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From protein sequence to dynamics and disorder with DynaMine

Author

Listed:
  • Elisa Cilia

    (MLG, Université Libre de Bruxelles
    Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus)

  • Rita Pancsa

    (Structural Biology Brussels, Vrije Universiteit Brussel
    VIB)

  • Peter Tompa

    (Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus
    Structural Biology Brussels, Vrije Universiteit Brussel
    VIB)

  • Tom Lenaerts

    (MLG, Université Libre de Bruxelles
    Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus
    AI-lab, Vrije Universiteit Brussel)

  • Wim F. Vranken

    (Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus
    Structural Biology Brussels, Vrije Universiteit Brussel
    VIB)

Abstract

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine—a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

Suggested Citation

  • Elisa Cilia & Rita Pancsa & Peter Tompa & Tom Lenaerts & Wim F. Vranken, 2013. "From protein sequence to dynamics and disorder with DynaMine," Nature Communications, Nature, vol. 4(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3741
    DOI: 10.1038/ncomms3741
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    1. Morgane Boone & Pathmanaban Ramasamy & Jasper Zuallaert & Robbin Bouwmeester & Berre Moer & Davy Maddelein & Demet Turan & Niels Hulstaert & Hannah Eeckhaut & Elien Vandermarliere & Lennart Martens & , 2021. "Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    2. Mónika Gönczi & João M. C. Teixeira & Susana Barrera-Vilarmau & Laura Mediani & Francesco Antoniani & Tamás Milán Nagy & Krisztina Fehér & Zsolt Ráduly & Viktor Ambrus & József Tőzsér & Endre Barta & , 2023. "Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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