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Obtaining Soft Matter Models of Proteins and their Phase Behavior

  • Irem AltanEmail author
  • Patrick Charbonneau
Protocol
Part of the Methods in Molecular Biology book series (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 Data and scripts relevant to this work have been archived and can be accessed at  https://doi.org/10.7924/r4ww7bs1p.

Key words

Soft matter Phase behavior Protein crystallization Coarse-grained simulation 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of ChemistryDuke UniversityDurhamUSA
  2. 2.Department of PhysicsDuke UniversityDurhamUSA

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