Acyl Chain Order Parameter Profiles in Phospholipid Bilayers: Computation from Molecular Dynamics Simulations and Comparison with 2H NMR Experiments

Overview

Journal Eur Biophys J

Specialty Biophysics

Date 2007 Jun 29

PMID 17598103

Citations 88

Authors

Louic S Vermeer

Bert L de Groot

Valerie Reat

Alain Milon

Jerzy Czaplicki

Affiliations

Soon will be listed here.

Abstract

Order parameters from deuterium NMR are often used to validate or calibrate molecular dynamics simulations. This paper gives a short overview of the literature in which experimental order parameters from (2)H NMR are compared to those calculated from MD simulations. The different ways in which order parameters from experiment are used to calibrate and validate simulations are reviewed. In the second part of this review, a case study of cholesterol in a DMPC bilayer is presented. It is concluded that the agreement between experimental data and simulation is favorable in the hydrophobic region of the membrane, for both the phospholipids and cholesterol. In the interfacial region the agreement is less satisfactory, probably because of the high polarity of this region which makes the correct computation of the electrostatics more complex.

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References

Mukhopadhyay P, Monticelli L, Tieleman D . Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. Biophys J. 2004; 86(3):1601-9. PMC: 1303994. DOI: 10.1016/S0006-3495(04)74227-7. View

Marsan M, Muller I, Ramos C, Rodriguez F, Dufourc E, CZAPLICKI J . Cholesterol orientation and dynamics in dimyristoylphosphatidylcholine bilayers: a solid state deuterium NMR analysis. Biophys J. 1999; 76(1 Pt 1):351-9. PMC: 1302524. DOI: 10.1016/S0006-3495(99)77202-4. View

Stockton G, Polnaszek C, Tulloch A, Hasan F, Smith I . Molecular motion and order in single-bilayer vesicles and multilamellar dispersions of egg lecithin and lecithin-cholesterol mixtures. A deuterium nuclear magnetic resonance study of specifically labeled lipids. Biochemistry. 1976; 15(5):954-66. DOI: 10.1021/bi00650a003. View

Feller S, Brown C, Nizza D, Gawrisch K . Nuclear Overhauser enhancement spectroscopy cross-relaxation rates and ethanol distribution across membranes. Biophys J. 2002; 82(3):1396-404. PMC: 1301941. DOI: 10.1016/S0006-3495(02)75494-5. View

Tobias D . Electrostatics calculations: recent methodological advances and applications to membranes. Curr Opin Struct Biol. 2001; 11(2):253-61. DOI: 10.1016/s0959-440x(00)00198-6. View

Sum A, de Pablo J . Molecular simulation study on the influence of dimethylsulfoxide on the structure of phospholipid bilayers. Biophys J. 2003; 85(6):3636-45. PMC: 1303668. DOI: 10.1016/S0006-3495(03)74781-X. View

Scott H . Modeling the lipid component of membranes. Curr Opin Struct Biol. 2002; 12(4):495-502. DOI: 10.1016/s0959-440x(02)00353-6. View

Rog T, Pasenkiewicz-Gierula M . Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study. Biochimie. 2005; 88(5):449-60. DOI: 10.1016/j.biochi.2005.10.005. View

Patel S, Brooks 3rd C . CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem. 2003; 25(1):1-15. DOI: 10.1002/jcc.10355. View

10.

Falck E, Patra M, Karttunen M, Hyvonen M, Vattulainen I . Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers. Biophys J. 2004; 87(2):1076-91. PMC: 1304448. DOI: 10.1529/biophysj.104.041368. View

11.

Lopez Cascales J, Otero T, Smith B, Gonzalez C, Marquez M . Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study. J Phys Chem B. 2006; 110(5):2358-63. DOI: 10.1021/jp0562680. View

12.

Takaoka Y, Pasenkiewicz-Gierula M, Miyagawa H, Kitamura K, Tamura Y, Kusumi A . Molecular dynamics generation of nonarbitrary membrane models reveals lipid orientational correlations. Biophys J. 2000; 79(6):3118-38. PMC: 1301188. DOI: 10.1016/S0006-3495(00)76546-5. View

13.

Chapman D, Owens N, Phillips M, Walker D . Mixed monolayers of phospholipids and cholesterol. Biochim Biophys Acta. 1969; 183(3):458-65. DOI: 10.1016/0005-2736(69)90160-6. View

14.

Douliez J, Leonard A, Dufourc E . Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings. Biophys J. 1995; 68(5):1727-39. PMC: 1282076. DOI: 10.1016/S0006-3495(95)80350-4. View

15.

Hofsass C, Lindahl E, Edholm O . Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophys J. 2003; 84(4):2192-206. PMC: 1302786. DOI: 10.1016/S0006-3495(03)75025-5. View

16.

Czub J, Baginski M . Comparative molecular dynamics study of lipid membranes containing cholesterol and ergosterol. Biophys J. 2006; 90(7):2368-82. PMC: 1403193. DOI: 10.1529/biophysj.105.072801. View

17.

Benz R, Castro-Roman F, Tobias D, White S . Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. Biophys J. 2004; 88(2):805-17. PMC: 1305157. DOI: 10.1529/biophysj.104.046821. View

18.

Petrache H, Dodd S, Brown M . Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by (2)H NMR spectroscopy. Biophys J. 2000; 79(6):3172-92. PMC: 1301193. DOI: 10.1016/S0006-3495(00)76551-9. View

19.

Lindahl E, Edholm O . Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J. 2000; 79(1):426-33. PMC: 1300946. DOI: 10.1016/S0006-3495(00)76304-1. View

20.

Chiu S, Jakobsson E, Scott H . Combined Monte Carlo and molecular dynamics simulation of hydrated lipid-cholesterol lipid bilayers at low cholesterol concentration. Biophys J. 2001; 80(3):1104-14. PMC: 1301307. DOI: 10.1016/S0006-3495(01)76088-2. View