Diffuse scattering provides material parameters and electron density profiles of biomembranes

Liu, Yufeng; Nagle, John F.

doi:10.1103/physreve.69.040901

Cited by 220 publications

(242 citation statements)

References 27 publications

Supporting

Mentioning

203

Contrasting

Order By: Relevance

“…The electron density profile of these membranes is also in agreement with experimental profiles (see supplementary material). 62 In our coordinate system, x and y axes are in the membrane plane and z is the plane normal. DOPC and peptide molecular interactions were represented by the CHARMM v.36 force field 63,64 and water was described by the TIP3P model.…”

Section: Computationalmentioning

confidence: 99%

Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

Lee

Kuczera

Middaugh

et al. 2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

The time-resolved parallel artificial membrane permeability assay with fluorescence detection and comprehensive computer simulations are used to study the passive permeation of three aromatic dipeptides—N-acetyl-phenylalanineamide (NAFA), N-acetyltyrosineamide (NAYA), and N-acetyl-tryptophanamide (NATA) through a 1,2-dioleoyl-sn-glycero-3-phospocholine (DOPC) lipid bilayer. Measured permeation times and permeability coefficients show fastest translocation for NAFA, slowest for NAYA, and intermediate for NATA under physiological temperature and pH. Computationally, we perform umbrella sampling simulations to model the structure, dynamics, and interactions of the peptides as a function of z, the distance from lipid bilayer. The calculated profiles of the potential of mean force show two strong effects—preferential binding of each of the three peptides to the lipid interface and large free energy barriers in the membrane center. We use several approaches to calculate the position-dependent translational diffusion coefficients D(z), including one based on numerical solution the Smoluchowski equation. Surprisingly, computed D(z) values change very little with reaction coordinate and are also quite similar for the three peptides studied. In contrast, calculated values of sidechain rotational correlation times τrot(z) show extremely large changes with peptide membrane insertion—values become 100 times larger in the headgroup region and 10 times larger at interface and in membrane center, relative to solution. The peptides’ conformational freedom becomes systematically more restricted as they enter the membrane, sampling α and β and C7eq basins in solution, α and C7eq at the interface, and C7eq only in the center. Residual waters of solvation remain around the peptides even in the membrane center. Overall, our study provides an improved microscopic understanding of passive peptide permeation through membranes, especially on the sensitivity of rotational diffusion to position relative to the bilayer.

show abstract

Section: Computationalmentioning

confidence: 99%

Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

Lee

Kuczera

Middaugh

et al. 2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…The radial electron density profile of the inner MT wall and outer tubulin monolayer are based on the fit to the MT scattering data. ** The parameters for the electron density profile of the lipid bilayer are based on literature data (3,30). Finally, the third tubulin layer is multiplied by the fraction, f, of tubulin coverage relative to the inner MT wall.…”

Section: Resultsmentioning

confidence: 99%

“…A chain packing statistical model of membranes (28) and experiments (29) show that k ϰ ␦ P , where ␦ is the membrane thickness. P Ϸ 3 in the case of fluid membrane, the C 12:0 and C 18:1 tails, for which ␦ Ϸ 1.2 and 1.4 nm, respectively (30). Membranes with ordered chains, the C 14:0 , C 16:0, and C 18:0 tails, for which ␦ Ϸ 1.5, 1.8, and 2 nm, respectively, are significantly more rigid, and the scaling of with ␦ is expected to be with a larger P (31, 32).…”

Section: Methodsmentioning

confidence: 99%

Cationic liposome–microtubule complexes: Pathways to the formation of two-state lipid–protein nanotubes with open or closed ends

Raviv

Needleman

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Intermolecular interactions between charged membranes and biological polyelectrolytes, tuned by physical parameters, which include the membrane charge density and bending rigidity, the membrane spontaneous curvature, the biopolymer curvature, and the overall charge of the complex, lead to distinct structures and morphologies. The self-assembly of cationic liposome-microtubule (MT) complexes was studied, using synchrotron x-ray scattering and electron microscopy. Vesicles were found to either adsorb onto MTs, forming a ''beads on a rod'' structure, or undergo a wetting transition and coating the MT. Tubulin oligomers then coat the external lipid layer, forming a tunable lipid-protein nanotube. The beads on a rod structure is a kinetically trapped state. The energy barrier between the states depends on the membrane bending rigidity and charge density. By controlling the cationic lipid͞tubulin stoichiometry it is possible to switch between two states of nanotubes with either open ends or closed ends with lipid caps, a process that forms the basis for controlled chemical and drug encapsulation and release.polyelectrolyte lipid complexes ͉ small angle x-ray scattering ͉ nanotubebased drug delivery ͉ membrane ͉ tubulin

show abstract

“…To analyze quantitatively the molecular layer stack of the Sdocosanylcysteine thin films in the present study, we have considered possible models including the Hosemann paracrystal model (Hosemann & Bagchi, 1962), the Cialle model (Liu & Nagle, 2004) and the modified Cialle model (Pabst et al, 2000), and found that the paracrystal model is the most suitable for a layer lattice in our study, as shown in Fig. 1.…”

Section: Theorymentioning

confidence: 99%

Quantitative analysis of molecularly stacked layer structures in supported organic thin films by synchrotron grazing-incidence X-ray scattering

et al. 2007

View full text Add to dashboard Cite

In this study, we derive a grazing‐incidence X‐ray scattering (GIXS) formula to analyze quantitatively GIXS patterns for molecularly stacked layer structures in substrate‐supported nanoscale thin films. We apply this formula in the quantitative analysis of GIXS patterns obtained for S‐docosanylcysteine thin films on silicon substrates with native oxide layers. This analysis successfully provides information on the structural parameters and orientation of the molecular layer stack developed in S‐docosanylcysteine thin films.

show abstract

Diffuse scattering provides material parameters and electron density profiles of biomembranes

Cited by 220 publications

References 27 publications

Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study

Cationic liposome–microtubule complexes: Pathways to the formation of two-state lipid–protein nanotubes with open or closed ends

Quantitative analysis of molecularly stacked layer structures in supported organic thin films by synchrotron grazing-incidence X-ray scattering

Contact Info

Product

Resources

About