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Are proteins well-packed?

J Liang1, K A Dill

  • 1Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607-7052, USA. jliang@uic.edu

Biophysical Journal
|July 21, 2001
PubMed
Summary
This summary is machine-generated.

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Proteins are not as well-packed as crystals. Their internal free volume distributions resemble liquids and glasses, with larger proteins being less densely packed. Folding enthalpies are independent of packing density.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Proteins exhibit high average packing densities, comparable to crystalline solids.
  • However, the distribution of free volumes within proteins remains underexplored.

Purpose of the Study:

  • To investigate the packing characteristics of proteins beyond average densities.
  • To analyze the distribution of free volumes and their implications for protein structure and folding.

Main Methods:

  • Utilized a novel Delaunay triangulation method to define interior and surface packing densities.
  • Analyzed free volume distributions, volume-to-surface ratios, and void cluster properties.

Main Results:

  • Protein free volume distributions resemble those of liquids and glasses, not crystalline solids.

Related Experiment Videos

  • Protein interiors are more akin to randomly packed spheres near the percolation threshold.
  • Larger proteins demonstrate looser packing than smaller proteins.

    • Conclusions:

    • Proteins' internal structure is characterized by broad free volume distributions, suggesting a more dynamic packing than previously assumed.
    • Packing density does not significantly influence protein folding enthalpies, indicating van der Waals forces are not primary drivers of folding.