Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data

Abstract

Quantitative structures were obtained for the fully hydrated fluid phases of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) bilayers by simultaneously analyzing x-ray and neutron scattering data. The neutron data for DOPC included two solvent contrasts, 50% and 100% D(2)O. For DPPC, additional contrast data were obtained with deuterated analogs DPPC_d62, DPPC_d13, and DPPC_d9. For the analysis, we developed a model that is based on volume probability distributions and their spatial conservation. The model's design was guided and tested by a DOPC molecular dynamics simulation. The model consistently captures the salient features found in both electron and neutron scattering density profiles. A key result of the analysis is the molecular surface area, A. For DPPC at 50 degrees C A = 63.0 A(2), whereas for DOPC at 30 degrees C A = 67.4 A(2), with estimated uncertainties of 1 A(2). Although A for DPPC agrees with a recently reported value obtained solely from the analysis of x-ray scattering data, A for DOPC is almost 10% smaller. This improved method for determining lipid areas helps to reconcile long-standing differences in the values of lipid areas obtained from stand-alone x-ray and neutron scattering experiments and poses new challenges for molecular dynamics simulations.

FIGURE 1

NSLD and ED profiles of a simulated DOPC bilayer versus the distance z along the bilayer normal. The left-hand side of the figure shows the individual lipid moieties (e.g., phosphate, choline, glycerol); the right-hand panel shows the partially combined components, thus reducing the total number of parameters needed for the SDP model. The combined component groups are as follows: carbonyl + glycerol (CG), phosphate+CH₂CH₂N (PCN), and the three CH₃ choline groups (CholCH3). Broken curves represent the partially (d9) and fully (d13) deuterated headgroup components (i.e., CD₂CD₂N and CholCD3). The choice of this combination is driven by the fact that each of the component groups has nearly the same functional form for all the different contrast conditions (e.g., ED of CholCH3 and NSLD of CholCH3 and CholCD3). Broken vertical lines mark the positions of the different groups.

FIGURE 2

The solid lines show the volume probability (volume fraction) distributions for the various SDP model components and combination components defined in Fig. 1. The probabilities were calculated from the symmetrized MD number histograms according to the procedure in Petrache et al. (26). The dashed lines show the best fits of SDP model functional forms to the corresponding component group distribution. The vertical dash-dot lines show the Gibbs dividing surface at position D_C for the hydrocarbon region with total thickness 2D_C and at position D_B/2 for water, where D_B is the Luzzati thickness of the entire bilayer. The top panel shows the sum of all probabilities.

FIGURE 3

The lines show fits using the SDP model to (A) x-ray and (B) neutron scattering form factors F(q) obtained from an MD simulation. In the main panels, the simulated form factors, depicted by dots, were constrained to the typical experimental range and noise was added at the typical experimental level (NRS). In the insets, the data are noise free and cover an extended q range (SES).

FIGURE 4

The solid lines show the volume probabilities obtained from the MD simulation (same as in Fig. 2). The dashed lines show the best fit to the full NRS data in column NRS/all in Table 1. An additional combination of methylene and methine groups is described by the gray lines (CH2+CH).

FIGURE 5

The solid lines show the result of simultaneous SDP fit to (A) x-ray and (B) neutron scattering data from DPPC at 50°C. X-ray experimental data are from Kučerka et al. (30) with the estimated uncertainties (±1 standard deviation) corresponding to the size of the data symbols for q < 0.6 Å⁻¹. The insets display the total ED and NSLD profiles for half the bilayer. (C) The SDP volume probability distributions.

FIGURE 6

The solid gray lines show the best results of the simultaneous SDP fit to (A) x-ray and (B) neutron scattering data from DOPC at 30°C; the dashed line in A and solid black lines in B show poorer fits when A was constrained to 72.4 Ų. X-ray experimental data were adapted from Kučerka et al. (19) and Kučerka et al. (29) with the estimated uncertainties (±1 standard deviation) being the size of the data symbols for q < 0.6 Å⁻¹. The insets display the total ED and NSLD profiles for half the bilayer. (C) The results of the best fit in terms of SDP volume probability distributions.

FIGURE 7

The results of component ED distributions obtained from the SDP simultaneous analysis of x-ray and neutron CV scattering data of DOPC at 30°C (solid lines) and those reported in Kučerka et al. (29) (broken lines). The methylene and methine groups are combined into one group (CH2CH), and the water + PC group accounts for the entire phosphatidylcholine and water distributions.