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Sequence and structure conservation in a protein core

M A Rodionov1, T L Blundell

  • 1Department of Biochemistry, University of Cambridge, United Kingdom.

Proteins
|November 26, 1998
PubMed
Summary

Protein structural analysis reveals that conserved polar residues in the protein core are linked to better atom packing. This finding suggests improved structural stability due to protected hydrogen bonds in homologous protein families.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Protein science

Background:

  • Sequence conservation is crucial for understanding protein function and evolution.
  • Amino acid properties and their structural environments influence protein stability.
  • Homologous protein families share conserved structural and functional features.

Purpose of the Study:

  • To investigate the relationship between sequence conservation and structural properties in homologous proteins.
  • To determine if atom packing density in the protein core correlates with residue conservation.
  • To elucidate the role of residue environment in sequence conservation patterns.

Main Methods:

  • Analysis of 585 proteins across 128 homologous families using structural alignment.
  • Quantification of residue conservation based on average similarity in aligned sequences.
  • Calculation of atom packing density and solvent accessibility for protein core residues.
  • Utilizing log-odd substitution tables considering amino acid environments in 3D structures.

Main Results:

  • No significant correlation found between sequence conservation and atom packing for nonpolar residues (e.g., leucine, valine, isoleucine).
  • A significant positive correlation observed between sequence conservation and atom packing for polar residues within the protein core.
  • Protein core residues with less than 7% solvent accessibility were analyzed for packing density.

Conclusions:

  • The structural environment, particularly atom packing of polar residues in the protein core, is a significant factor in sequence conservation.
  • Protected polar residues, involved in hydrogen bonds, contribute to enhanced structural stability.
  • Understanding these structure-sequence relationships aids in predicting protein function and evolution.

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