Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain.

ABSTRACT: Although we understand many aspects of how small proteins (number of residues less than about hundred) fold, it is a major challenge to quantitatively describe how large proteins self-assemble. To partially overcome this challenge, we performed simulations using the self-organized polymer model with side chains (SOP-SC) in guanidinium chloride (GdmCl), using the molecular transfer model (MTM), to describe the folding of the 110-residue PDZ3 domain. The simulations reproduce the folding thermodynamics accurately including the melting temperature (T_m), the stability of the folded state with respect to the unfolded state. We show that the calculated dependence of ln k_obs (k_obs is the relaxation rate) has the characteristic chevron shape. The slopes of the chev

SUBMITTER: Liu Z 

PROVIDER: S-EPMC5893999 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature