Parallels between Enzyme Action and Tryptophan Fluorescence Brightness in Proteins

Abstract

Thousands of scientists studying proteins rely on the intensity, wavelength, and lifetimes of emitted light (fluorescence) from the amino acid tryptophan (Trp) because it is extremely sensitive to its “environment” in a protein. But, what exactly does “environment” mean? In the last several years, we have combined classical molecular dynamics with simplified quantum mechanics and electrostatics to gain considerable insight into what environments promote and quench Trp fluorescence. Close parallels can be drawn between our simulations of Trp fluorescence brightness and simulations of enzyme effectiveness, especially for the “single electron transfer” mechanism. We have carried out MD simulations of Staphylococcal nuclease and ribonuclease T1 and determined the electric potential difference between the phosphorus subject to nucleophilic attack and the putative electrophile. These are characterized by potential differences of 2-3 volts, with fluctuations spanning 1.5 volts, quite similar to the energy gaps between the fluorescing state of Trp and charge transfer states that result in fluorescence quenching. We shall report results for a variety of enzymes representing six major classes of enzymes.