A multiscale computational model for simulating the kinetics of protein complex assembly

Jiawen Chen, Yinghao Wu

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Proteins fulfill versatile biological functions by interacting with each other and forming high-order complexes. Although the order in which protein subunits assemble is important for the biological function of their final complex, this kinetic information has received comparatively little attention in recent years. Here we describe a multiscale framework that can be used to simulate the kinetics of protein complex assembly. There are two levels of models in the framework. The structural details of a protein complex are reflected by the residue-based model, while a lower-resolution model uses a rigid-body (RB) representation to simulate the process of complex assembly. These two levels of models are integrated together, so that we are able to provide the kinetic information about complex assembly with both structural details and computational efficiency.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages401-411
Number of pages11
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1764
ISSN (Print)1064-3745

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Proteins
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Protein Subunits

Keywords

  • Coarse-grained simulation
  • Diffusion-reaction algorithm
  • Kinetic Monte Carlo
  • Multiscale modeling
  • Protein association rate
  • Protein complex assembly

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Chen, J., & Wu, Y. (2018). A multiscale computational model for simulating the kinetics of protein complex assembly. In Methods in Molecular Biology (pp. 401-411). (Methods in Molecular Biology; Vol. 1764). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7759-8_26

A multiscale computational model for simulating the kinetics of protein complex assembly. / Chen, Jiawen; Wu, Yinghao.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 401-411 (Methods in Molecular Biology; Vol. 1764).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chen, J & Wu, Y 2018, A multiscale computational model for simulating the kinetics of protein complex assembly. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1764, Humana Press Inc., pp. 401-411. https://doi.org/10.1007/978-1-4939-7759-8_26
Chen J, Wu Y. A multiscale computational model for simulating the kinetics of protein complex assembly. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 401-411. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7759-8_26
Chen, Jiawen ; Wu, Yinghao. / A multiscale computational model for simulating the kinetics of protein complex assembly. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 401-411 (Methods in Molecular Biology).
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