Reconstruction of 3D density from solution scattering

Grant, Thomas D.

doi:10.1016/bs.mie.2022.09.018

Cited by 2 publications

(1 citation statement)

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“…GNOM files were used as inputs to calculate electron density maps for each sample using DENSS in the RAW interface, using the slow mode to average 100 reconstructions together and the NifL dimer model as a reference structure. The proposed publication metrics for DENSS models are included in SI Appendix , Table S1 F ( 64 ). Alignment of the NifL dimer model to electron density maps was performed internally by DENSS, and the correlation between the NifL dimer model and the final electron density map is reported for each conformation in SI Appendix , Table S1 .…”

Section: Methodsmentioning

confidence: 99%

Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system

Boyer

Tokmina‐Lukaszewska

Batista

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ 54 -dependent activator NifA to control the transcription of nitrogen fixation ( nif ) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL–NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph, Azotobacter vinelandii .

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Section: Methodsmentioning

confidence: 99%