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Related Experiment Videos

Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins.

Susanne Moelbert1, Eldon Emberly, Chao Tang

  • 1NEC Laboratories America, Princeton, NJ 08540, USA.

Protein Science : a Publication of the Protein Society
|February 10, 2004
PubMed
Summary
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Protein structure is influenced by hydrophobicity, but the correlation between a protein's amino acid sequence and its surface exposure is not perfect. This imperfect correlation is mainly due to mutations and other forces beyond hydrophobicity.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Hydrophobicity is a key driver of protein folding, with hydrophobic residues typically buried in the core and polar residues exposed on the surface.
  • Understanding the relationship between a protein's amino acid sequence and its three-dimensional structure is fundamental to molecular biology.

Purpose of the Study:

  • To quantify the correlation between a protein's hydrophobicity sequence and its surface exposure pattern.
  • To assess the statistical significance of this correlation across different hydrophobicity scales.
  • To identify factors contributing to deviations from an optimal correlation.

Main Methods:

  • Analysis of known protein structures from databases.
  • Statistical assessment of hydrophobicity sequence versus surface exposure.

Related Experiment Videos

  • Comparison with an off-lattice hydrophobic-polar model.

    • Main Results:

    • A significant but suboptimal correlation was found between hydrophobicity sequence and surface exposure.
    • The suboptimal correlation is primarily attributed to the tolerance of natural proteins to mutations.
    • Other forces, in addition to hydrophobicity, also contribute to surface-exposure patterns.

    Conclusions:

    • While hydrophobicity is a major determinant, it does not perfectly predict surface exposure in natural proteins.
    • Protein evolution and other biophysical forces modulate the direct hydrophobicity-surface exposure relationship.
    • Database findings align with predictions from simplified hydrophobic-polar models, validating their utility.