title: Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study.
abstract: Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods.
authors.affiliation: Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6.
authors.forename: Maria S
authors.initials: MS
authors.lastname: Shadrina
authors.affiliation: Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6.
authors.forename: Ann M
authors.initials: AM
authors.lastname: English
authors.affiliation: Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6.
authors.forename: Gilles H
authors.initials: GH
authors.lastname: Peslherbe
mesh_terms: D000818:Animals; D004058:Diffusion; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism*; D010100:Oxygen / Q000032:analysis / Q000378:metabolism*; D011487:Protein Conformation; D050661:Sperm Whale / Q000378:metabolism*
chemical_list: D009211:Myoglobin; D010100:Oxygen