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 Data and scripts relevant to this work have been archived and can be accessed at https://doi.org/10.7924/r4ww7bs1p.
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01 July 2020
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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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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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