Structural changes of homodimers in the PDB

Area of Science:

• Structural biology
• Computational biology
• Biophysics

Background:

• Protein complexes drive biological processes, relying on structural flexibility for function.
• Understanding large-scale structural changes in complexes is crucial but challenging.

Purpose of the Study:

• To develop and apply an automated computational pipeline for analyzing structural dynamics in protein complexes.
• To characterize complex-specific motions in homodimers and correlate them with interface characteristics.

Main Methods:

• Combined two novel applications: SCPC for binding mode matching and Motion Tree for rigid-body motion identification.
• Applied the pipeline to all available homodimer structures in the Protein Data Bank (PDB).
• Defined and classified two types of motions: interface motion and subunit-spanning motion.

Main Results:

• Complex-specific motions were identified in approximately 40% of homodimer families.
• Interface motion is associated with small, flat interfaces and drastic contact changes.
• Subunit-spanning motion correlates with large, rugged interfaces and moderate contact changes.

Conclusions:

• Homodimer interface properties dictate the type of complex-specific motion observed.
• The SCPC and Motion Tree pipeline is effective for large-scale structural analysis of protein complexes.
• This work provides insights into the relationship between protein complex structure, dynamics, and interface features.