Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Single-molecule force spectroscopy is crucial for understanding protein folding dynamics.
• Identifying transiently populated states during folding remains a challenge.

Purpose of the Study:

• To investigate the nature of populated states during polyubiquitin folding using mechanical force.
• To elucidate the structural basis for observed unfolding force distributions.

Main Methods:

• Atomic force spectroscopy (AFM) with force-pulse protocols.
• Molecular dynamics simulations using coarse-grained ubiquitin dimer models.
• Brownian dynamics simulations for force unfolding.

Main Results:

• AFM revealed an ensemble of minimum energy compact structures (MECS) during polyubiquitin folding.
• Forced unfolding of MECS showed broad extension distributions (up to 30 nm).
• Simulations identified domain swapping between ubiquitin modules as the cause of MECS formation, with ~100-fold lower mechanical stability than the native state.

Conclusions:

• Domain swapping is proposed as a general mechanism for forming populated intermediates in multi-subunit protein assembly.
• The study provides quantitative agreement between experimental and simulation data.
• Understanding these intermediates offers insights into protein folding pathways and stability.