Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Chemistry

Background:

• Understanding HIV-1 protease function is crucial for developing antiviral therapies.
• The binding mechanism of substrates to HIV-1 protease influences drug efficacy.

Purpose of the Study:

• To elucidate the binding mechanism of a specific peptide substrate to wild-type HIV-1 protease.
• To investigate the binding pathway and energetics using advanced simulation techniques.

Main Methods:

• Biased all-atom molecular dynamics simulations (1.6 micros) in explicit water.
• Bias-exchange metadynamics technique to explore configuration space by biasing seven reaction coordinates.
• Calculation of binding free energy and kinetic constants for association and dissociation.

Main Results:

• The Michaelis complex structure was obtained with high accuracy (backbone rmsd of 0.9 A).
• Calculated binding free energy (-6 kcal/mol) and kinetic constants (1.3 x 10^6 M^-1 s^-1 association, 57 s^-1 dissociation) align with experimental data.
• The primary binding pathway involves substrate sliding through a lateral channel without significant flap opening.

Conclusions:

• The binding mechanism observed differs from the expected natural polyprotein substrate binding, which likely involves flap opening.
• This distinction suggests that mutations in HIV-1 protease could differentially impact the binding kinetics of peptidomimetic drugs and natural substrates.
• Findings provide insights into substrate specificity and potential drug resistance mechanisms.