III. Geometrical framework for thinking about globular proteins: Turns in proteins

Area of Science:

• Structural biology
• Biophysics
• Computational biology

Background:

• Protein structure formation is governed by pairwise interactions.
• Secondary structures like alpha-helices and beta-sheets arise from repetitive, geometry-constrained interactions.
• Tertiary structure formation involves weaker, less constrained pairwise interactions.

Purpose of the Study:

• To demonstrate that protein turns are instances of pairwise poking contacts.
• To provide a unifying geometrical definition for protein turns (e.g., beta-turns, hairpin bends).
• To systematically analyze the structural classes and amino acid preferences of protein turns.

Main Methods:

• Applying the 'poking pairwise interactions' framework to protein turns.
• Analyzing geometrical constraints and contact patterns in protein turns.
• Classifying turn structures and identifying associated amino acid preferences.

Main Results:

• Protein turns are characterized by local, isolated poking pairwise contacts.
• Geometrical constraints for turns are partially relaxed compared to secondary structures.
• Systematic analysis revealed distinct structural classes and amino acid preferences for protein turns.

Conclusions:

• A simple, purely geometrical definition unifies various types of protein turns.
• The poking interaction model successfully explains the formation of secondary, tertiary, and turn structures.
• Understanding turn formation through geometry and amino acid preferences advances protein structure prediction.