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Related Experiment Videos

Polymer collapse, protein folding, and the percolation threshold.

Hagai Meirovitch1

  • 1University of Pittsburgh, School of Medicine, Center for Computational Biology and Bioinformatics (CCBB), Pennsylvania 15213, USA. hagaim@pitt.edu

Journal of Computational Chemistry
|March 27, 2002
PubMed
Summary

This study models polymer folding using the HP model, finding that the arrangement and fraction of hydrophobic monomers influence transitions. Randomly distributed hydrophobic monomers above a threshold promote polymer collapse, relevant to protein folding.

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Area of Science:

  • Polymer Physics
  • Computational Chemistry
  • Biophysics

Background:

  • Polymers exhibit temperature-dependent conformational transitions.
  • The Hydrophobic-Polar (HP) model simplifies polymer behavior, representing hydrophobic (H) and polar (P) monomers.
  • This model is analogous to protein folding, with H residues mimicking hydrophobic amino acids and P residues mimicking polar ones.

Purpose of the Study:

  • To investigate the transition of polymers from a swollen state to low-temperature structures.
  • To analyze the influence of monomer type, fraction, and arrangement on polymer collapse.
  • To relate lattice model findings to protein folding mechanisms.

Main Methods:

  • Simulations using the scanning method on square and simple cubic lattices.

Related Experiment Videos

  • Modeling polymers as self-avoiding walks (SAW) with self-attracting H monomers.
  • Analyzing the effect of H monomer fraction (g) and distribution on polymer conformation.

    • Main Results:

    • The polymer's ground state and transition sharpness are dependent on the lattice type, H monomer fraction (g), and their sequence.
    • A collapsed transition is highly probable when H monomers are randomly distributed and their fraction exceeds the lattice's site percolation threshold.
    • An effective lattice model suggests protein folding behavior aligns with these findings.

    Conclusions:

    • The arrangement and proportion of hydrophobic monomers critically determine polymer folding transitions.
    • Lattice-based HP model simulations provide insights applicable to real protein folding.
    • The average hydrophobic amino acid fraction in globular proteins is near the effective lattice percolation threshold.