Structural Determinants of Misfolding in Multidomain Proteins

Area of Science:

• Protein biophysics
• Computational biology
• Molecular dynamics

Background:

• Single molecule experiments (AFM, FRET) reveal stable misfolded structures in multidomain proteins.
• Topology-based simulations successfully model domain-swapped misfolded structures consistent with experimental data.

Purpose of the Study:

• Investigate factors governing the propensity of multidomain protein folds to undergo domain-swapped misfolding.
• Determine the key determinants of misfolding propensity beyond initial folding kinetics.

Main Methods:

• Utilized a coarse-grained simulation model to study multidomain protein folding.
• Analyzed the relationship between domain stability, folding rates, and misfolding propensity.
• Explored the impact of interdomain linker length on misfolding.

Main Results:

• Misfolding propensity is primarily linked to the relative stability of domains in folded versus misfolded intermediates, not folding rates or barrier heights.
• Findings are consistent with a single folding funnel model where commitment to folded or misfolded states occurs late in the folding process.
• Interdomain linker length was investigated for its influence on domain-swapped misfolding.

Conclusions:

• Domain stability, rather than kinetic factors, is the critical determinant for domain-swapped misfolding in multidomain proteins.
• The folding funnel landscape suggests late-stage commitment to specific protein structures.
• An alchemical model is proposed for predicting domain-swapped misfolding propensity.