Calculation of IR dichroic values and order parameters from molecular dynamics simulations and their application to structure determination of lipid bilayers

Abstract

In polarized infrared (IR) absorption experiments, dichroic values are used to study the structure and orientation of lipid molecules. From computer simulations, we obtained angular distributions of IR transition moment (TM) orientations of the stretch vibrations of CH 2 groups of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholin (POPC) lipid bilayers in the gel (L/~) and fluid (L a) phases. From these distributions, we calculated dichroic absorption values, as well as order parameters. We established a connection between the dichroic ratio R am, which is measured in IR-ATR setups, with the dichroic ratio D and the order parameter Szz.The calculated values compare well with experimental results for the fluid phase. In addition, we computed angular distributions of transition moments with respect to the tail director orientation for the gel and the fluid phases. Only small differences were found between the distributions in the symmetric stretch orientation, the asymmetric stretch orientation, and the C-H bond orientation of CH 2 groups. The distributions of tail directors of POPC showed average tilts of 14.7 ° in the gel phase and 32.9 ° in the fluid phase. We developed a theory which makes it possible to calculate average tilt angles of tail directors in the gel phase from dichroic absorption values obtained from IR measurements for a wide range of lipids. Legendre coefficients were calculated from TM distributions. Order parameters, defined as the second Legendre polynomial, were found to closely approximate the TM distribution in lipid bilayers in the fluid phase.

Combinatorial microscopy for the study of protein–membrane interactions in supported lipid bilayers: Order parameter measurements by combined polarized TIRFM/AFM

“…The technique of polarized total internal reflection fluorescence microscopy (pTIRFM) is able to infer the time-and ensemble-averaged orientational order related to a collection of fluorescent probe molecules located within an interfacial system such as a substrate-supported bilayer through a quantity known as the orientational order parameter, hP 2 i (Axelrod, 1989(Axelrod, , 2001Burghardt, 1984;Oreopoulos and Yip, 2009;Sund et al, 1999;Thompson et al, 1984;Timbs and Thompson, 1990). This order parameter is similar to those encountered in other orientation-sensitive spectroscopies and has an analogous interpretation Bolterauer and Heller, 1996;Douliez et al, 1998;Lafrance et al, 1995;Lopes and Castanho, 2005;Schafer et al, 1998;Vermeer et al, 2007). In addition to the co-localization of sample fluorescence and topography that can be achieved by combined optical and atomic force microscopy, pTIRFM also allows hP 2 i associated with the fluorescent probes to be spatially mapped via the (probe concentration-independent) order parameter image.…”

Effects of phospholipid unsaturation on the bilayer nonpolar region

“…Among several reports on computer simulations of unsaturated PC bilayers (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38), cis -and trans -unsaturated bilayers were compared in two of them (27,36). In a Langevin dynamics simulation study, Pearce and Harvey (27) showed that structural and dynamic properties of PCs with a trans double bond are similar to those of saturated PCs, whereas PCs with a cis double bond behave differently.…”

Effects of heat on new and aged polyamide 6,6 textiles during pest eradication

“…Polarized ATR (Pol ATR) experiments were employed to monitor alterations in the anisotropy (directionality). A polarizer set to 0 was placed between the source and the ATR crystal and the fibre sample was rotated between 0 and 90 [32]. Dichroic peaks were identified at 1196 cm À1 (parallel), 1416 cm À1 (perpendicular) and 1631 cm À1 (perpendicular).…”