The study by Vivian and Callis explores the mechanisms behind the fluorescence wavelength shifts of tryptophan (Trp) in proteins, using a hybrid quantum mechanical-classical molecular dynamics method. The researchers predict the fluorescence wavelengths of 19 Trps in 16 proteins, starting from crystal structures. By adjusting only one parameter—scale factor for quantum mechanical atomic charges—the mean absolute deviation between predicted and observed fluorescence maximum wavelengths is 6 nm. The study highlights the importance of modeling electrostatic interactions, including hydration, in proteins to understand their function and structure. The results provide a rigorous test of the internal Stark effect (ISE) hypothesis, which suggests that the fluorescence wavelength shift is primarily influenced by the electric field produced by the protein and solvent environment. The analysis decomposes the spectral shifts into contributions from individual amino acid residues, solvent molecules, and protein atoms, revealing that red shifts are more common than blue shifts. The study also examines the contributions from water and protein residues, finding that both solvent and protein residues significantly influence the fluorescence wavelength. The findings offer insights into the complex interactions between Trp and its environment, contributing to a better understanding of protein dynamics and structure.The study by Vivian and Callis explores the mechanisms behind the fluorescence wavelength shifts of tryptophan (Trp) in proteins, using a hybrid quantum mechanical-classical molecular dynamics method. The researchers predict the fluorescence wavelengths of 19 Trps in 16 proteins, starting from crystal structures. By adjusting only one parameter—scale factor for quantum mechanical atomic charges—the mean absolute deviation between predicted and observed fluorescence maximum wavelengths is 6 nm. The study highlights the importance of modeling electrostatic interactions, including hydration, in proteins to understand their function and structure. The results provide a rigorous test of the internal Stark effect (ISE) hypothesis, which suggests that the fluorescence wavelength shift is primarily influenced by the electric field produced by the protein and solvent environment. The analysis decomposes the spectral shifts into contributions from individual amino acid residues, solvent molecules, and protein atoms, revealing that red shifts are more common than blue shifts. The study also examines the contributions from water and protein residues, finding that both solvent and protein residues significantly influence the fluorescence wavelength. The findings offer insights into the complex interactions between Trp and its environment, contributing to a better understanding of protein dynamics and structure.