Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Fluorescence spectroscopy is vital for analyzing protein dynamics and solvation.
• Tryptophan (Trp) residues are intrinsic fluorescent probes, emitting between 308-360 nm based on their environment.
• Computational modeling of fluorescence, due to electronic transitions, presents significant challenges.

Purpose of the Study:

• To develop a computational method for predicting tryptophan residue emission wavelengths in proteins.
• To correlate fluorescence emission with protein structural and environmental factors.
• To enable interpretation of complex fluorescence spectra.

Main Methods:

• Utilized classical molecular dynamics simulations.
• Calculated solvent-accessible surface area and electrostatic interactions of the indole group.
• Developed linear parametric models to predict emission wavelengths.

Main Results:

• Predicted maximum emission wavelengths with standard errors around 5 nm.
• Achieved a standard error of 4.89 nm and a correlation coefficient of 0.81 for 19 proteins.
• Demonstrated the models' ability to capture environmental influences on Trp fluorescence.

Conclusions:

• Classical molecular dynamics simulations can effectively predict Trp fluorescence emission wavelengths.
• The developed models offer a valuable tool for interpreting protein fluorescence spectra.
• This approach aids in studying proteins with multiple Trp residues or complex local environments.