Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules

Costa, Luca; Andriatis, A.; Brennich, Martha; Teulon, Jean‐Marie; Chen, Shu‐wen W.; Pellequer, Jean‐Luc; Round, Adam

doi:10.1186/s12900-016-0068-2

Cited by 15 publications

(13 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Compared with the results from Caspar (1956), our proposed reconstruction is able to accurately approximate the radius of the inner core and of the overall structure and locate the peak density as well as the hollowness of the inner core. Compared with Costa et al (2016) and Lee et al (2007), our reconstruction presents similar features to theirs, in the sense that the approximate radii of the low, high and intermediate density cylindrical compartments agree with our reconstruction, as does the total density per compartment. However, owing to the absence of the cylindrical assumption, our method can better resolve features such as the hollowness of the core and the radius and thickness of the RNA ring of the virus (orange ring in Fig.…”

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virussupporting

confidence: 66%

“…We also present the average radial electron distribution of the reconstruction in Fig. 3(d) compared with the three-cylinder model used in Costa et al (2016) and Lee et al (2007) estimated from SAXS data and the distribution of a TMV oriented gel sample from Caspar (1956). Compared with the results from Caspar (1956), our proposed reconstruction is able to accurately approximate the radius of the inner core and of the overall structure and locate the peak density as well as the hollowness of the inner core.…”

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virusmentioning

confidence: 98%

“…TMV is a 3000 Å long virion structured as a cylindrical shell with an outer diameter of about 180 Å and an inner diameter of roughly 40 Å (Caspar, 1956). We use the SAXS intensity (data kindly provided by Marta Brennich, ESRF) from a 26 mg ml À1 unoriented solution of TMV collected on BM29 at ESRF (Costa et al, 2016). The corresponding equatorial intensity is generated by applying the geometric correction described in Section 2 to the SAXS data and is shown as a solid line in Fig.…”

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virusmentioning

confidence: 99%

“…(c) Side-by-side comparison of the reconstructed cross-section and PDB entry 2tmv(Namba et al, 1989). (d) Radial density distribution of TMV for the proposed approach, the threecylinder model used inCosta et al (2016) andLee et al (2007) and the radial distribution of a TMV oriented gel sample fromCaspar (1956)…”

mentioning

confidence: 99%

See 3 more Smart Citations

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Roig-Solvas

Brooks

Makowski

2020

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

Ab initio reconstruction methods have revolutionized the capabilities of smallangle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/ connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed. research papers Acta Cryst. (2020). D76, 102-117 Roig-Solvas et al. FiXR 103 research papers 116 Roig-Solvas et al. FiXR Acta Cryst. (2020). D76, 102-117 Figure 10Normalized error between the original matrices B q and the proposed approximationB B q as a function of q and the percentage of eigenvectors used. The white lines indicate iso-error contours.

show abstract

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virussupporting

confidence: 66%

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virusmentioning

confidence: 98%

Section: Experiments 2: Saxs Measurements Of Tobacco Mosaic Virusmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Roig-Solvas

Brooks

Makowski

2020

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

show abstract

“…The AFM head was mounted on a commercial inverted optical microscope (Axio Observer, Carl Zeiss). [37,38]. °C.…”

Section: Characterization Techniquesmentioning

confidence: 99%

Physico-chemical properties and surface characterization of renewable hybrid nanofilms interacting with model proteins

Theodoratou

Costa

Bonnet

et al. 2019

European Polymer Journal

Self Cite

View full text Add to dashboard Cite

A comprehensive characterization of physical-chemical properties and biological interactions of ca. 200-nm-thick hybrid films based on silylated (inorganic part) castor oil (organic part) is proposed. A series of such nanofilms was fabricated and cross-linked by a sol-gel procedure, and their properties such as hydrophilicity, hardness and water vapour transmission rate were systematically studied as a function of the ratio of silylated agent to castor oil. It was found that the nanofilms have contact angles always below 90°, tunable Young modulus and hardness in the MPa range. Moreover, their water vapour transmission rates are increased by decreasing the silica ratio. The protein adsorption and cytocompatibility were evaluated using model proteins and cells. The adsorption of the proteins bovine serum albumin (BSA) and lysozyme was characterized using a quartz crystal microbalance in energy dissipation mode (QCM-D), and atomic force microscopy (AFM). The combination of the latter provided evidence for the different affinities of the proteins with the films. It was found that BSA and lysozyme form rigid layers on the surface with surface coverage close to 30 %, and that both protein layers decrease their thickness after their dehydration. Finally, cell culture experiments exhibited a good viability of the fibroblasts compared to ultra-low adhesion surfaces, which makes them potential candidates for biomedical applications.

show abstract

High Resolution AFM and Its Applications

Sun¹,

Ye²,

Sun³

2018

Atomic Force Microscopy in Molecular and Cell Biology

View full text Add to dashboard Cite

Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules

Cited by 15 publications

References 65 publications

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Physico-chemical properties and surface characterization of renewable hybrid nanofilms interacting with model proteins

High Resolution AFM and Its Applications

Contact Info

Product

Resources

About