water-water interaction parameters for a coarse-grained model J. Phys. Chem. B 118 6 2014 1603 1611
7. N.P. Franks, and W.R. Lieb The structure of lipid bilayers and the effects of general anaesthetics: an x-ray and neutron diffraction study J. Mol. Biol. 133 4 1979 469 500
8. Andrew Gelman, John B. Carlin, Hal S. Stern, David B. Dunson, Aki Vehtari, and Donald B. Rubin Bayesian Data Analysis third edition 2013 Chapman and Hall/CRC
9. Peter Heftberger, Benjamin Kollmitzer, Frederick A. Heberle, Jianjun Pan, Michael Rappolt, Heinz Amenitsch, Norbert Kučerka, John Katsaras, and Georg Pabst Global small-angle x-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile model J. Appl. Crystallogr. 47 1 Feb 2014 173 180
10. Berk Hess, Carsten Kutzner, David van der Spoel, and Erik Lindahl Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 3 2008 435 447
11. Jeffery B. Klauda, Norbert Kucerka, Bernard R. Brooks, Richard W. Pastor, and John F. Nagle Simulation-based methods for interpreting x-ray data from lipid bilayers Biophys. J. 90 8 Apr 2006 2796 2807
12. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, and Richard W. Pastor Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types J. Phys. Chem. B 114 23 2010 7830 7843
13. Norbert Kučerka, Bryan W. Holland, Chris G. Gray, Bruno Tomberli, and John Katsaras Scattering density profile model of POPG bilayers as determined by molecular dynamics simulations and small-angle neutron and x-ray scattering experiments J. Phys. Chem. B 116 1 2012 232 239
14. Norbert Kučerka, John F. Nagle, Jonathan N. Sachs, Scott E. Feller, Jeremy Pencer, Andrew Jackson, and John Katsaras Lipid bilayer structure determined by the simultaneous analysis of neutron and x-ray scattering data Biophys. J. 95 5 2008 2356 2367
15. Norbert Kučerka, Mu-Ping Nieh, and John Katsaras Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature Biochim. Biophys. Acta Biomembr. 1808 11 2011 2761 2771
16. Jahur A. Mondal, Satoshi Nihonyanagi, Shoichi Yamaguchi, and Tahei Tahara Three distinct water structures at a zwitterionic lipid/water interface revealed by heterodyne-detected vibrational sum frequency generation J. Am. Chem. Soc. 134 18 2012 7842 7850
17. J.F. Nagle, and S. Tristram-Nagle Structure of lipid bilayers Biochim. Biophys. Acta 1469 3 Nov 2000 159 195
18. J.A. Nelder, and R. Mead A simplex method for function minimization Comput. J. 7 4 1965 308 313
19. J. Nocedal, and S. Wright Numerical optimization Springer Series in Operations Research and Financial Engineering 2006 Springer
20. Sagar A. Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, and H.L. Scott Cholesterol packing around lipids with saturated and unsaturated chains: a simulation study Langmuir 24 13 2008 6858 6865
21. Jianjun Pan, Xiaolin Cheng, Luca Monticelli, Frederick A. Heberle, Norbert Kucerka, D. Peter Tieleman, and John Katsaras The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations Soft Matter 10 2014 3716 3725
22. Jianjun Pan, Frederick A. Heberle, Stephanie Tristram-Nagle, Michelle Szymanski, Mary Koepfinger, John Katsaras, and Norbert Kučerka Molecular structures of fluid phase phosphatidylglycerol bilayers as determined by small angle neutron and x-ray scattering Biochim. Biophys. Acta Biomembr. 1818 9 2012 2135 2148
23. V.A. Parsegian, and R.P. Rand Interaction in membrane assemblies R. Lipowsky, E. Sackmann, Structure and Dynamics of Membranes Volume 1 of Handbook of Biological Physics 1995 North-Holland 643 690
24. Brian Richard Pauw Everything SAXS: small-angle scattering pattern collection and correction J. Phys. Condens. Matter 25 38 2013 383201
25. B.R. Pauw Corrigendum: everything SAXS: small-angle scattering pattern collection and correction (2013 J. Phys.: Condens. Matter 25 383201) J. Phys. Condens. Matter 26 23 2014 239501
26. Nam Dinh Pham, and Bogdan M. Wilamowski Improved Nelder Mead's simplex method and applications J. Comput. 3 3 2011
27. K. Tu, D.J. Tobias, and M.L. Klein Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer Biophys. J. 69 6 1995 2558 2562
28. M.C. Wiener, and S.H. White Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution Biophys. J. 59 1 1991 162 173
29. M.C. Wiener, and S.H. White Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure Biophys. J. 61 2 1992 434 447