Fluorescent proteins

This chapter covers molecular modeling methods utilized to study the main photophysical and photochemical events in fluorescent proteins. Among them, GFP-like proteins are the most investigated and those demonstrate a wider range of photochemical events and photophysical features, compared with the flavin-based fluorescent proteins and phytochromes. Therefore, those are discussed to illustrate applications of different methods of computational chemistry in the study of fluorescent proteins. We cover methods aiming to estimate vertical transition energies between different electronic states, energy transfer processes between fluorescent proteins, and photochemical reactions. These tasks can be solved using a large variety of modern molecular modeling methods including methods of quantum chemistry, combined quantum mechanics/molecular mechanics, and molecular dynamic methods. We point out that quantitative structure-property relationships are successfully utilized instead of direct computations of the property of interest.