Acta NaturaeActa NaturaeActa Naturae2075-8251Acta Naturae Ltd1080710.32607/20758251-2009-1-2-33-43ArticlesСтатьиResearch ArticleComputer Modeling of the Structure and Spectra of Fluorescent ProteinsComputer Modeling of the Structure and Spectra of Fluorescent ProteinsNemukhinA Vanemukhin@yahoo.comGrigorenkoB LSavitskyA PDepartment of Chemistry, M.V. Lomonosov Moscow State UniversityN.M. Emanuel Institute of Biochemical Physics, Russian Academy of SciencesDepartment of Chemistry, M.V. Lomonosov Moscow State UniversityA.N. Bach Institute of Biochemisty, Russian Academy of Sciences1509200912NO2 (2009)№2 (2009)334317012020Copyright ©; 2009, Nemukhin A.V., Grigorenko B.L., Savitsky A.P.Copyright ©; 2009, Nemukhin A.V., Grigorenko B.L., Savitsky A.P.2009Nemukhin A.V., Grigorenko B.L., Savitsky A.P.Nemukhin A.V., Grigorenko B.L., Savitsky A.P.https://creativecommons.org/licenses/by/4.0https://actanaturae.ru/2075-8251/article/view/10807

Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical–molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers.

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