Modeling structure and spectra of red fluorescent proteins

Abstract

Modern molecular modeling tools are intensively used to gain knowledge of events occurring upon photoexcitation of organic chromophores in the gas-phase, in solution and in protein matrices. We applied quantum mechanical approach to estimate equilibrium geometry configurations as well as positions and intensities of spectral bands for a number of red fluorescent proteins, including the DsRed from Discosoma coral, and its mutants of the so-called mFruits series. As demonstrated in our previous simulations for GFP and blue fluorescent proteins, this strategy was proven to be productive for modeling. The model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. Mechanisms of photoexcitation, identification of the functional states of the chromophores, elucidation the role of point mutations in the photoreceptor proteins are considered on the basis of simulations.