Two sterols, two bilayers: insights on membrane structure from molecular dynamics

References

• Simons K, Ikonen E. How cells handle cholesterol. Science. 2000;290:1721–1726.
   PubMed Web of Science ®Google Scholar
• Maxfield FR, Tabas I. Role of cholesterol and lipid organization in disease. Nature. 2005;438:612–621.10.1038/nature04399
   PubMed Web of Science ®Google Scholar
• Marquardt D, Kučerka N, Wassall SR, et al. Cholesterol’s location in lipid bilayers. Chem Phys Lipid. 2016;199:17–25.10.1016/j.chemphyslip.2016.04.001
   PubMed Web of Science ®Google Scholar
• Kessel A, Ben-Tal N, May S. Interactions of cholesterol with lipid bilayers: the preferred configuration and fluctuations. Biophys J. 2001;81:643–658.10.1016/S0006-3495(01)75729-3
   PubMed Web of Science ®Google Scholar
• Martinez-Seara H, Róg T, Karttunen M, et al. Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes. PLoS ONE. 2010;5:e11162.10.1371/journal.pone.0011162
   PubMed Web of Science ®Google Scholar
• Boughter CT, Monje-Galvan V, Im W, et al. Influence of cholesterol on phospholipid bilayer structure and dynamics. J Phys Chem B. 2016;120:11761–11772.10.1021/acs.jpcb.6b08574
   PubMed Web of Science ®Google Scholar
• Khelashvili G, Harries D. How cholesterol tilt modulates the mechanical properties of saturated and unsaturated lipid membranes. J Phys Chem B. 2013;117:2411–2421.10.1021/jp3122006
   PubMed Web of Science ®Google Scholar
• Marquardt D, Heberle FA, Greathouse DV, et al. Lipid bilayer thickness determines cholesterol’s location in model membranes. Soft Matter. 2016;12:9417–9428.10.1039/C6SM01777K
   PubMed Web of Science ®Google Scholar
• van Meer G, Voelker DR, Feigenson GW. Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol. 2008;9:112–124.10.1038/nrm2330
   PubMed Web of Science ®Google Scholar
• Róg T, Pasenkiewicz-Gierula M. Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study. FEBS Lett. 2001;502:68–71.10.1016/S0014-5793(01)02668-0
   PubMed Web of Science ®Google Scholar
• Bui TT, Suga K, Umakoshi H. Roles of sterol derivatives in regulating the properties of phospholipid bilayer systems. Langmuir. 2016;32:6176–6184.10.1021/acs.langmuir.5b04343
   PubMed Web of Science ®Google Scholar
• Czub J, Baginski M. Comparative molecular dynamics study of lipid membranes containing cholesterol and ergosterol. Biophys J. 2006;90:2368–2382 . Epub 2006 Jan 10.10.1529/biophysj.105.072801
   PubMed Web of Science ®Google Scholar
• Pitman MC, Suits F. Molecular-level organiztion of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochemistry. 2004;43:15318–15328.10.1021/bi048231w
   PubMed Web of Science ®Google Scholar
• Pöyry S, Róg T, Karttunen M, et al. Significance of cholesterol methyl groups. J Phys Chem B. 2008;112:2922–2929.10.1021/jp7100495
   PubMed Web of Science ®Google Scholar
• Róg T, Pasenkiewicz-Gierula M, Vattulainen I, et al. What happens if cholesterol is made smoother. Biophys J. 2007;92:3346–3357.10.1529/biophysj.106.095497
   PubMed Web of Science ®Google Scholar
• Cournia Z, Ullmann GM, Smith JC. Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study. J Phys Chem B. 2007;111:1786–1801.10.1021/jp065172i
   PubMed Web of Science ®Google Scholar
• Endress E, Bayerl S, Prechtel K, et al. The effect of cholesterol, lanosterol, and ergosterol on lecithin bilayer mechanical properties at molecular and microscopic dimensions: a solid-state NMR and micropipet study. Langmuir. 2002;18:3293–3299.10.1021/la011596 m
   Web of Science ®Google Scholar
• Mannock DA, Lewis RN, McMullen TP, et al. The effect of variations in phospholipid and sterol structure on the nature of lipid-sterol interactions in lipid bilayer model membranes. Chem Phys Lipid. 2010;163:403–448.10.1016/j.chemphyslip.2010.03.011
   PubMed Web of Science ®Google Scholar
• Mannock DA, Lewis RN, McElhaney RN. A calorimetric and spectroscopic comparison of the effects of ergosterol and cholesterol on the thermotropic phase behavior and organization of dipalmitoylphosphatidylcholine bilayer membranes. Biochim Biophys Acta. 2010;1798:376–388.10.1016/j.bbamem.2009.09.002
   PubMed Web of Science ®Google Scholar
• Hung W-C, Lee M-T, Chung H, et al. Comparative study of the condensing effects of ergosterol and cholesterol. Biophys J. 2016;110:2026–2033.10.1016/j.bpj.2016.04.003
   PubMed Web of Science ®Google Scholar
• Monje-Galvan V, Klauda JB. Modelling yeast organelle membranes and how lipid diversity influences bilayer properties. Biochemistry. 2015;54:6852–6861. Epub 2015 Oct 26.
   PubMed Web of Science ®Google Scholar
• Tuller G, Nemec T, Hrastnik C, et al. Lipid composition of subcellular membranes of an FY1679-derived haploid yeast wild-type strain grown on different carbon sources. Yeast. 1999;15:1555–1564.10.1002/(ISSN)1097-0061
   PubMed Web of Science ®Google Scholar
• Klemm RW, Ejsing CS, Surma MA, et al. Segregation of sphingolipids and sterols during formation of secretory vesicles at the trans-Golgi network. J Cell Biol. 2009;185:601–612.10.1083/jcb.200901145
   PubMed Web of Science ®Google Scholar
• Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Klauda JB, Venable RM, Freites JA, et al. 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
   PubMed Web of Science ®Google Scholar
• Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A. 1985;31:1695–1697.
   PubMed Web of Science ®Google Scholar
• Frenkel D, Smit B. Understanding molecular simulation from algorithms to applications. 2 ed. Cambridge (MA): Academic Press; 2001.
   Google Scholar
• Leach AR. Molecular modeling principles and applications. 2nd ed. Great Britain: Pearson Education; 2001.
   Google Scholar
• Feller SE, Zhang Y, Pastor RW, et al. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995;103:4613–4621.10.1063/1.470648
   Web of Science ®Google Scholar
• Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Steinbach PJ, Brooks BR. New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem. 1994;15:667–683.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Klauda JB. Free programs, molecular coordinates, & Files University of Maryland. [cited Jun 2015]. Available from: https://terpconnect.umd.edu/~jbklauda/research/download.html.
   Google Scholar
• Barber CB, Dobkin DP, Huhdanpaa H. The quickhull algorithm for convex hulls. ACM Trans Math Software (TOMS). 1996;22:469–483.10.1145/235815.235821
   Web of Science ®Google Scholar
• Lim JB, Rogaski B, Klauda JB. Update of the cholesterol force field parameters in CHARMM. J Phys Chem B. 2011;116:203–210.
   PubMed Web of Science ®Google Scholar
• Kučerka N, Nagle JF, Sachs JN, et al. Lipid bilayer structure determined by the simultaneous analysis of neutron and X-Ray scattering data. Biophys J. 2008;95:2356–2367 . Epub 2008 May 27.10.1529/biophysj.108.132662
   PubMed Web of Science ®Google Scholar
• Pan J, Marquardt D, Heberle FA, et al. Revisiting the bilayer structures of fluid phase phosphatidylglycerol lipids: accounting for exchangeable hydrogens. Biochim Biophys Acta. 2014;1838:2966–2969.10.1016/j.bbamem.2014.08.009
   PubMed Web of Science ®Google Scholar
• Kučerka N, Katsaras J. Nagle JF. Comparing membrane simulations to scattering experiments: introducing the SIMtoEXP software. J Membr Biol. 2010;235:43–50.10.1007/s00232-010-9254-5
   PubMed Web of Science ®Google Scholar
• Lomize MA, Lomize AL, Pogozheva ID, et al. OPM: orientations of proteins in membranes database. Bioinformatics (Oxford, England). 2006;22:623–625. Epub 2006 Jan 7.
   Google Scholar
• Leftin A, Brown MF. An NMR database for simulations of membrane dynamics. Biochim Biophys Acta. 2011;1808:818–839 . Epub 2010 Dec 8.10.1016/j.bbamem.2010.11.027
   PubMed Web of Science ®Google Scholar
• Seelig A, Seelig J. Dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry. 1974;13:4839–4845.10.1021/bi00720a024
   PubMed Web of Science ®Google Scholar
• Seelig A, Seelig J. Bilayers of dipalmitoyl-3-sn-phosphatidylcholine. Conformational differences between the fatty acyl chains. Biochem Biophys Acta. 1975;406:1–5 . Epub 1975 Sep 16.
   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 . Epub 1978/08/08.10.1021/bi00609a021
   PubMed Web of Science ®Google Scholar
• Klauda JB, Eldho NV, Gawrisch K, et al. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. J Phys Chem B. 2008;112:5924–5929 . Epub 2008/01/09.10.1021/jp075641w
   PubMed Web of Science ®Google Scholar
• Perly B, Smith IC, Jarrell HC. Acyl chain dynamics of phosphatidylethanolamines containing oleic acid and dihydrosterculic acid: deuteron NMR relaxation studies. Biochemistry. 1985;24:4659–4665 . Epub 1985 Aug 13.10.1021/bi00338a027
   PubMed Web of Science ®Google Scholar
• Klauda JB, Roberts MF, Redfield AG, et al. Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics. Biophys J. 2008;94:3074–3083.10.1529/biophysj.107.121806
   PubMed Web of Science ®Google Scholar
• Long RA, Hruska F, Gesser HD. Membrane condensing effect of cholesterol and the role of its hydroxyl group. Biochem Biophys Res Commun. 1970;41:321–327.10.1016/0006-291X(70)90506-1
   PubMed Web of Science ®Google Scholar
• O’Connor JW, Klauda JB. Lipid membranes with a majority of cholesterol: applications to the ocular lens and aquaporin 0. J Phys Chem B. 2011;115:6455–6464.10.1021/jp108650u
   PubMed Web of Science ®Google Scholar
• Pan JJ, Tristram-Nagle S, Nagle JF. Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation. Phys Rev E. 2009;80:12.
   Web of Science ®Google Scholar
• Arora A, Raghuraman H, Chattopadhyay A. Influence of cholesterol and ergosterol on membrane dynamics: a fluorescence approach. Biochim Biophys Acta (BBA) Res Commun. 2004;318:920–926.
   PubMed Web of Science ®Google Scholar