Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics

Area of Science:

• Biochemistry and Structural Biology
• Computational Chemistry
• Enzymology

Background:

• Enzymes utilize structural tunnels for transporting molecules, crucial for their function.
• Studying these transient tunnels is experimentally challenging.
• Molecular dynamics (MD) simulations are used to explore enzyme tunnels, but conventional MD (cMD) has sampling limitations.

Purpose of the Study:

• To evaluate Gaussian accelerated MD (GaMD) for improved exploration of enzyme tunnel networks.
• To investigate tunnel dynamics in haloalkane dehalogenase LinB and its variants.
• To identify previously uncharacterized transient pathways.

Main Methods:

• Gaussian accelerated MD (GaMD) simulations.
• Analysis of tunnel networks in haloalkane dehalogenase LinB and two engineered variants.
• Characterization of transient side tunnel (ST) opening mechanisms.

Main Results:

• GaMD successfully identified all known tunnels in LinB and its mutants.
• A previously unknown transient side tunnel (ST) was discovered and characterized.
• GaMD provided detailed insights into variant-specific ST opening dynamics, overcoming cMD sampling limitations.

Conclusions:

• GaMD significantly enhances sampling efficiency for studying enzyme tunnels compared to cMD.
• The discovered ST shows functional relevance, offering new avenues for protein engineering.
• GaMD is a powerful tool for identifying rare enzyme tunnels, aiding drug development and precision medicine.