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Ordering a dynamic protein via a small-molecule stabilizer.

Ningkun Wang1, Chinmay Y Majmudar, William C Pomerantz

  • 1Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.

Journal of the American Chemical Society
|February 7, 2013
PubMed
Summary
This summary is machine-generated.

Researchers used Tethering to stabilize the GACKIX domain, enabling its structural characterization. This method aids in discovering small molecules that modulate conformationally flexible proteins like CBP/p300 coactivators.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • The GACKIX domain of CBP/p300 is a master coactivator that binds diverse transcriptional activators.
  • Its conformational dynamics present challenges for structural characterization.
  • Understanding these dynamics is crucial for deciphering transcriptional regulation.

Purpose of the Study:

  • To overcome the challenges in structurally characterizing the dynamic GACKIX domain.
  • To identify small molecules that stabilize the GACKIX domain for structural studies.
  • To explore the utility of the Tethering strategy for conformationally malleable proteins.

Main Methods:

  • Utilized the ligand discovery strategy of Tethering to identify stabilizing small-molecule fragments.
  • Performed crystallographic characterization of the GACKIX domain complexed with a small molecule.
  • Conducted molecular dynamics simulations on the obtained structure.

Main Results:

  • Successfully identified small-molecule fragments that stabilize the GACKIX domain.
  • Achieved the first crystallographic characterization of the GACKIX domain at 2.0 Å resolution.
  • Molecular dynamics revealed side-chain motions crucial for accommodating diverse binding partners.

Conclusions:

  • The Tethering strategy is effective for stabilizing conformationally flexible proteins, facilitating structural characterization.
  • This approach accelerates the discovery of small-molecule modulators for proteins like CBP/p300.
  • The findings provide insights into the mechanism of activator binding by the GACKIX domain.