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The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.

R V Pappu1, R Srinivasan, G D Rose

  • 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 9, 2000
PubMed
Summary

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Short polyalanyl chains exhibit steric effects beyond nearest neighbors, challenging the isolated-pair hypothesis. This finding reduces the calculated entropy cost for adopting specific protein conformations.

Area of Science:

  • Computational chemistry
  • Biophysics
  • Protein folding

Background:

  • Flory's isolated-pair hypothesis simplifies protein folding by assuming steric independence of phi,psi pairs.
  • This hypothesis is fundamental to helix-coil theories and understanding protein conformational landscapes.

Purpose of the Study:

  • To reevaluate Flory's isolated-pair hypothesis using an all-atom representation of short polyalanyl chains.
  • To investigate the extent of steric effects in intrachain interactions and their impact on conformational space.

Main Methods:

  • Exhaustive enumeration of sterically allowed conformations for short polyalanyl chains.
  • Inclusion of intrachain interactions and a single adjustable parameter for backbone energy (e.g., peptide hydrogen bond).

Related Experiment Videos

Main Results:

  • Steric effects were found to extend beyond nearest-chain neighbors, contradicting the isolated-pair hypothesis.
  • The accessible conformational space was significantly restricted by these non-local steric interactions.
  • The calculated entropy cost for adopting specific conformations was substantially lower than previously estimated.

Conclusions:

  • Flory's isolated-pair hypothesis is an oversimplification, as steric effects are more pervasive.
  • A more accurate understanding of protein folding and conformational entropy requires considering these extended steric interactions.
  • The reduced entropy price has significant implications for predicting protein stability and folding pathways.