The objective of this project is to carry out computations to provide a detailed understanding of the widely exploited phenomenon of fluorescence quenching in any biological (and other) setting in terms of structure and dynamics. The project builds on previous support, which led to unprecedented progress in understanding tryptophan (Trp) fluorescence wavelength variability in proteins using electrostatics, and on unprecedented progress in understanding of the enigmatic--and more widely exploited--Trp fluorescence intensity changes accompanying changes in protein structure, that was primarily focused on the amide groups. In this project, higher-level computations will be done to greatly solidify this understanding. The scope will broaden to include less common (but potent when nearby) quenchers in proteins: histidine cation, disulfide, cysteine, and methionine. In addition, the generality of the concepts and methods will be tested by branching out to other widely exploited fluorescent systems that are often quenched, including flavins, NADH, and fluorescent dyes attached to proteins and nucleic acids. A convenient twist is that the software developed by the PI provides a transparent transition from a focus on the quenching of Trp fluorescence by numerous electron acceptors to quenching of numerous other fluorophores by Trp as one of the stronger one-electron donors in biology. A major goal is to expand the method to include realistic evaluation of the electron transfer coupling element during dynamics simulations, a parameter that is currently treated as an empirical constant. The PI will work closely with experimental groups to ensure that the computations are relevant and to help with interpreting the experiments.
Quenching is considered an obscure subject, and the biological community is in need of rational means for prediction and understanding of this subject. Experiment is well ahead of theory at this point, and a large amount of potentially revealing data is being generated. Fluorescence quenching processes are modulated by protein motions, but structural information gained from the correlation functions is of little use without an accurate physical understanding of exactly what is causing the modulations of the quenching. The PI's teaching interests have led to an integrated grasp of quantum mechanics, kinetics, and thermodynamics, all of which play important roles in electron transfer processes. The PI has established a graduate course in the physical chemistry of electron transfer and works with undergraduates, graduate students, and postdoctoral associates in his laboratory. The PI plans to establish a web site that will make available analysis software that will aid researchers and students in making predictions concerning fluorescence quenching in proteins.
