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Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.

Nishita Mandal^1,2, Bartlomiej Surpeta^1,2, Jan Brezovsky^1,2

¹Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland.

Journal of Chemical Information and Modeling

|August 15, 2024

Summary

This summary is machine-generated.

Gaussian accelerated molecular dynamics (GaMD) simulations effectively identify enzyme tunnels, including a novel transient side tunnel in haloalkane dehalogenase LinB. This method overcomes sampling limitations of conventional MD for protein engineering and drug discovery.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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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.