Proteopedia: 3D visualization and annotation of transcription factor–DNA readout modes

Authors

  • Ana Carolina Dantas Machado,

    1. Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, California 90089
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  • Skyler B. Saleebyan,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Bailey T. Holmes,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Maria Karelina,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Julia Tam,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Sharon Y. Kim,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Keziah H. Kim,

    1. Flintridge Preparatory School, 4543 Crown Avenue, La Cañada Flintridge, California 91011
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    • Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, and Keziah H. Kim contributed equally to this work.

  • Iris Dror,

    1. Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, California 90089
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  • Eran Hodis,

    1. Harvard/MIT MD-PhD Program, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115
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  • Eric Martz,

    1. Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, Massachusetts 01003
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  • Patricia A. Compeau,

    1. La Cañada High School, 4463 Oak Grove Drive, La Cañada Flintridge, California 91011
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  • Remo Rohs

    Corresponding author
    1. Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, California 90089
    • Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, California 90089
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Abstract

3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology

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