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A physical basis for protein secondary structure.

R Srinivasan1, G D Rose

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

Proceedings of the National Academy of Sciences of the United States of America
|December 10, 1999
PubMed
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Protein secondary structure arises from local effects favoring hydrogen bonds versus opposing sidechain entropy loss. These biases preorganize folding, anticipating native structures.

Area of Science:

  • * Biophysics and Structural Biology
  • * Computational Biology and Bioinformatics

Background:

  • * Protein secondary structure formation is crucial for protein function.
  • * Understanding the physical underpinnings of secondary structure propensity is key.
  • * Existing models may not fully capture the interplay of local forces.

Purpose of the Study:

  • * To propose and test a physical theory for protein secondary structure.
  • * To identify the primary local factors governing secondary structure propensities.
  • * To investigate how these factors influence protein folding preorganization.

Main Methods:

  • * Development of a novel physical theory for protein secondary structure.
  • * Implementation of simplified Monte Carlo simulations for testing the theory.

Related Experiment Videos

  • * Analysis of local energetic and entropic contributions to structure formation.

    • Main Results:

    • * Secondary structure propensities are driven by two competing local effects: hydrogen bond formation and sidechain conformational entropy.
    • * These sequence-specific biases are distributed throughout the unfolded polypeptide chain.
    • * The identified biases largely, though imperfectly, predict the native secondary structure.

    Conclusions:

    • * A simple physical model can explain key aspects of protein secondary structure.
    • * Local energetic and entropic factors are dominant in determining secondary structure propensities.
    • * The theory provides insights into the preorganization of protein folding pathways.