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Modeling absorption of the kindling fluorescent protein with the neutral form of the chromophore

Authors

  • Igor Topol,

    Corresponding author
    1. Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, Maryland 21702-1201
    • Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, Maryland 21702-1201
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  • Jack Collins,

    1. Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, Maryland 21702-1201
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  • Vladimir Mironov,

    1. Department of Chemistry, M.V. Lomonosov Moscow State University, 1/3 Leninskie Gory, Moscow 119991, Russian Federation
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  • Alexander Savitsky,

    1. Department of Chemistry, M.V. Lomonosov Moscow State University, 1/3 Leninskie Gory, Moscow 119991, Russian Federation
    2. A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Prospekt, Moscow 119071, Russian Federation
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  • Alexander Nemukhin

    1. Department of Chemistry, M.V. Lomonosov Moscow State University, 1/3 Leninskie Gory, Moscow 119991, Russian Federation
    2. N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, Moscow 119334, Russian Federation
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Abstract

Kindling fluorescent protein (KFP) is an important member of the colored proteins family widely used as biomarkers in living cells. We apply quantum chemistry modeling of KFP properties by computing structure and spectra of a large molecular cluster mimicking the chromophore-containing pocket, assuming the protonated (neutral) form of the chromophore in the trans configuration. We provide evidence that this protein conformation accounts for the previously observed but unassigned absorption band at 445 nm. We demonstrate that the structure and charge of the amino acid residues nearest to the chromophore play a role in the shifts in the absorption wave length, thus underlying a strong role of intermolecular interactions when considering properties of the fluorescent proteins. © 2012 Wiley Periodicals, Inc.

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