Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques

Shekhar, Prabhanshu; Nanda, Hirsh; Lösche, Mathias; Heinrich, Frank

doi:10.1063/1.3661986

Cited by 63 publications

(90 citation statements)

References 47 publications

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“…Data fitting was performed using IGOR Pro 6.32A (Wavemetrics). The one-dimensional structural profile along the lipid bilayer normal was obtained from NR using a hybrid of a stratified slab model for the solid substrate (44), a continuous distribution model for the stBLM (45), and a monotonic Hermite spline for the model-free envelope of the protein (28). Individual slabs were implemented for the bulk silicon, the silicon oxide, the chromium, and the gold layers.…”

Section: Methodsmentioning

confidence: 99%

Structural Features of Membrane-bound Glucocerebrosidase and α-Synuclein Probed by Neutron Reflectometry and Fluorescence Spectroscopy

Yap¹,

Jiang²,

Heinrich

et al. 2015

Journal of Biological Chemistry

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Background: A specific interaction exists between ␣-synuclein and glucocerebrosidase on the lipid membrane, resulting in enzyme inhibition. Results: Binding glucocerebrosidase has a profound effect on ␣-synuclein, moving roughly half of its embedded helical region above the membrane plane. Conclusion: A model is proposed with structural insights into glucocerebrosidase inhibition by ␣-synuclein. Significance: ␣-Synuclein-glucocerebrosidase interaction provides a molecular connection between Parkinson and Gaucher diseases.

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Section: Methodsmentioning

confidence: 99%

Structural Features of Membrane-bound Glucocerebrosidase and α-Synuclein Probed by Neutron Reflectometry and Fluorescence Spectroscopy

Yap¹,

Jiang²,

Heinrich

et al. 2015

Journal of Biological Chemistry

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“…Data were analyzed by fitting an area-fraction distribution of substrate, membrane, and protein layers along the z axis. A composition space model that represents the lipid membrane in terms of overlapping distributions of the different molecular groups (lipid chain, head group, and tether) (20) was used to represent , Cr, and Au) as well as the tether layer were conserved among all the models. Lipid thickness and the protein profile were allowed to vary between experimental conditions.…”

Section: Gagmentioning

confidence: 99%

Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein

Dick

Datta

Nanda

et al. 2015

J Virol

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Previously, no retroviral Gag protein has been highly purified in milligram quantities and in a biologically relevant and active form. We have purified Rous sarcoma virus (RSV) Gag protein and in parallel several truncation mutants of Gag and have studied their biophysical properties and membrane interactions in vitro. RSV Gag is unusual in that it is not naturally myristoylated. From its ability to assemble into virus-like particles in vitro, we infer that RSV Gag is biologically active. By size exclusion chromatography and small-angle X-ray scattering, Gag in solution appears extended and flexible, in contrast to previous reports on unmyristoylated HIV-1 Gag, which is compact. However, by neutron reflectometry measurements of RSV Gag bound to a supported bilayer, the protein appears to adopt a more compact, folded-over conformation. At physiological ionic strength, purified Gag binds strongly to liposomes containing acidic lipids. This interaction is stimulated by physiological levels of phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] and by cholesterol. However, unlike HIV-1 Gag, RSV Gag shows no sensitivity to acyl chain saturation. In contrast with full-length RSV Gag, the purified MA domain of Gag binds to liposomes only weakly. Similarly, both an N-terminally truncated version of Gag that is missing the MA domain and a C-terminally truncated version that is missing the NC domain bind only weakly. These results imply that NC contributes to membrane interaction in vitro, either by directly contacting acidic lipids or by promoting Gag multimerization. IMPORTANCERetroviruses like HIV assemble at and bud from the plasma membrane of cells. Assembly requires the interaction between thousands of Gag molecules to form a lattice. Previous work indicated that lattice formation at the plasma membrane is influenced by the conformation of monomeric HIV. We have extended this work to the more tractable RSV Gag. Our results show that RSV Gag is highly flexible and can adopt a folded-over conformation on a lipid bilayer, implicating both the N and C termini in membrane binding. In addition, binding of Gag to membranes is diminished when either terminal domain is truncated. RSV Gag membrane association is significantly less sensitive than HIV Gag membrane association to lipid acyl chain saturation. These findings shed light on Gag assembly and membrane binding, critical steps in the viral life cycle and an untapped target for antiretroviral drugs. Many of the principles underlying retrovirus assembly are understood. For example, the retrovirus structural protein, Gag, is able to assemble into morphologically normal virus-like particles (VLPs) in cells (1) and as a purified protein in vitro (2). The structures and functions of the multiple Gag domains are known. Thus, the MA domain mediates binding to the plasma membrane (PM), where for most retroviruses the Gag lattice is formed and budding occurs, the CA domain and immediately adjoining sequences engage in critical contacts to form the hexagonal Gag lattice, t...

