Wide-angle X-ray Scattering Data Research Articles

Effects of processing on structural, mechanical and biological properties of collagen-based substrates for regenerative medicine

The aim of this work was to investigate the structural features of type I collagen isoforms and collagen-based films at atomic and molecular scales, in order to evaluate whether and to what extent different protocols of slurry synthesis may change the protein structure and the final properties of the developed scaffolds. Wide Angle X-ray Scattering data on raw materials demonstrated the preferential orientation of collagen molecules in equine tendon-derived collagens, while randomly oriented molecules were found in bovine skin collagens, together with a lower crystalline degree, analyzed by the assessment of FWHM (Full Width at Half Maximum), and a certain degree of salt contamination. WAXS and FT-IR (Fourier Transform Infrared) analyses on bovine collagen-based films, showed that mechanical homogenization of slurry in acidic solution was the treatment ensuring a high content of super-organization of collagen into triple helices and a high crystalline domain into the material. In vitro tests on rat Schwannoma cells showed that Schwann cell differentiation into myelinating cells was dependent on the specific collagen film being used, and was found to be stimulated in case of homogenization-treated samples. Finally DHT/EDC crosslinking treatment was shown to affect mechanical stiffness of films depending on collagen source and processing conditions.

SUNBIM a package for X-ray imaging of materials with SWAXS & GISWAXS techniques

SUNBIM (Supramolecular & SUbmolecular Nano & Bio Materials X-ray IMaging Project) is a suite of integrated programs developed, in collaboration with Rigaku Innovative Technologies, to treat Small and Wide Angle X-ray Scattering data, collected either in transmission geometry (SAXS/WAXS) or in reflection geometry (GISAXS/GIWAXS). In addition, a specific routine to collect and analyze data in SAXS scanning transmission microscopy has been developed as additional tool to investigate tissues or material science samples through a focused X-ray beam which is used to raster scan a specimen while acquiring SAXS scattering patterns with a 2D detector. Indeed, a first-generation-synchrotron-class FrE+ SuperBright Rigaku microsource, coupled to a three pinhole S-MAX3000 camera, was recently installed at the X-ray MicroImaging Laboratory (XMI-L@b) and used with success in SAXS/WAXS/GISAXS/GIWAXS experiments (De Caro et al, 2012; 2013)and for SAXS scanning microscopy (Altamura et al, 2012; Giannini et al, 2013). The SUNBIM package was developed and interfaced to the XMI-L@b to perform: i) q-scale calibration and 2D->1D folding on SAXS/GISAXS/WAXS data, including also possible eccentricity corrections studied in the case of WAXS/GIWAXS data (Cervellino et al., 2006; 2008); ii) background evaluation and subtraction, denoising and primary beam angular divergence deconvolution on SAXS/GISAXS profiles (De Caro et al, 2012; 2013); iii) indexing of 2D GISAXS frames (Tate et al., 2006) and extraction of 1D GISAXS profiles along specific cuts; iv) scanning SAXS microscopy: collection of SAXS data in a mesh across mm2 area, composite of the as-collected 2D SAXS frames into a single image, analysis of the composed data to derive the transmitted intensity microscopy as well as the distribution and orientation of nano-scale structures over the analyzed area (Bunk et al., 2009).

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

Wide-angle x-ray scattering (WAXS) experiments of biomolecules in solution have become increasingly popular because of technical advances in light sources and detectors. However, the structural interpretation of WAXS profiles is problematic, partly because accurate calculations of WAXS profiles from structural models have remained challenging. In this work, we present the calculation of WAXS profiles from explicit-solvent molecular dynamics (MD) simulations of five different proteins. Using only a single fitting parameter that accounts for experimental uncertainties because of the buffer subtraction and dark currents, we find excellent agreement to experimental profiles both at small and wide angles. Because explicit solvation eliminates free parameters associated with the solvation layer or the excluded solvent, which would require fitting to experimental data, we minimize the risk of overfitting. We further find that the influence from water models and protein force fields on calculated profiles are insignificant up to q≈15nm−1. Using a series of simulations that allow increasing flexibility of the proteins, we show that incorporating thermal fluctuations into the calculations significantly improves agreement with experimental data, demonstrating the importance of protein dynamics in the interpretation of WAXS profiles. In addition, free MD simulations up to one microsecond suggest that the calculated profiles are highly sensitive with respect to minor conformational rearrangements of proteins, such as an increased flexibility of a loop or an increase of the radius of gyration by < 1%. The present study suggests that quantitative comparison between MD simulations and experimental WAXS profiles emerges as an accurate tool to validate solution ensembles of biomolecules.

WAXS studies of global molecular orientation induced in nematic liquid crystals by simple shear flow

Global molecular orientation function coefficients for the nematic liquid crystal 4-cyano 4'-nn -pentylbiphenyl (5CB) in shear flow are presented, being extracted from 2-dimensional Wide-Angle X-ray Scattering data. A linear increase in orientation parameter P2 is observed with a logarithmic increase in shear rate. It is proposed that this arises from an increased number of LC directors aligning to the shear axis. Upon cessation of shear flow, the anisotropy is seen to relax away completely, over a time scale which is inversely proportional to the previously applied shear rate.