Computational Approach to Elucidating Insulin-Protamine Binding Interactions and Dynamics in Insulin NPH Formulations

Area of Science:

• Biochemistry
• Structural Biology
• Pharmacology

Background:

• Insulin NPH is an intermediate-acting insulin formulation.
• Its prolonged action is attributed to insulin-protamine complexes.
• The precise binding mechanism of protamine to insulin remains unclear.

Purpose of the Study:

• To elucidate the binding epitope and mode of protamine peptides interacting with the insulin R6 hexamer.
• To compute binding sites and energetics of insulin-protamine complexes using computational methods.

Main Methods:

• Utilized bioinformatics tools, including molecular docking and 200 ns molecular dynamics (MD) simulations.
• Docked four naturally occurring protamine peptides to the insulin R6 hexamer.
• Analyzed binding interactions (hydrogen bonding, hydrophobic, electrostatic) and estimated binding energies.

Main Results:

• Arginine-rich protamine peptides bind to the insulin hexamer surface.
• Binding is mediated by hydrogen bonding, hydrophobic, and electrostatic interactions, supported by negative binding energies.
• The insulin hexamer structure remained stable, with dynamic termini residues in the protamine peptides.

Conclusions:

• Protamine binding to insulin R6 is characterized by specific interactions and negative binding energies.
• The insulin hexamer exhibits dynamic stability within the complex.
• Computational approaches effectively model the dynamics and energetics of insulin-protamine interactions.