Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Ribonuclease A (RNase A) is the most studied member of ribonucleases - a group of enzymes responsible for catalyzing RNA degradation. RNase A contains four disulfide bonds, which were found to be necessary for the native structure of the protein to form. In this work the kinetics and thermodynamics of RNase unfolding were studied by means of a series of coarse-grained canonical molecular-dynamics simulations, run at various temperatures, and replica-exchange molecular dynamics simulations with the UNRES force field, which is capable of dynamic formation and breaking the disulfide bonds during the course of the simulations. It was found that the Cys40-Cys95 bond was the first to break, while the Cys26-Cys84 bond was the last to break, independent of temperature, in agreement with available experimental data. Except for the Cys40-Cys95 bond, all disulfide bonds were relatively stable during the simulations. The formation/disruption of disulfide bonds was found to be temperature dependent for three out of four disulfide bonds in RNase A, except for the most stable disulfide bond between Cys65 and Cys72. A stable intermediate without the Cys40-Cys9S disulfide bond, with structure similar to that of the most common folding intermediate observed experimentally, was found in simulated unfolding. In agreement with experiment, non-native disulfide bonds were also observed. By analyzing residue-position fluctuations, it was found that native disulfide bonds are located in the highly flexible regions of the protein, which is probably why their presence is necessary for the stability of RNase A.