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A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly

  • Jiawen Chen
  • Yinghao Wu
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

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.

Key words

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

Notes

Acknowledgments

This work was supported in part by the National Institutes of Health (Grant No. R01GM120238) and a start-up grant from the Albert Einstein College of Medicine.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxUSA

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