Impact of Hydration on the α-Helical Structure of S-Peptide in RNase-S

The folded conformation of a protein is essential for its enzymatic function, as it provides the structural framework required for substrate recognition, active site organization, stability, conformational flexibility, catalytic activity, and regulatory control. Ribonucleases (RNases) play a critical role in biological systems by catalyzing the degradation of RNA into smaller fragments. RNase-S is a heterodimeric protein composed of two subunits: the S-Peptide and the S-Protein. The S-Peptide serves as the catalytic component, enabling ribonuclease activity, while the S-Protein maintains the structural integrity of the enzyme. The proper folding of the S-Peptide in RNase-S is vital for enzymatic function, as it ensures the formation of the active site, facilitates substrate recognition and binding, maintains structural stability and flexibility, and enables efficient catalysis. Any disruption in its folded conformation can compromise enzymatic activity and hinder RNA cleavage. From classical molecular dynamics and constant-force MD simulations, we find that the S-Peptide is significantly more stable in complex with the S-Protein than in its isolated form. This increased stability is due to differences in hydration levels, which help preserve its intramolecular noncovalent interactions. Our findings also reveal that the S-Peptide binds to the S-Protein through an induced fit mechanism rather than conformational selection.