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Coarse-Grained Simulations of Protein Aggregation

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Therapeutic Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 899))

Abstract

Protein aggregation is believed to be responsible for a number of human diseases and limits the yields of pharmaceutical proteins during production. Computer simulations can be used to develop novel experimentally testable hypotheses pertaining to aggregation. While all-atom simulations with explicit solvent are too computationally intensive to address the multitude of relevant time scales, coarse-grained models make it possible to observe the transition of monomers to an equilibrium containing aggregates. Here, we provide the reader with background information and a list of steps for setting up, performing, and analyzing computer simulations of aggregating coarse-grained (CG) proteins.

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Author information

Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA

    Troy Cellmer & Nicolas L. Fawzi

Authors
  1. Troy Cellmer
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  2. Nicolas L. Fawzi
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Corresponding author

Correspondence to Troy Cellmer .

Editor information

Editors and Affiliations

  1. MedImmune, LLC, MedImmune Way One, Gaithersburg, 20878, USA

    Vladimir Voynov

  2. , Department of Physical Biochemistry, Biogen Idec, Cambridge Center 14, Cambridge, 02142, Massachusetts, USA

    Justin A. Caravella

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Cellmer, T., Fawzi, N.L. (2012). Coarse-Grained Simulations of Protein Aggregation. In: Voynov, V., Caravella, J. (eds) Therapeutic Proteins. Methods in Molecular Biology, vol 899. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-921-1_27

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  • DOI: https://doi.org/10.1007/978-1-61779-921-1_27

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-920-4

  • Online ISBN: 978-1-61779-921-1

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