Correlation to Protein Conformation of Wide-Angle X-ray Scatter Parameters

Abstract

In the last decade, several studies have reported that Wide-Angle X-ray Scattering (WAXS) from protein in solution contains valuable information about protein secondary and tertiary structures. Nevertheless, the use of such information will remain limited until a clear understanding of the correlation between protein structural elements and WAXS profile regions is established. In this work, large number of possible protein conformations is generated using comparative modeling (LOOPP & PHYRE servers) of nine different proteins representing six main protein classes (SCOP database). After model validation (SAVES server), protein structural elements of the selected models are retrieved (Swiss PDB Viewer & VORONOIA) and their corresponding WAXS profiles are generated (CRYSOL). The correlations between seven elements of protein structure (alpha helix, beta sheet and random coil content, alpha to beta ratio, alpha to random coil ratio, average packing density and number of residues) and seven WAXS profile parameters (Full Width at Half Maximum of two main scattering peaks of interest, their areas, positions and ratio of intensities) are investigated. Results revealed high (up to 0.75) and moderate (0.30-0.50) correlations between some of the suggested profile parameters and investigated protein structural elements indicating that these parameters represent a useful probe of protein conformation. Moreover, a high observed correlation between the degree of fitting of model to reference structures and the degree of fitting of their corresponding WAXS profiles suggests that the latter can be used in experimental model validation.

Solid-State Nanostructured Materials from Self-Assembly of a Globular Protein–Polymer Diblock Copolymer

“…The larger domain spacing peak is attributed to either inter-sheet spacing or inter-helix spacing for proteins containing β-sheets or α-helices, respectively. 62 The smaller domain spacing peak arises from inter-strand hydrogen bonding in β-sheet proteins, or backbone hydrogen bonding in α-helices. 62 Given that circular dichroism and the known crystal structure of mCherry suggest a predominantly β-sheet secondary structure, these peaks are inferred to result from inter-sheet spacing and inter-strand hydrogen bonding between β-strands.…”

“…62 The smaller domain spacing peak arises from inter-strand hydrogen bonding in β-sheet proteins, or backbone hydrogen bonding in α-helices. 62 Given that circular dichroism and the known crystal structure of mCherry suggest a predominantly β-sheet secondary structure, these peaks are inferred to result from inter-sheet spacing and inter-strand hydrogen bonding between β-strands. Because the q values of these peaks do not change between samples, it is concluded that the inter-sheet and inter-strand spacing is not changed significantly by the processing method used to induce self-assembly.…”

Thermal Transitions and Structural Relaxations in Protein‐Based Thermoplastics

“…Two peaks are typically observed in proteins. The first corresponds to a d ‐spacing of approximately 10 Å, and has been attributed to both inter‐helix packing in proteins with predominantly helical structures and to inter‐sheet separation in proteins with a large proportion of β‐sheets . The second is a d ‐spacing of 4–5 Å attributed to repeating distances within each structure, due to hydrogen bonding either along the backbone of α‐helical proteins or between strands in β‐sheets …”

Thermal and Mechanical Properties of Bloodmeal-Based Thermoplastics Plasticized with Tri(ethylene glycol)

“…The first is attributed to inter‐helix packing in helix rich proteins and inter‐sheet separation in beta sheet rich proteins. The second peak is similarly attributed to either hydrogen bonding along the backbone in helices, or to bonding between strands in β‐sheets . Both were seen in thermoplastics derived from bloodmeal (Figure ).…”

“…The second peak is similarly attributed to either hydrogen bonding along the backbone in helices, or to bonding between strands in b-sheets. [17] Both were seen in thermoplastics derived from bloodmeal ( Figure 5). The former peak reduced in size when TEG was included, suggesting some disruption to the packing of ordered secondary structures when TEG was included.…”