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Related Experiment Videos

Protein unfolding: rigidity lost.

A J Rader1, Brandon M Hespenheide, Leslie A Kuhn

  • 1Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 14, 2002
PubMed
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Protein unfolding is linked to structural rigidity loss. A universal rigid-to-floppy transition occurs during denaturation, analogous to network glasses, with mean coordination as the key variable.

Area of Science:

  • Biophysics
  • Materials Science
  • Statistical Mechanics

Background:

  • Proteins exhibit complex unfolding pathways involving loss of structural stability.
  • Rigidity and flexibility are mathematically defined concepts applicable to network materials.
  • Understanding protein unfolding is crucial for molecular biology and drug design.

Purpose of the Study:

  • To establish a connection between protein unfolding and the concepts of rigidity and flexibility.
  • To simulate protein unfolding by weakening noncovalent bonds and observe the emergence of flexible regions.
  • To identify a universal reaction coordinate for protein unfolding across diverse protein architectures.

Main Methods:

  • Simulating the weakening of noncovalent bonds in proteins.

Related Experiment Videos

  • Analyzing the emergence of flexible regions (floppy modes) during unfolding.
  • Determining the transition state from the inflection point of floppy modes versus mean atomic coordination.
  • Calculating specific heat-like quantities from the derivatives of floppy modes.

    • Main Results:

    • The fraction of floppy modes during unfolding mirrors the fraction-folded curve.
    • A peak in a specific heat-like quantity occurs at a mean coordination of = 2.41.
    • Proteins transition from rigid to flexible states, retaining a stable core before full denaturation.
    • This behavior is analogous to the rigid-to-floppy phase transition observed in network glasses.

    Conclusions:

    • Protein unfolding can be universally described as a rigid-to-floppy phase transition.
    • Mean atomic coordination serves as the relevant structural variable (reaction coordinate) for protein unfolding.
    • This framework unifies the understanding of phase transitions in both proteins and glasses.