Easy adaptation of protein structure to sequence

Area of Science:

• Structural biology
• Protein bioinformatics
• Computational biophysics

Background:

• Protein tertiary structures exhibit conserved features across families.
• Understanding structural conservation aids in predicting protein function and evolution.

Purpose of the Study:

• To investigate the conservation patterns of coarse, medium, and fine-grained structural properties in protein families.
• To correlate structural conservation with protein structural deviation and identify conserved core sizes.
• To evaluate factors influencing side chain torsion angle conservation for homology modeling.

Main Methods:

• Analysis of 175 protein tertiary structures from 34 families.
• Characterization of conserved sites within each protein family.
• Correlation analysis between structural properties, structural deviation, and sequence deviation.
• Estimation of minimal conserved core size.

Main Results:

• Coarse and medium-grained structural properties correlate with structural deviation.
• Fine-grained properties are poorly conserved, except in functional sites, indicating local structural adaptability.
• A minimal conserved core size of approximately 35% of the protein fold was estimated.
• Side chain torsion angle conservation, structural/sequence deviation, and resolution were used to identify suitable protein pairs for homology modeling tests.

Conclusions:

• Protein folding can be viewed as an optimization process allowing local adaptation to sequence variations.
• The identified conserved cores provide insights into essential structural elements.
• The study provides a framework for selecting protein structure pairs to test automatic homology modeling algorithms.