Comparative Molecular Dynamics Analysis of RNase-S Complex Formation

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Ribonuclease A (RNase-A) proteolysis yields S-peptide and S-protein.
• Binding of S-peptide to S-protein forms active RNase-S.
• S-peptide transitions from disordered to helical upon binding, modeling coupled folding-binding.

Purpose of the Study:

• Investigate the dynamics of the RNase-S complex and its components.
• Understand the conformational changes during S-peptide binding to S-protein.
• Elucidate the contributions of S-peptide residues to complex stability.

Main Methods:

• Comparative molecular dynamics simulations.
• In silico Alanine scanning free-energy simulations.
• Analysis of conformational fluctuations and helical structure.

Main Results:

• Isolated S-peptide exhibits disorder with minimal helical structure.
• In the RNase-S complex, S-peptide's N-terminal helix fluctuates, while C-terminal residues remain helical.
• S-protein is more flexible alone, undergoing a pincer-like motion that narrows the binding cleft, which is reversed upon S-peptide binding.

Conclusions:

• The C-terminal helical turn of S-peptide is crucial for RNase-S complex stability.
• S-peptide binding stabilizes S-protein and influences binding kinetics.
• Global protein motions coupled to peptide binding are relevant for other protein-surface interactions.