Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers

References

• 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.
   PubMed Web of Science ®Google Scholar
• Maxfield FR, Tabas I. Role of cholesterol and lipid organization in disease. Nature. 2005;438:612–621.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Hénin J, Shinoda W, Klein ML. Models for phosphatidylglycerol lipids put to a structural test. J Phys Chem B. 2009;113:6958–6963.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Feller SE. Molecular dynamics simulations of lipid bilayers. Curr Opin Colloid Interface Sci. 2000;5:217–223.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Zhao W, Rόg T, Gurtovenko AA, Vattulainen I, Karttunen M. Role of phosphatidylglycerols in the stability of bacterial membranes. Biochimie. 2008;90:930–938.
   PubMed Web of Science ®Google Scholar
• Feller SE, MacKerell Jr AD. An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B. 2000;104:7510–7515.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Lim JB, Rogaski B, Klauda JB. Update of the cholesterol force field parameters in CHARMM. J Phys Chem B. 2012;116:203–210.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Durell SR, Brooks BR, Bennaim A. Solvent-induced forces between two hydrophilic groups. J Phys Chem. 1994;98:2198–2202.
   Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: an NLog(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Web of Science ®Google Scholar
• Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995;103:4613–4621.
   Web of Science ®Google Scholar
• Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994;101:4177–4189.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• KuČerka N, Katsaras J, Nagle J. Comparing membrane simulations to scattering experiments: introducing the SIMtoEXP software. J Membr Biol. 2010;235:43–50.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Seelig A, Seelig J. Bilayers of dipalmitoyl-3-sn-phosphatidylcholine conformational differences between the fatty acyl chains. Biochim Biophys Acta. 1975;406:1–5.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Seelig J, Waespe-Sarcevic N. Molecular order in cis and trans unsaturated phospholipid bilayers. Biochemistry. 1978;17:3310–3315.
   PubMed Web of Science ®Google Scholar