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Characterization of MLKL-mediated Plasma Membrane Rupture in Necroptosis
Published on: August 7, 2018
BcL-xL conformational changes upon fragment binding revealed by NMR
Clémentine Aguirre1, Tim Ten Brink, Olivier Walker
1UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France.
Plos One
|May 30, 2013
Summary
A new NMR method accurately detects subtle protein conformational changes upon fragment binding. This technique aids fragment-based drug design by simulating chemical shift perturbations for improved inhibitor development.
Area of Science:
- Structural Biology
- Biophysics
- Medicinal Chemistry
Background:
- Protein-protein interactions (PPIs) are crucial therapeutic targets.
- Fragment-based drug design (FBDD) offers a promising strategy for PPI inhibitor development.
- Understanding protein conformational changes upon ligand binding is vital for FBDD.
Purpose of the Study:
- To present a rapid Nuclear Magnetic Resonance (NMR) method for detecting subtle protein conformational changes induced by fragment binding.
- To validate the method using the Bcl-xL protein and a known inhibitor fragment.
- To establish Chemical Shift Perturbation (CSP) simulation as a tool for assessing ligand-induced protein dynamics in FBDD.
Main Methods:
- Utilized fragment-induced Chemical Shift Perturbation (CSP) of amine protons.
- Compared experimental CSP data with simulated CSP values based on docked fragment poses, incorporating ring-current effects.
- Employed residual dipolar coupling (RDC) measurements for corroboration.
- Performed retrospective analysis on the Bcl-xL/4'-fluoro-[1,1'-biphenyl]-4-carboxylic acid complex.
Main Results:
- The NMR method successfully identified subtle conformational rearrangements in Bcl-xL upon fragment binding, particularly in helices H2, H3, and the start of H5.
- Results were consistent with residual dipolar coupling (RDC) data and prior molecular dynamics (MD) simulations.
- Demonstrated the reliability of protein amine proton CSPs as structural probes for ligand interactions.
Conclusions:
- The developed fast NMR approach effectively probes subtle protein conformational changes during fragment binding.
- CSP simulation is a valuable tool for assessing protein structural adaptations in fragment-based drug design.
- This method enhances the early stages of drug discovery targeting protein-protein interactions.
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