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Understanding domain swapping in the c-Src SH3 domain through hinge-loop mutagenesis.

M Carmen Salinas-Garcia1, Marina Plaza-Garrido1, Jose C Martinez2

  • 1Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, Carretera de Sacramento s/n, 04120 Almeria, Spain.

Acta Crystallographica. Section D, Structural Biology
|August 27, 2025
PubMed
Summary

Investigating the c-Src SH3 domain, researchers swapped loop regions between c-Src and Abl SH3 proteins. Loop composition influences stability and 3D domain swapping, but is not the sole driver of dimer formation.

Keywords:
3D domain swappingSH3 domainsclosed/primary interfacehinge loopopen/secondary interface

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Area of Science:

  • Biophysics
  • Structural Biology
  • Protein Folding

Background:

  • The c-Src SH3 domain is a well-characterized model protein.
  • It exhibits noncanonical folding, forming 3D domain-swapped oligomers and amyloid fibrils.
  • Understanding residues involved in unfolding and hinge loop dynamics is crucial for studying 3D domain swapping.

Purpose of the Study:

  • To investigate the role of specific residues in the unfolding and 3D domain swapping of the c-Src SH3 domain.
  • To construct chimeric proteins by interchanging RT and n-Src loops between c-Src SH3 and Abl SH3 domains.
  • To analyze the impact of these loop interchanges on protein stability and oligomer formation.

Main Methods:

  • Construction of chimeric SH3 proteins by site-directed mutagenesis.
  • Interchange of RT and n-Src loop residues between c-Src SH3 and Abl SH3 domains.
  • Biophysical characterization including stability assays and structural analysis of domain-swapped forms.

Main Results:

  • Chimeric c-Src SH3 domain with Abl SH3 loops showed minor stability changes but retained the ability to form domain-swapped dimers.
  • Interchanging one or two loops in Abl SH3 domain significantly reduced stability but did not promote 3D domain-swapped oligomer formation.
  • The hinge loop composition appears to influence structural element interchange but is not the sole determinant of intertwined dimer formation.

Conclusions:

  • The study elucidates the role of RT and n-Src loops in c-Src SH3 domain folding and 3D domain swapping.
  • While hinge loop composition is important, other factors also contribute to the formation of 3D domain-swapped oligomers.
  • Findings provide insights into the mechanisms of alternative protein folding and amyloid formation.