Computer Modeling of the Structure and Spectra of Fluorescent Proteins

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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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The discovery and use of colored proteins from the family of the green fluorescent protein [1–7] stimulated an avalanchelike growth of interest in these amazing species. Their practical value is explained by their ability to label cell clones with colored proteins and then literally trace the inner cell events. Biotechnology perspectives are promising because of multicolor labeling, in particular, the ability to observe interprotein interactions in living systems. These proteins are well characterized in crystallography studies. The β-sheets form the walls of the can (Fig.1) which efficiently shield the chromophore from the external media. The latter is represented by the hydroxybenzylidene-imidazoline molecule (Fig.2), which is formed in nature from three amino-acid residues inside the protein globule. The photophysical properties of fluorescent proteins are explained by transformations occurring with this chromophore group inside the macromolecule upon light illumination at certain wavelengths. Researchers from different fields concentrate on studies of all the aspects of the structure and mechanism of fluorescent proteins. In this review, we primarily analyze works on the computer modeling of the structure and spectra of these species. Using modern tools of molecular modeling [8] may provide considerable support to experimental studies, allowing one to save time and resources for a comprehensive examination of the processes occurring in such complex molecular systems. Obviously, a description of the transitions between the electronic states of chromophore molecules responsible for light absorption and emission requires the use of the quantum theory; correspondingly, quantum chemistry is an appropriate modeling tool. The conformational states of the protein macromolecule and the structure of the chromophorecontaining domain are also important for the properties of fluorescent proteins, thus requesting the application of molecular mechanics and molecular dynamics methods. To employ all these approaches, substantial computer resources, as well as efficient numerical algorithms and computer programs, are necessary. Quantum chemistry models are based on a nuclear-electron picture of a molecular system that requires a numerical solution of the Schroedinger equation by using approximations of different accuracy levels. Presently, a developed hierarchy of quantum chemistry approaches is known, each of which is oriented toward performing certain tasks. In particular, for calculating structural parameters, i.e., geometrical configurations corresponding to the minimum energy points on the ground electronic state potential energy surface for a given model molecular system, as well as to calculate vibrational spectra, electronic density functional theory approaches are often operative.
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