Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator...

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Molecular dynamics (MD) is commonly used to calculate slow-motional electron paramagnetic resonance (EPR) spectra of spin-labeled biomolecules.
• Existing MD methods often rely on trajectory-based calculations, which can be computationally intensive.
• The stochastic Liouville equation (SLE) formalism is another widely used approach for calculating slow-motional EPR line shapes.

Purpose of the Study:

• To present an alternative computational approach for calculating slow-motional EPR spectra.
• To adapt MD trajectories for direct input into the diffusion operator-based SLE formalism.
• To improve computational efficiency and enable deconvolution of local and global molecular motions.

Main Methods:

• Utilized molecular dynamics (MD) trajectories to derive diffusion parameters (rotational diffusion tensor, tilt angles, orienting potential coefficients).
• Integrated these derived diffusion parameters as direct inputs into the stochastic Liouville equation (SLE) line shape program.
• Validated the method by comparing MD-predicted line shapes with experimental high-frequency (250 GHz) EPR spectra.

Main Results:

• Developed an efficient computational approach by combining MD with the SLE formalism.
• Achieved significant improvements in computational efficiency compared to traditional trajectory-based MD methods, especially for high-frequency, high-field EPR.
• Demonstrated the capability to distinguish between local spin label motion and overall molecular motion.

Conclusions:

• The presented MD-SLE approach offers a computationally efficient alternative for analyzing slow-motional EPR spectra.
• This method facilitates the separation of local and global motions in spin-labeled biomolecules.
• The validated approach provides a powerful tool for characterizing molecular dynamics using EPR spectroscopy.