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SAXS/WAXS data of conformationally flexible ribose binding protein.

ABSTRACT: Modern artificial intelligence-based protein structure prediction methods, such as Alphafold2, can predict structures of folded proteins with reasonable accuracy. However, Alphafold2 provides a static view of a protein, which does not show the conformational variability of the protein, domain movement in a multi-domain protein, or ligand-induced conformational changes it might undergo in solution. Small-angle X-ay scattering (SAXS) and wide-angle X-ray scattering (WAXS) are solution techniques that can aid in integrative modeling of conformationally flexible proteins, or in validating their predicted ensemble structures. While SAXS is sensitive to global structural features, WAXS can expand the scope of structural modeling by including information about local structural changes. We present SAXS and WAXS datasets obtained from conformationally flexible d-ribose binding protein (RBP) from Escherichia coli in the ribose bound and unbound forms. SAXS/WAXS datasets of RBP provided here may aid in method development efforts for more accurate prediction of structural ensembles of conformationally flexible proteins, and their conformational changes.

SUBMITTER: Choudhury J

PROVIDER: S-EPMC10764985 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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SAXS/WAXS data of conformationally flexible ribose binding protein.

Choudhury Jagrity J Yonezawa Kento K Anu Anu A Shimizu Nobutaka N Chaudhuri Barnali B

Data in brief 20231209

Modern artificial intelligence-based protein structure prediction methods, such as Alphafold2, can predict structures of folded proteins with reasonable accuracy. However, Alphafold2 provides a static view of a protein, which does not show the conformational variability of the protein, domain movement in a multi-domain protein, or ligand-induced conformational changes it might undergo in solution. Small-angle X-ay scattering (SAXS) and wide-angle X-ray scattering (WAXS) are solution techniques t ...[more]

PMID: 38178847

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Project description:Electrospinning is a versatile technique to produce nanofibrous membranes with applications in filtration, biosensing, biomedical and tissue engineering. The structural and therefore physical properties of electrospun fibers can be finely tuned by changing the electrospinning parameters. The large parameter window makes it challenging to optimize the properties of fibers for a specific application. Therefore, a fundamental understanding of the multiscale structure of fibers and its correlation with their macroscopic behaviors is required for the design and production of systems with dedicated applications. In this study, we demonstrate that the properties of poly(vinylidene fluoride-co-hexafluoro propylene) (PVDF-HFP) electrospun fibers can be tuned by changing the rotating drum speed used as a collector during electrospinning. Indeed, with the help of multiscale characterization techniques such as scanning electron microscopy (SEM), small-angle X-ray scattering (SAXS), and wide-angle X-ray scattering (WAXS), we observe that increasing the rotating drum speed not only aligns the fibers but also induces polymeric chain rearrangements at the molecular scale. Such changes result in enhanced mechanical properties and an increase of the piezoelectric β-phase of the PVDF-HFP fiber membranes. We detect nanostructural deformation behaviors when the aligned fibrous membrane is uniaxially stretched along the fiber alignment direction, while an increase in the alignment of the fibers is observed for randomly aligned samples. This was analyzed by performing in situ SAXS measurements coupled with uniaxial tensile loading of the fibrous membranes along the fiber alignment direction. The present study shows that fibrous membranes can be produced with varying degrees of fiber orientation, piezoelectric β-phase content, and mechanical properties by controlling the speed of the rotating drum collector during the fiber production. Such aligned fiber membranes have potential applications for neural or musculoskeletal tissue engineering.

Dataset Information

SAXS/WAXS data of conformationally flexible ribose binding protein.

Publications

SAXS/WAXS data of conformationally flexible ribose binding protein.

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