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Side-chain entropy and packing in proteins

S Bromberg1, K A Dill

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204.

Protein Science : a Publication of the Protein Society
|July 1, 1994
PubMed
Summary

Side chains in proteins increase entropy in open states but oppose folding in compact states due to steric hindrance. Side-chain ordering near maximum compactness influences protein structure.

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Area of Science:

  • Computational biology
  • Protein structure and stability
  • Statistical mechanics

Background:

  • Protein stability is crucial for function.
  • Understanding the role of side chains in protein folding is essential.

Purpose of the Study:

  • To investigate the role of side-chain packing in protein stability and structure.
  • To compare lattice models with and without side chains.

Main Methods:

  • Enumeration of self-avoiding configurations in 2D and 3D.
  • Monte Carlo sampling for chains up to 50 monomers.
  • Comparison of side-chain lattice models (SCM) and linear lattice models (LCM).

Main Results:

  • Side chains increase entropy in open conformations but decrease it in compact ones, opposing folding.
  • Side-chain ordering (freezing) occurs near maximum compactness, reducing entropy.
  • Contact frequencies (mm, ms, ss) in compact models resemble those in protein data banks.

Conclusions:

  • Side-chain packing significantly impacts protein entropy and stability.
  • Compactness may promote main-chain hydrogen bonding.
  • Protein packing is analogous to dense packing of objects rather than precise matching.

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