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Open Dataset XS97QA1S


Oxidized and X-ray-reduced Apoptosis-Inducing Factor with Allosteric Fragment Binders Examined by Time-resolved HT-SAXS

Abstract

This dataset applies time-resolved HT-SAXS to identify and triage allosteric fragment binders of oxidized and X-ray-reduced Apoptosis-Inducing Factor (AIF). Fragment hits of AIF were identified by high-throughput differential scanning fluorescence (HT-DSF), then validated by DSF and microscale thermophoresis (MST). SAXS data with 300-ms framing were collected on 39 AIF-fragment complexes and analyzed at 0.3-s and 2.1-s exposures to determine fragment impact on oxidized and X-ray-reduced AIF redox states, respectively. These datasets revealed fragments capable of stimulating dimerization of X-ray-reduced AIF and triaged fragment binders into conformational chemotypes. This dataset is described in detail in Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Nature Chemical Biology DOI: 10.1038/s41589-024-01609-1.

Experimental description

N-terminally truncated AIF (78-613) was expressed in bacteria and purified as described in Brosey et al, Structure, 2016. Purified AIF was exchanged into SAXS buffer by size-exclusion chromatography (Superdex 200 10/300) to ensure monodisperse protein. SAXS samples were prepared at 4 mg/mL with direct addition of DMSO or library fragments (10 mg/mL) to protein and SEC-matched buffers (Brosey et al, Methods in Enzymology, 2023). HT-SAXS data were collected by mail-in service at ALS beamline 12.3.1 (SIBYLS) at Lawrence Berkeley National Laboratory. **For deposition, this dataset was reprocessed and rescaled from the original image files to ensure correct intensity errors.**

File description

Two zip files containing 0.3 s (oxidized) and 2.1 s (X-ray-reduced) SAXS curves for AIF-fragment complexes. File names are descriptive of DMSO or fragment identifier.

Created

2023-03-23

Updated

2024-05-30

Data collection technique

HT-SAXS

Journal DOI

Source

Advanced Light Source

Beamline

SIBYLS BL12.3.1

Wavelength

1.27 Å

Sample to Detector Distance

2.0 m


Submitting Author

Chris Brosey

University of Texas MD Anderson Cancer Center

United States of America

[email protected]

Collaborators

Project Leader

John Tainer

[email protected]


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Complete Set of SAS Data Files

The complete SAS dataset is downloadable as a zip file.


Individual SAS Data Files (total 1)

These are individual SAS data files that may be raw or processed (merged, etc.). These may or not be included in a zip file containing a larger dataset.


Supplemental Data and Supporting Materials (total 0)

These data and materials may include X-ray crystal structure coordinates, multi-angle light scattering data, .etc. It may also include additional details or methods pertaining to the SAXS experiments, or the researcher's interpretations of the results.


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SAXS Similarity SAXS FrameSlice


Sample:

  • Macromolecule 1: AIF
    • Sample Full Name: Apoptosis-inducing Factor
    • Sample Type: Protein
    • Source Organism: Homo sapiens
    • Source Organism NCBI Taxonomy ID: 9606
    • Expression System: Escherichia coli
    • Expression NCBI Taxonomy ID: 562
    • Uniprot ID: O95831
    • Sequence or Chemical Formula:
    • MVGAGAYAYKTMKEDEKRYNERISGLGLTPEQKQKKAALSASEGEEVPQDKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESEASEITIPPSTPAVPQAPVQGEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHEDLEVLFQ