Characterization and comparison of protein structures. Part I-characterization

Area of Science:

• Structural bioinformatics
• Computational biology
• Protein structure analysis

Background:

• Understanding protein structure regularity is crucial for predicting function.
• Existing methods may not fully capture subtle periodicities and symmetries.
• Correlating sequence properties with 3D conformation remains a challenge.

Purpose of the Study:

• To present quantitative criteria for Calpha-backbone regularity in protein structures.
• To develop a Fourier-based technique for analyzing protein structural periodicity.
• To investigate correlations between physicochemical properties and polypeptide chain conformation.

Main Methods:

• Fourier remapping of Calpha-chain Cartesian coordinates.
• Analysis of Fourier spectra to identify periodicities and symmetries.
• Assessment of integral regularity using spectral structural entropies.
• Statistical comparison with random protein counterparts.

Main Results:

• Fourier spectra effectively identify hidden periodicities and symmetries.
• Spectral structural entropies quantify integral regularity.
• Significant correlations found between amino acid sequence properties and spatial conformation.
• Hydrophobicity and side-chain volumes show strong correlations, with hydrophobicity being more dominant.

Conclusions:

• The Fourier remapping technique provides novel insights into protein backbone regularity.
• Physicochemical characteristics along the amino acid sequence directly influence protein spatial conformation.
• This approach enhances the understanding of structure-function relationships in proteins.