Simulating FRET from tryptophan: is the rotamer model correct?

Area of Science:

• Computational biophysics
• Protein spectroscopy
• Molecular modeling

Background:

• Time-resolved fluorescence spectra of tryptophan in proteins often show multiple lifetimes.
• This is typically attributed to protein structural dynamics and tryptophan rotamer states.
• The tetracycline repressor (TetR) protein complex with tetracycline is a model for studying transcriptional regulation and FRET.

Purpose of the Study:

• To develop and validate a computational model for simulating time-resolved tryptophan fluorescence spectra in proteins.
• To investigate the influence of FRET on fluorescence decay curves in the TetR-tetracycline complex.
• To assess the applicability of the classical rotamer model in systems with FRET acceptors.

Main Methods:

• Combined classical molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) calculations.
• Semiempirical configuration interaction (CI) calculations for spectroscopic properties.
• Simulation of fluorescence decay curves incorporating FRET rate constants, Einstein coefficients, and nonradiative decay rates.

Main Results:

• The computational model successfully simulates fluorescence decay curves with and without FRET.
• The study demonstrates the extension of the rotamer model to protein systems containing FRET acceptors.
• Calculated FRET rate constants provide insights into energy transfer dynamics.

Conclusions:

• The classical rotamer model can be extended to explain tryptophan fluorescence decay in proteins with FRET.
• The interpretation of fitted fluorescence lifetimes requires adjustment when FRET acceptors are present.
• This computational approach provides a framework for analyzing complex protein fluorescence dynamics.