Using biased molecular dynamics and Brownian dynamics in the study of fluorescent proteins
Résumé
The present article presents a theoretical study of the dynamics of the chromophore of the Green Fluorescent Protein in its excited state on a long time scale (a few ten nanoseconds) in order to help the interpretation of time resolved experiments. The starting hypothesis is that the quenching of fluorescence is related to the internal motion of the chromophore, usually called 'φ torsion'. In fact, that motion is hindered by the protein and cannot be studied by standard molecular dynamics. Therefore we have developed a different approach involving three steps. First the potential of mean force (PMF) along the considered torsion is obtained by biased molecular dynamics (umbrella sampling). Then, a long time scale, single particle Brownian dynamics is performed using that PMF and an appropriate diffusion constant. Finally we determine the nth passage time (NPT) distribution functions at geometries or regions where nonradiative ground state recovery may occur. The NPT distributions generalize the more usual 'mean first passage time' and allow determining different quantities like fluorescence decay profiles, mean fluorescence lifetime, quantum yield etc. These quantities are used here in a qualitative discussion of the fluorescence decay in Green Fluorescent Protein.