SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues

Abstract

This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.

The hierarchical response of human corneal collagen to load

“…All analysis was carried out using bespoke software developed in-house in the Matlab (Mathworks) environment. A detailed explanation of the analysis procedures for SAXS and WAXS of collagen can be found elsewhere [36] , [37] and is described briefly here. Images were centred and converted to cylindrical polar form, with z representing pixel intensity, and data were split into two circumferential populations: parallel (within ±45° of applied load in the positive and negative directions), and perpendicular ( Fig.…”

Revealing the Assembly of Filamentous Proteins with Scanning Transmission Electron Microscopy

“…Although different methods can be used for measuring the molecular packing structure of proteins, e.g., small angle scattering and turbidity techniques, they rely on bulk measurements and often involve assumptions about the network or protein structure to support the data analysis. 36,37 The spatial resolution and correlative image-mass analysis of our approach allows us to retrieve, in a label-free manner, information about the filament mass per length, molecular We have demonstrated the potential of this technique by studying the structure of a wide range of biopolymers important in the cellular cytoskeleton and in the extracellular matrix. Our findings demonstrate that STEM has a wide mass range, from 17 kDa/nm for Fd bacteriophages and actin filaments to 20 MDa/nm for collagen bundles.…”

The effect of bacteriochlorophyll derivative WST-D and near infrared light on the molecular and fibrillar architecture of the corneal stroma

“…The corneo-scleral discs (cornea with a 2-mm scleral rim) were removed, placed in storage medium and transported to Diamond Light Source for examination on small-and wide-angle x-ray scattering beamlines (I22 and I02 respectively). Due to beamline access restrictions, the 4 pairs of corneo-scleral discs destined for wide-angle x-ray scattering studies (samples [13][14][15][16] were stored in Optisol (Chiron Ophthalmics, Irvine, California) for 8 days prior to data collection and the 6 pairs of corneo-scleral discs for small-angle x-ray scattering studies (samples [17][18][19][20][21][22] were stored in minimal essential medium with 6% dextran for 2 days prior to data collection.…”

“…Small-angle x-ray scattering patterns were calibrated against the 58.380 Å d 001 lattice reflection in powder diffraction patterns of silver behenate. Using methods detailed previously, data were analysed using an integrated software tool specifically designed for the analysis of fibrous collagen-based tissues (SAXS4COLL), to generate average measurements of collagen D-periodicity, fibril diameter and inter-fibrillar spacing 20 .…”

“…(1). Using the analysis technique described previously 20 , wide-angle x-ray scatter patterns were calibrated against the 0.305 nm d 104 lattice reflection in powder diffraction patterns of calcium carbonate and the modal average inter-molecular spacing of corneal collagen was determined from the position of the intermolecular equatorial reflection peak. The relationship between x-ray Bragg spacing and the corresponding centre-to-centre distance of the parameter under investigation (collagen inter-molecular or inter-fibrillar spacing) depends on the precise packing of the molecules within the fibrils, or of the fibrils within the stroma.…”