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The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles

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Allostery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2253))

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Abstract

PyInteraph is a software package designed for the analysis of structural communication from conformational ensembles, such as those derived from in silico simulations, under the formalism of protein structure networks. We demonstrate its usage for the calculation and analysis of intramolecular interaction networks derived from three different types of interactions, as well as with a more general protocol based on distances between centers of mass. We use the xPyder PyMOL plug-in to visualize such networks on the three-dimensional structure of the protein. We showcase our protocol on a molecular dynamics trajectory of the Cyclophilin A wild-type enzyme, a well-studied protein in which different allosteric mechanisms have been investigated.

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Acknowledgments

The authors would like to thank Elena Papaleo and Emmanuelle Bignon for fruitful comments and suggestions. This work was supported by Carlsberg Foundation Distinguished Fellowship (CF18-0314), The Danish Council for Independent Research, Natural Science, Project 1 (102517), Danmarks Grundforskningsfond (DNRF125) to our group.

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  1. Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark

    Matteo Lambrughi, Valentina Sora & Matteo Tiberti

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  1. Matteo Lambrughi
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  2. Valentina Sora
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  1. Unit of Chemical-Physics Fundamentals in Chemical Engineering Department of Engineering, Universitá Campus Bio-Medico di Rome, Rome, Italy

    Luisa Di Paola

  2. Environment and Health Department, Instituto Superiore di Sanità, Rome, Italy

    Alessandro Giuliani

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Lambrughi, M., Sora, V., Tiberti, M. (2021). The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles. In: Di Paola, L., Giuliani, A. (eds) Allostery. Methods in Molecular Biology, vol 2253. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1154-8_10

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  • DOI: https://doi.org/10.1007/978-1-0716-1154-8_10

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