Intrachain contact dynamics in unfolded cytochrome cb562

Area of Science:

• Biophysics
• Protein Dynamics
• Chemical Kinetics

Background:

• Understanding protein folding and dynamics is crucial for deciphering biological function.
• Intrachain contact formation governs protein structure and stability.
• Cytochrome cb562 serves as a model system for studying protein dynamics.

Purpose of the Study:

• To investigate intrachain contact dynamics in unfolded cytochrome cb562.
• To explore the influence of protein folding and loop formation on contact kinetics.
• To determine the timescale and mechanisms of diffusion in denatured proteins.

Main Methods:

• Utilized ruthenium photosensitizers covalently bound to cytochrome cb562.
• Monitored heme quenching of excited ruthenium complexes to track contacts.
• Analyzed rate constants for contact formation as a function of residue separation.
• Examined contact formation in both unfolded and loop-forming states.

Main Results:

• Intrachain diffusion in chemically denatured proteins occurs on the microsecond timescale (≤0.1 μs).
• Rate constants show a power-law dependence on the number of peptide bonds (exponent -1.5).
• Loop formation accelerated contact kinetics at specific labeling sites (Ru66) due to reduced peptide length.
• Quenching rates were modestly reduced at other sites within the stable loop compared to the open chain.

Conclusions:

• Intrachain diffusion in unfolded proteins is a microsecond process consistent with Gaussian chain models.
• Protein structural elements, like loops, significantly modulate intrachain contact dynamics.
• The findings provide insights into the interplay between protein structure and dynamics.