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Multi-domain protein ER-60. (a) Four domains constituting ER-60. (b) Structural model of ER-60 based on a crystal structure (PDBID: 3F8U)³³. PyMOL³⁹ was used to model the missing C-terminal residues and replace the mutated C60A with cysteine. In the ribbon model, the a domain in shown in blue, the b domain in green, the b′ domain in yellowish green, and the a′ domain in red. The other parts are gray. The reactive cysteines in the CGHC motif are orange. Gly¹³³ and Leu³⁶⁵ are hinge regions between the a and the b domain, and the b′ and the a′ domain, respectively.
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Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To exami...
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Citations
Aggregates cause a fatal problem in the structural analysis of a biomacromolecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC–SAS, was developed as a new approach to overcome this problem. However, the original version of AUC–SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC–SAS approach is identified. The improved AUC–SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).
