Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using...

Area of Science:

• Biophysics
• Computational Chemistry
• Protein Dynamics

Background:

• Protein side chains, specifically aromatic ones like phenylalanine and tyrosine, undergo 180° ring flips.
• Nuclear magnetic resonance (NMR) experiments study these dynamics to understand local conformational fluctuations.
• Ring flips are classified as slow (milliseconds) or fast (nanoseconds to milliseconds) based on NMR timescales.

Purpose of the Study:

• Investigate the infrequent metadynamics approach for estimating protein ring flip rates.
• Discriminate between slow and fast ring flips for eight aromatic side chains in a model protein.
• Assess the sufficiency of collective variables (CVs) in metadynamics simulations of ring flips.

Main Methods:

• Performed well-tempered metadynamics simulations on eight aromatic side chains of the basic pancreatic trypsin inhibitor.
• Estimated ring-flipping free-energy surfaces using collective variables.
• Evaluated the impact of using χ₂ alone versus χ₂ combined with χ₁ as collective variables.

Main Results:

• Using χ₂ alone as a collective variable was insufficient for consistent results.
• Incorporating a complementary CV, such as χ₁, improved the classification of fast and slow ring flips for most residues.
• Observed multiple pathways and recrossing events for certain residues, suggesting the influence of librational motions and friction effects.

Conclusions:

• Infrequent metadynamics can successfully estimate ring flip rates and classify their dynamics.
• The choice and combination of collective variables are crucial for accurate simulations of protein ring flips.
• Librational motions and friction effects play a significant role in the mechanisms of protein side chain ring flips.