Integrative Structural Biology: Using X-ray Crystallography, Small-Angle X-ray Scattering, and Cryogenic Electron Microscopy to Determine Protein Structures

Author(s):  
Jamie R. Wallen
2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  

Soft Matter ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. 3096-3104
Author(s):  
Valeria Castelletto ◽  
Jani Seitsonen ◽  
Janne Ruokolainen ◽  
Ian W. Hamley

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties.


AIP Advances ◽  
2013 ◽  
Vol 3 (3) ◽  
pp. 032139 ◽  
Author(s):  
E. Carvou ◽  
J. L. Le Garrec ◽  
J. Pérez ◽  
J. Praquin ◽  
M. Djeddi ◽  
...  

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.


2020 ◽  
Vol 223 (18) ◽  
pp. jeb228387
Author(s):  
Katarzyna Janas ◽  
Anna Łatkiewicz ◽  
Andrew Parnell ◽  
Dorota Lutyk ◽  
Julia Barczyk ◽  
...  

ABSTRACTThe costs associated with the production and maintenance of colour patches is thought to maintain their honesty. Although considerable research on sexual selection has focused on structurally coloured plumage ornaments, the proximate mechanisms of their potential condition dependence, and thus their honesty, is rarely addressed, particularly in an experimental context. Blue tit (Cyanistes caeruleus) nestlings have ultraviolet (UV)–blue structurally coloured tail feathers, providing a unique opportunity for investigation of the causes of variation in their colour. Here, we examined the influence of early growing conditions on the reflectance and structural properties of UV–blue-coloured tail feathers of blue tit nestlings. We applied a two-stage brood size manipulation to determine which stage of development more strongly impacts the quality of tail feather colouration and microstructure. We used small-angle X-ray scattering (SAXS) and electron microscopy to characterise the nanoscale and microscale structure of tail feather barbs. Nestlings from the broods enlarged at a later stage of growth showed a sex-specific rectrix development delay, with males being more sensitive to this manipulation. Contrary to predictions, treatment affected neither the quality of the barbs’ nanostructures nor the brightness and UV chroma of feathers. However, at the microscale, barbs’ keratin characteristics were impaired in late-enlarged broods. Our results suggest that nanostructure quality, which determines the UV–blue colour in tail feathers, is not sensitive to early rearing conditions. Furthermore, availability of resources during feather growth seems to impact the quality of feather microstructure more than body condition, which is likely to be determined at an earlier stage of nestling growth.


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