3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops

Area of Science:

• Protein structure and dynamics
• Molecular biology
• Biochemistry

Background:

• Src Homology 3 (SH3) domains bind proline-rich motifs (PRMs) via RT and n-Src loops.
• Distal and diverging turns are crucial for SH3 domain protein folding.
• Domain swapping is a significant protein dimerization mechanism.

Purpose of the Study:

• To investigate the structural consequences of creating a chimeric c-Src-SH3 domain with Abl-SH3 loop residues.
• To characterize the folding and dimerization behavior of this chimeric mutant.
• To explore the role of specific loops in 3D domain swapping.

Main Methods:

• X-ray crystallography to determine the structure of the chimeric c-Src-SH3 domain.
• Analysis of protein structure to identify secondary structures and quaternary arrangements.
• Comparison of chimeric structure with wild-type SH3 domains.

Main Results:

• The chimeric c-Src-SH3 domain crystallized as a domain-swapped dimer.
• The RT- and n-Src-loops of the chimeric mutant function as hinge loops in the dimer.
• A structured diverging type II β-turn was observed in an unfolded-like intermediate, stabilized by interactions within or between polypeptide chains.
• The fold of the diverging type II β-turn and distal loop were conserved.

Conclusions:

• The study provides the first evidence of a structured diverging type II β-turn in an unfolded-like intermediate of the c-Src-SH3 domain.
• The observed domain-swapped dimer structure offers a platform to study how hinge loop amino acid sequences influence 3D domain swapping in c-Src-SH3.
• This research deepens the understanding of SH3 domain structure, folding, and dimerization mechanisms.