Diffusion of Unfolded Acyl-Coenzyme A-Binding Protein Over a Complete Range of Denaturant

Abstract

The unfolded states of acyl-coenzyme A-binding protein (ACBP) were studied from the point of view of diffusion dynamics. Using the method of Trp/Cys contact quenching, we monitored the intramolecular diffusion of the unfolded chain over a wide range of denaturant in both equilibrium and using a novel microfluidic mixer to capture dynamics before folding. Theoretically, both a worm-like chain model and molecular dynamics (MD) have been used to generate loop terminal distance distributions required for data analysis. MD simulation also provides a direct comparison to measured rates through mean squared displacement over time. We observed a deep compaction of protein conformation from 6M GuHCL to 0.2M GuHCL resulting in a 100-fold decrease of intramolecular diffusion coefficient. This protein, however, is still shown to be more diffusive than protein L in physiological conditions, suggesting a strong sequence dependence of intramolecular diffusion.