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Microsecond subdomain folding in dihydrofolate reductase.

Munehito Arai1, Masahiro Iwakura, C Robert Matthews

  • 1Protein Design Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan. arai@bio.c.u-tokyo.ac.jp

Journal of Molecular Biology
|May 11, 2011
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Summary
This summary is machine-generated.

Understanding protein folding dynamics is key. This study reveals microsecond folding mechanisms of dihydrofolate reductase (DHFR), showing early collapse and hierarchical subdomain assembly critical for complex protein structures.

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Area of Science:

  • Protein dynamics and biophysics
  • Molecular biology and biochemistry

Background:

  • Characterizing microsecond dynamics in multisubdomain protein folding is challenging.
  • Dihydrofolate reductase (DHFR) is a two-subdomain protein with folding initiated in the microsecond range.

Purpose of the Study:

  • To investigate the microsecond folding dynamics of dihydrofolate reductase (DHFR).
  • To elucidate the folding mechanisms of multisubdomain proteins at the microsecond timescale.

Main Methods:

  • Utilized a continuous-flow mixing device for rapid sample manipulation.
  • Employed fluorescence lifetime detection to monitor local Trp environments.
  • Applied Förster resonance energy transfer (FRET) to assess global dimensions of folding intermediates.

Main Results:

  • Observed substantial collapse in both subdomains of DHFR within 35 μs from the unfolded state.
  • Detected further contraction of the discontinuous loop subdomain and Trp burial during the fastest observable phase (∼550 μs).
  • Both subdomains reached similar compactness during the rapid folding phase.

Conclusions:

  • A hierarchical assembly model for DHFR folding emerges: independent subdomain folding, docking, and annealing after initial collapse.
  • Chain entropy plays a significant role in organizing the folding of both multisubdomain and single-domain proteins.
  • Subdomain folding explains the complex kinetics observed in protein folding.