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A minimalist model protein with multiple folding funnels.

C R Locker1, R Hernandez

  • 1Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

Proceedings of the National Academy of Sciences of the United States of America
|July 27, 2001
PubMed
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Proteins can adopt multiple stable structures beyond their native state. A minimalist model demonstrates this, suggesting protein folding landscapes can include misfolded, long-lived states.

Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Studies suggest proteins, like prions, can exist in multiple stable, long-lived states beyond their native conformation.
  • These states differ structurally and their stability isn't always due to cooperative nucleation effects.

Purpose of the Study:

  • To design a minimalist model protein to explore the dynamics of wild-type proteins exhibiting multiple long-lived states.
  • To investigate the generalizability of the rugged energy landscape model to include protein misfolding.

Main Methods:

  • Designed a 27-monomer minimalist protein model on a cubic lattice with three monomer types.
  • Introduced a 'winding index' as an order parameter to quantify protein folding extent.
  • Evaluated the winding index's advantages over native contact parameters for characterizing protein states.

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Main Results:

  • The minimalist model successfully exhibited multiple long-lived states.
  • The winding index proved effective in distinguishing enantiomers and was computationally efficient.
  • Demonstrated that protein folding energy landscapes can encompass stable, misfolded states.

Conclusions:

  • The minimalist protein model provides proof-of-existence for multiple stable protein states.
  • The concept of rugged energy landscapes can be extended to include protein misfolding into long-lived conformations.
  • This work offers insights into the complex dynamics of protein folding and misfolding relevant to diseases like prion disorders.