Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications...

Area of Science:

• Protein structure analysis
• Structural bioinformatics
• Molecular biology

Background:

• Beta-turns are defined by residue distances (i, i+3).
• Protein secondary structures include alpha-helices and beta-sheets, connected by turns.
• Understanding turn structures is crucial for protein folding and function.

Purpose of the Study:

• To identify and characterize alpha-turns using a distance criterion (i, i+4).
• To classify alpha-turns based on residue torsion angles (phi, psi).
• To investigate the role of alpha-turns in protein tertiary structure and helix formation.

Main Methods:

• Analysis of a database of known protein structures.
• Application of a distance criterion (i, i+4) for alpha-turn identification.
• Classification of alpha-turns based on the phi, psi angles of central residues (i+1 to i+3).

Main Results:

• At least 15 classes of alpha-turns were identified, including the AAA class with conventional helical angles.
• A shift towards more negative phi angles was observed towards the C-terminal end of AAA turns, reducing electrostatic repulsion.
• Alpha-turns are prevalent in beta-hairpin loops, and proline at position i+1 influences hydrogen bonding.
• The residue composition at the C-terminal end (i+4) suggests a helix capping mechanism.

Conclusions:

• Alpha-turns represent a distinct structural motif in proteins.
• The C-terminal capping signal at position i+4 of AAA alpha-turns may prevent their elongation into helices.
• These findings contribute to understanding alpha-helix nucleation and protein folding processes.