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Obtaining Soft Matter Models of Proteins and their Phase Behavior

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Protein Self-Assembly

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2039))

Abstract

Globular proteins are roughly spherical biomolecules with attractive and highly directional interactions. This microscopic observation motivates describing these proteins as patchy particles: hard spheres with attractive surface patches. Mapping a biomolecule to a patchy model requires simplifying effective protein–protein interactions, which in turn provides a microscopic understanding of the protein solution behavior. The patchy model can indeed be fully analyzed, including its phase diagram. In this chapter, we detail the methodology of mapping a given protein to a patchy model and of determining the phase diagram of the latter. We also briefly describe the theory upon which the methodology is based, provide practical information, and discuss potential pitfalls. Data and scripts relevant to this work have been archived and can be accessed at https://doi.org/10.7924/r4ww7bs1p.

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Change history

  • 01 July 2020

    The acknowledgement section text has been updated in the chapter.

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Acknowledgments

We thank Diana Fusco for guiding discussions. The authors acknowledge support from National Science Foundation Grant no. NSF DMR-1749374. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, as well as the Duke Compute Cluster.

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Authors and Affiliations

  1. Department of Chemistry, Duke University, Durham, NC, USA

    Irem Altan

  2. Department of Physics, Duke University, Durham, NC, USA

    Patrick Charbonneau

Authors
  1. Irem Altan
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  2. Patrick Charbonneau
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Correspondence to Irem Altan .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Maynooth University, Maynooth, Co. Kildare, Ireland

    Jennifer J. McManus

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Altan, I., Charbonneau, P. (2019). Obtaining Soft Matter Models of Proteins and their Phase Behavior. In: McManus, J. (eds) Protein Self-Assembly. Methods in Molecular Biology, vol 2039. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9678-0_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9678-0_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9677-3

  • Online ISBN: 978-1-4939-9678-0

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