Direct observation of parallel folding pathways revealed using a symmetric repeat protein system

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Determining a polypeptide's native fold from its primary structure is an ongoing challenge.
• Protein folding pathways are typically predicted to be diverse, but experimental evidence remains elusive.
• Theoretical models suggest proteins fold via parallel pathways on energy landscapes.

Purpose of the Study:

• To experimentally detect and characterize diverse protein folding pathways.
• To investigate the role of protein size and repeat number in folding dynamics.
• To provide a detailed energy landscape for protein folding.

Main Methods:

• Utilized linear repeat proteins with high translational symmetry and variable lengths.
• Compared folding rates of consensus ankyrin repeat proteins (CARPs) of varying sizes.
• Employed a parallel-Ising pathway model for global fitting and rate measurement.

Main Results:

• Observed an increase in folding rates with increasing protein size and repeat number.
• Found that transition state size remained constant regardless of protein size.
• Directly measured nucleation and propagation rates, quantifying fluxes along parallel pathways.
• Demonstrated parallel pathways in CARPs, contrasting with single pathways in sequence-variable repeats.

Conclusions:

• The increase in folding rate with chain length provides direct evidence for parallel folding pathways.
• Parallel pathways are likely common in proteins with high structural and topological variation.
• This study offers a quantitative energy landscape for protein folding, advancing our understanding of protein dynamics.