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Packing regularities in biological structures relate to their dynamics.

Robert L Jernigan1, Andrzej Kloczkowski

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Summary

Protein packing density influences cooperative motions and residue conservation. This finding supports elastic network models for predicting protein dynamics and functional mechanisms, even for complex structures like the ribosome.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Proteins exhibit high packing density, leading to geometric regularities and cooperative domain motions.
  • Residue orientations in proteins are influenced by hydrophobicity and resemble dense sphere packing (face-centered cubic lattice).
  • Packing density correlates with residue conservation, showing distinct regimes relating sequence entropy and inverse packing density.

Purpose of the Study:

  • To investigate the relationship between protein packing density, residue orientation, and conservation.
  • To provide justification for the use of elastic network models in predicting protein dynamics.
  • To explore the application of elastic network models to study the functional motions of large molecular machines like the ribosome.

Main Methods:

  • Analysis of geometric regularities and packing densities in protein structures.
  • Statistical analysis of residue packing densities and sequence entropy.
  • Application of elastic network models to simulate protein dynamics and functional motions, including ribosome dynamics.

Main Results:

  • Protein packing density dictates geometric regularities and cooperativity in domain motions.
  • Three distinct regimes were identified for the relationship between sequence entropy and inverse packing density.
  • Elastic network models are validated by packing results and successfully applied to study ribosome functional motions.

Conclusions:

  • Protein internal geometry and packing density are fundamental to their dynamic behavior and stability.
  • Elastic network models offer a robust framework for understanding protein dynamics and can be extended to partially denatured states.
  • The study demonstrates the utility of elastic network models for elucidating functional mechanisms of complex systems like the ribosome, bridging static structures with dynamic processes.