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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Area of Science:

  • Structural Biology
  • Protein Dynamics
  • Biochemistry

Background:

  • Aromatic residues are crucial for protein core stability.
  • Nuclear magnetic resonance (NMR) studies indicated aromatic side chains can rotate (ring flips) within proteins.
  • Protein 'breathing' motions were hypothesized to facilitate these ring flips, but structural details were lacking.

Purpose of the Study:

  • To elucidate the structural rearrangements accompanying ring flipping of a buried tyrosine residue in an SH3 domain.
  • To provide high-resolution structural insights into protein breathing motions associated with side chain dynamics.

Main Methods:

  • Utilized NMR spectroscopy to observe tyrosine side chain flipping.
  • Performed proteome-wide sequence analysis to design stabilizing mutants.
  • Employed X-ray crystallography to determine the high-resolution structure of the minor state.

Main Results:

  • Demonstrated that the tyrosine side chain transitions to a low-populated minor state.
  • Identified the generation of void volume around the tyrosine ring during the transition.
  • Captured the high-resolution structure of the stabilized minor state.

Conclusions:

  • The study reveals the structural basis for protein breathing motions enabling aromatic side chain ring flipping.
  • Findings offer insights into the interplay between local protein environment and amino acid side chain conformations.
  • Results have implications for protein design and structure prediction.