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“…Early so-called strip models used constant ρ(z) in different z regions [92]. This has been improved by using error functions to smear the artificially sharp edges of the strip model [93,94]. When the width of two error function interfaces are wide compared to the distances between the edges, the profile becomes a Gaussian.…”

Section: Modeling the Bilayer Structurementioning

confidence: 99%

Structure Determination of HIV-1 Tat/Fluid Phase Membranes and DMPC Ripple Phase Using X-Ray Scattering

Akabori¹

2015

Springer Theses

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This thesis employs X-ray scattering to study the structure of two different stacked lipid membrane systems. The first part reports the effect on lipid bilayers of the Tat peptide Y 47 GRKKRRQRRR 57 from the HIV-1 virus transactivator of translation (Tat) protein. Synergistic use of low angle X-ray scattering (LAXS) and atomistic molecular dynamics (MD) simulations indicated Tat peptide binding to neutral dioleoylphosphatidylcholine (DOPC) headgroups. This binding induced the nearby lipid phosphate groups to move 3Å closer to the bilayer center. Many of the Tat arginines were as close to the bilayer center as the locally thinned lipid phosphate groups. Analysis of LAXS from DOPC, DOPC/dioleoylphosphatidylethanolamine (DOPE), DOPC/dioleoylphosphatidylserine (DOPS), and a mimic of the nuclear membrane indicated that the Tat peptide decreased the bilayer bending modulus K c and increased the area per lipid, possibly facilitating Tat membrane translocation. Although a mechanism for translocation remains elusive, this study suggests that Tat translocates from the headgroup region.The second study presents the structure of the asymmetric ripple phase formed by dimyristoylphosphatidylcholine. We determined the most detailed ripple phase structure by combining synchrotron LAXS and wide angle X-ray scattering (WAXS) from highly aligned multilamellar samples. We derived three intensity corrections to calculate the X-ray form factors from the 52 measured reflections. The LAXS analysis provided a high resolution two-dimensional electron density map. The ripple major arm was demonstrated to be consistent with the gel phase, and the major and minor arm structures were clearly different, supporting the coexistence of different molecular organizations. The minor arm electron density profile was qualitatively consistent with interdigitated chain packing previously proposed by MD simulations. Analysis of high resolution near grazing incidence WAXS showed that major arm hydrocarbon chains were tilted parallel to the ripple plane by 18°with respect to the bilayer local normal, toward the next nearest neighbor similarly to the gel L βF rather than the L βI phase. By measuring the Bragg rod lengths in transmission WAXS, we determined that major arm chains in opposing leaflets were coupled. The LAXS and WAXS results together indicated that chains in the major arm were shorter by 1.3Å compared to the gel phase, suggesting a gauche-trans-gauche kink in the ripple major arm. In contrast to the LAXS analysis, the measured nGIWAXS was consistent with disordered chains in the minor arm similarly to the fluid L α phase.

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Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques

Cited by 63 publications

References 47 publications

Structural Features of Membrane-bound Glucocerebrosidase and α-Synuclein Probed by Neutron Reflectometry and Fluorescence Spectroscopy

Structural Features of Membrane-bound Glucocerebrosidase and α-Synuclein Probed by Neutron Reflectometry and Fluorescence Spectroscopy

Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein

Structure Determination of HIV-1 Tat/Fluid Phase Membranes and DMPC Ripple Phase Using X-Ray Scattering

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