Rate of intrachain contact formation in an unfolded protein: temperature and denaturant effects.

This research article discusses the effects of temperature and denaturant concentration on the rate of intrachain diffusion in an unfolded protein, specifically horse cytochrome c. The study found that as denaturant concentration decreases, the chain’s diffusion accelerates, while higher denaturant concentrations indicate an Arrhenius activation barrier comparable to solvent viscosity effects. The findings suggest that inter-residue energetic interactions do not control conformational diffusion in unfolded states, even under folding conditions.

Research Methodology

The researchers used several technical methods to assess the rate of intrachain diffusion in an unfolded protein:

• A ligand was photodissociated from the heme iron of unfolded horse cytochrome c, a protein. This method allowed for the stimulation of the protein.
• Transient optical absorption spectroscopy was utilized to measure the timescale of the diffusive motions that bring the heme into contact with its native ligand, Met80. This spectroscopy measurement provided a quantifiable rate of how fast the protein changes its structure.
• The rate at which a 62 residue intrachain loop formed under both folding and unfolding conditions was evaluated to determine the dynamics of the chain.

Key Findings

The study unveiled a few primary findings:

• The diffusion of the chain accelerates as the concentration of the denaturant decreases. When absent of denaturant, the contact formation rate approached a value around 6×10(5) s(-1). This shows that lower denaturant levels allow the protein to reconfigure at a faster pace.
• The temperature dependence of the rate of contact formation indicated an Arrhenius activation barrier, or the minimum energy necessary to start a chemical reaction. This was noted to be approximately 20 kJ/mol at high denaturant concentrations, which is comparable to what is expected from solvent viscosity effects alone.
• It was also revealed that although the Arrhenius activation energy (Ea) increased as the concentration of the denaturant decreased, the overall rate of diffusion increased. This suggests that reducing the denaturant concentration, though it raises the energy barrier, actually increases the rate of protein structure change.
• The research concluded that inter-residue energetic interactions do not control conformational diffusion in unfolded states, even under folding conditions. This means that the energy interactions between residues do not have a dominant influence on the rate at which the protein changes its conformation.

These results provide valuable insights into protein dynamics and may have applications in understanding and treating diseases related to protein misfolding such as Alzheimer’s and Parkinson’s.