Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking

Hosoe, Yuhi; Sekiguchi, Hiroshi; Sasaki, Yuji; Oda, Masayuki

doi:10.1016/j.bpc.2021.106669

Cited by 2 publications

(3 citation statements)

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“…Because gold nanocrystals with diameters of 40–80 nm are larger than the proteins with a diameter of 5–10 nm discussed in this review, multiple proteins may bind to a single gold nanocrystal. DXT experiments were performed using the c-Myb R2R3 C130I/H135M/M189A mutant at different protein immobilization densities [ 32 ]. In the absence of DNA, no differences were observed between the two immobilization densities.…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

“…The histograms were compared in the presence of DNA at low ( A ) and high ( B ) immobilization densities. The figures were slightly modified from Figure 1 A,B in [ 32 ].…”

Section: Figurementioning

confidence: 99%

“…Using DXT, the structural dynamics of various proteins and those in ligand–protein interactions have been analyzed [ 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. We used DXT to analyze the change in structural dynamics of relatively smaller globular proteins, a single-chain variable fragment (scFv) antibody (26 k), a de novo designed protein (8 k), and a DNA-binding protein (12 k), as they interacted with other molecules [ 29 , 30 , 31 , 32 ]. When a protein binds to another molecule, various types of conformational changes are observed, which are closely correlated with subsequent events such as signal transduction and transcriptional regulation.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking

Oda

2023

IJMS

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Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.

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Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

“…The histograms were compared in the presence of DNA at low ( A ) and high ( B ) immobilization densities. The figures were slightly modified from Figure 1 A,B in [ 32 ].…”

Section: Figurementioning

confidence: 99%