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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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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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Probing single-molecule enzyme active-site conformational state intermittent coherence.

Yufan He1, Yue Li, Saptarshi Mukherjee

  • 1Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.

Journal of the American Chemical Society
|August 10, 2011
PubMed
Summary

Enzyme catalysis involves dynamic protein movements. Researchers used single-molecule FRET to observe enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) conformational changes during reactions, revealing key dynamics.

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Area of Science:

  • Enzymology
  • Biophysics
  • Biochemistry

Background:

  • Protein conformational dynamics are crucial for enzyme function.
  • Understanding enzyme mechanisms requires studying dynamic states.
  • Enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in folate biosynthesis.

Purpose of the Study:

  • To investigate the relationship between protein conformational dynamics and enzymatic reactions.
  • To identify and characterize conformational states of HPPK during catalysis.
  • To elucidate the mechanism of substrate-enzyme complex formation and product release.

Main Methods:

  • Single-molecule fluorescence resonance energy transfer (smFRET) was employed to monitor enzyme conformational changes in real-time.
  • Statistical data analysis, including correlation function analysis, was used to interpret smFRET trajectories.
  • Enzyme HPPK was studied in its catalytic reaction with substrates.

Main Results:

  • Intermittently appearing coherence in enzymatic conformational states was identified in single-molecule FRET trajectories.
  • Coherent conformational dynamics suggest a multistep motion related to substrate binding and product release.
  • Coherence frequency increased with substrate concentration, supporting a multiple-conformational state model for HPPK.

Conclusions:

  • Enzymatic catalysis involves dynamic conformational changes that can be observed at the single-molecule level.
  • The observed intermittent coherence in HPPK suggests a common mechanism in conformation-regulated enzymatic reactions.
  • Results support a model combining conformation selection and induced-fit mechanisms for substrate-enzyme complex formation.