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      Computer Modeling of the Structure and Spectra of Fluorescent Proteins

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      1 , 2 , , 1 , 1 , 3
      Acta Naturae
      A.I. Gordeyev

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          Abstract

          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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          Most cited references152

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          The green fluorescent protein.

          R Tsien (1998)
          In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.
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            Failure of time-dependent density functional theory for long-range charge-transfer excited states: the zincbacteriochlorin-bacteriochlorin and bacteriochlorophyll-spheroidene complexes.

            It is well-known that time-dependent density functional theory (TDDFT) yields substantial errors for the excitation energies of charge-transfer (CT) excited states, when approximate standard exchange-correlation (xc) functionals are used, for example, SVWN, BLYP, or B3LYP. Also, the correct 1/R asymptotic behavior of CT states with respect to a distance coordinate R between the separated charges of the CT state is not reproduced by TDDFT employing these xc-functionals. Here, we demonstrate by analysis of the TDDFT equations that the first failure is due to the self-interaction error in the orbital energies from the ground-state DFT calculation, while the latter is a similar self-interaction error in TDDFT arising through the electron transfer in the CT state. Possible correction schemes, such as inclusion of exact Hartree-Fock or exact Kohn-Sham exchange, as well as aspects of the exact xc-functional are discussed in this context. Furthermore, a practical approach is proposed which combines the benefits of TDDFT and configuration interaction singles (CIS) and which does not suffer from electron-transfer self-interaction. The latter approach is applied to a (1,4)-phenylene-linked zincbacteriochlorin-bacteriochlorin complex and to a bacteriochlorophyll-spheroidene complex, in which CT states may play important roles in energy and electron-transfer processes. The errors of TDDFT alone for the CT states are demonstrated, and reasonable estimates for the true excitation energies of these states are given.
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              Molecular polarizabilities calculated with a modified dipole interaction

              B.T. Thole (1981)
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                Author and article information

                Journal
                Acta Naturae
                Acta Naturae
                Acta Naturae
                Acta Naturae
                A.I. Gordeyev
                2075-8251
                July 2009
                : 1
                : 2
                : 33-43
                Affiliations
                [1 ]Department of Chemistry, M.V. Lomonosov Moscow State University;
                [2 ]N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences;
                [3 ]A.N. Bach Institute of Biochemisty, Russian Academy of Sciences
                Author notes
                Article
                3347511
                22649601
                e23fe625-4df0-4986-9207-7341c0141451
                Copyright © 2009 Park-media Ltd.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Review
                Molecular Biology

                Life sciences
                Life sciences

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