Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers

Molecular Simulation

Volumn 41, Issue 10-12, 2015, Pages 948-954

  Kang, Hojin ^a   Klauda, Jeffery B ^a  

^a UNIVERSITY OF MARYLAND   (United States)

Author keywords

lipid bilayer; molecular simulations; POPG

Indexed keywords

BIOINFORMATICS; CYTOLOGY; DEUTERIUM; LIPIDS; MOLECULAR DYNAMICS; NEUTRON SCATTERING; X RAYS;

FUNCTIONAL FORMS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; NEUTRON FORM FACTORS; ORDER PARAMETER; PHOSPHATIDYLGLYCEROLS; POPG; STRUCTURAL MODELING;

LIPID BILAYERS;

EID: 84931008594     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2014.926548     Document Type: Conference Paper

References (43)

1. van Meer G, Voelker DR, Feigenson GW. Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol. 2008; 9: 112-124.
2. Maxfield FR, Tabas I. Role of cholesterol and lipid organization in disease. Nature. 2005; 438: 612-621.
3. Ingram LO. Changes in lipid composition of Escherichia coli resulting from growth with organic solvents and with food additives. Appl Environ Microbiol. 1977; 33: 1233-1236.
4. Oursel D, Loutelier-Bourhis C, Orange N, Chevalier S, Norris V, Lange CM. Lipid composition of membranes of Escherichia coli by liquid chromatography/tandem mass spectrometry using negative electrospray ionization. Rapid Commun Mass Spectrom. 2007; 21: 1721-1728.
5. Ishida Y, Kitagawa K, Nakayama A, Ohtani H. Complementary analysis of lipids in whole bacteria cells by thermally assisted hydrolysis and methylation-GC and MALDI-MS combined with on-probe sample pretreatment. J Anal Appl Pyrolysis. 2006; 77: 116-120.
6. Zhao W, Róg T, Gurtovenko AA, Vattulainen I, Karttunen M. Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions. Biophys J. 2007; 92: 1114-1124.
7. Hénin J, Shinoda W, Klein ML. Models for phosphatidylglycerol lipids put to a structural test. J Phys Chem B. 2009; 113: 6958-6963.
8. Kwon B, Waring AlanJ, Hong M. A 2H solid-state NMR study of lipid clustering by cationic antimicrobial and cell-penetrating peptides in model bacterial membranes. Biophys J. 2013; 105: 2333-2342.
9. Borle F, Seelig J. Ca2+ binding to phosphatidylglycerol bilayers as studied by differential scanning calorimetry and 2H-and 31P-nuclear magnetic resonance. Chem Phys Lipids. 1985; 36: 263-283.
10. Perly B, Smith ICP, Jarrell HC. Effects of the replacement of a double bond by a cyclopropane ring in phosphatidylethanolamines: a deuterium NMR study of phase transitions and molecular organization. Biochemistry. 1985; 24: 1055-1063.
11. KuČerka N, Holland BW, Gray CG, Tomberli B, Katsaras J. 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. 2012; 116: 232-239.
12. Pan J, Heberle FA, Tristram-Nagle S, Szymanski M, Koepfinger M, Katsaras J, Kucerka N. Molecular structures of fluid phase phosphatidylglycerol bilayers as determined by small angle neutron and X-ray scattering. Biochim Biophys Acta Biomembr. 2012; 1818: 2135-2148.
13. Feller SE. Molecular dynamics simulations of lipid bilayers. Curr Opin Colloid Interface Sci. 2000; 5: 217-223.
14. Zhao C, Caplan DA, Noskov SY. Evaluations of the absolute and relative free energies for antidepressant binding to the amino acid membrane transporter LeuT with free energy simulations. J Chem Theory Comput. 2010; 6: 1900-1914.
15. Berger O, Edholm O, Jahnig F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J. 1997; 72: 2002-2013.
16. Zhao W, Rg T, Gurtovenko AA, Vattulainen I, Karttunen M. Role of phosphatidylglycerols in the stability of bacterial membranes. Biochimie. 2008; 90: 930-938.
17. Feller SE, MacKerell Jr AD. An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B. 2000; 104: 7510-7515.
18. Klauda JB, Venable RM, Freites JA, O'Connor JW, Mondragon-Ramirez C, Vorobyov I, Tobias DJ, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B. 2010; 114: 7830-7843.
19. Klauda JB, Monje V, Kim T, Im W. Improving the CHARMM force field for polyunsaturated fatty acid chains. J Phys Chem B. 2012; 116: 9424-9431.
20. Pandit KR, Klauda JB. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. Biochim Biophys Acta Biomembr. 2012; 1818: 1205-1210.
21. Lim JB, Klauda JB. Branching at the Iso-and anteiso-positions in complex chlamydia membranes: a molecular dynamics study. Biochim Biophys Acta Biomembr. 2011; 1808: 323-331.
22. Lim JB, Rogaski B, Klauda JB. Update of the cholesterol force field parameters in CHARMM. J Phys Chem B. 2012; 116: 203-210.
23. Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008; 29: 1859-1865.
24. Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophys J. 2009; 97: 50-58.
25. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem. 2005; 26: 1781-1802.
26. Durell SR, Brooks BR, Bennaim A. Solvent-induced forces between two hydrophilic groups. J Phys Chem. 1994; 98: 2198-2202.
27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983; 79: 926-935.
28. 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: 10089-10092.
29. Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995; 103: 4613-4621.
30. Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994; 101: 4177-4189.
31. Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem. 2009; 30: 1545-1614.
32. KuČerka N, Katsaras J, Nagle J. Comparing membrane simulations to scattering experiments: introducing the SIMtoEXP software. J Membr Biol. 2010; 235: 43-50.
33. Kucerka N, Nieh MP, Katsaras J. Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. BBA-Biomembranes. 2011; 1808: 2761-2771.
34. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996; 14: 33-38.
35. Benz RW, Castro-Roman F, Tobias DJ, White SH. Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. Biophys J. 2005; 88: 805-817.
36. Klauda JB, KuČerka N, Brooks BR, Pastor RW, Nagle JF. Simulation-based methods for interpreting X-ray data from lipid bilayers. Biophys J. 2006; 90: 2796-2807.
37. KuČerka N, Liu YF, Chu NJ, Petrache HI, Tristram-Nagle ST, Nagle JF. 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.
38. Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 united-atom chain model for lipids and surfactants. J Phys Chem B. 2014; 118: 547-556.
39. Seelig A, Seelig J. The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry. 1974; 13: 4839-4845.
40. Seelig A, Seelig J. Bilayers of dipalmitoyl-3-sn-phosphatidylcholine conformational differences between the fatty acyl chains. Biochim Biophys Acta. 1975; 406: 1-5.
41. Klauda JB, Eldho NV, Gawrisch K, Brooks BR, Pastor RW. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. J Phys Chem B. 2008; 112: 5924-5929.
42. Perly B, Smith ICP, Jarrell HC. Acyl chain dynamics of phosphatidylethanolamines containing oleic acid and dihydrosterculic acid: deuteron NMR relaxation studies. Biochemistry. 1985; 24: 4659-4665.
43. Seelig J, Waespe-Sarcevic N. Molecular order in cis and trans unsaturated phospholipid bilayers. Biochemistry. 1978; 17: 3310-3315.