In silico model of an antenna of a phycobilisome and energy transfer rates determination by theoretical Förster approach

Authors

  • Maximiliano Figueroa,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
    2. GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liege, Belgium
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  • José Martínez-Oyanedel,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
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  • Adelio R. Matamala,

    1. Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Chile
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  • Jorge Dagnino-Leone,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
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  • Claudia Mella,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
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  • Rubén Fritz,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
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  • José Sepúlveda-Ugarte,

    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
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  • Marta Bunster

    Corresponding author
    1. Laboratorio de Biofísica Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
    • Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla160-C, Concepción, Chile
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Abstract

Energy transfer (ET) in phycobilisomes, a macrocomplex of phycobiliproteins and linker proteins, is a process that is difficult to understand completely. A model for a rod composed of two hexamers of Phycocyanin and two hexamers of Phycoerythrin was built using an in silico approach and the three-dimensional structures of both phycobiliproteins from Gracilaria chilensis. The model was characterized and showed 125 Å wide and 230 Å high, which agree with the dimensions of a piling of four hexamers as observed in the images of subcomplexes of phycobilisomes obtained by transmission electron microscopy. ET rates between every pair of chromophores in the model were calculated using the Förster approach, and the fastest rates were selected to draw preferential ET pathways along the rod. Every path indicates that the ET is funneled toward the chromophores located at Cysteines 82 in Phycoerythrin and 84 in Phycocyanin. The chromophores that face the exterior of the rod are phycoerythrobilins, and they also show a preferential ET toward the chromophores located at the center of the rod. The values calculated, in general, agree with the experimental data reported previously, which validates the use of this experimental approach.

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