Location and dynamics of acyl chain NBD-labeled phosphatidylcholine (NBD-PC) in DPPC bilayers. A molecular dynamics and time-resolved fluorescence anisotropy study

Abstract

100-ns molecular dynamics simulations of fluid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers, both pure and containing 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) acyl-chain labeled fluorescent analogs (C6-NBD-PC and C12-NBD-PC), are described. These molecules are widely used as probes for lipid structure and dynamics. The results obtained here for pure DPPC agree with both experimental and theoretical published works. We verified that the NBD fluorophore of both derivatives loops to a transverse location closer to the interface than to the center of the bilayer. Whereas this was observed previously in experimental literature works, conflicting transverse locations were proposed for the NBD group. According to our results, the maximum of the transverse distribution of NBD is located around the glycerol backbone/carbonyl region, and the nitro group is the most external part of the fluorophore. Hydrogen bonds from the NH group of NBD (mostly to glycerol backbone lipid O atoms) and to the nitro O atoms of NBD (from water OH groups) are continuously observed. Rotation of NBD occurs with approximately 2.5-5 ns average correlation time for these probes, but very fast, unresolved reorientation motions occur in <20 ps, in agreement with time-resolved fluorescence anisotropy measurements. Finally, within the uncertainty of the analysis, both probes show lateral diffusion dynamics identical to DPPC.

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

“…33 Regarding the atoms of the NBD moiety, they are mainly located near the glycerol backbone of POPC (for example, note the similar hzi of POPC C13 and NBD-diC n PE N1 atoms), similarly to other NBD probes NBD-C n , 33 NBD-PC, 13 and NBD-cholesterol. 16 However, contrary to these probes, in which the NO 2 group was the outermost part of the fluorophore, the amine N1 is generally the most external atom of NBD, located further from the bilayer centre than the nitro N6 atom in all derivatives.…”

“…13,16,33 To verify whether this also applies to NBD-diC n PE, we studied the occurrence of H-bonds featuring probe atoms either as donors (Fig. 6A) or as acceptors (Fig.…”

“…The NBD transition dipole (parallel to the NBD short axis 13,86 ) has different orientation in NBD-diC n PE compared to NBD-PC. As commented above, whereas the nitro group of NBD-PC is pointed towards the water phase, that of NBD-diC n PE shows inward orientation (for a direct comparison of the angular distributions of the NBD long and short axes in NBD-PC and NBD-diC 16 PE, see Fig.…”

“…1) in the present study with our previous investigation of NBD-PC in fluid DPPC (323 K). 13 Fig. 12 depicts the mass distribution of NBD in the C6-NBD-PC/DPPC and NBD-diC 16 PE/ POPC systems, while values of relevant parameters are listed in Table 2.…”

Recent Developments in the Study of the Behavior of Fluorescent Membrane Probes in Lipid Bilayers: Molecular Dynamics Approach

“…1C), in fluid DPPC bilayers (0:64, 1:63, 4:60 NBD-PC/DPPC bilayers, T=323 K, t=100 ns) have been reported in two complementary studies. The first one addressed primarily the locations and dynamics of the probes (Loura & Prates Ramalho, 2007) whereas the second focused on their effects on the host bilayer properties (Loura et al, 2008). Parameterization of the NBD moiety required energy minimization for geometry and ab initio quantum mechanical calculations for partial atomic charges.…”