A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
M D Shahinuzzaman, Dipak Barua

Abstract

This article introduces a multiscale framework for spatiotemporal modeling of protein-protein interaction. Cellular protein molecules represent multivalent species that contain modular features, such as binding domains and phosphorylation motifs. The binding and transformations of these features occur at a small time and spatial scale. On the other hand, space and time involved in protein diffusion, colocalization, and formation of complexes could be relatively large. Here, we present an agent-based framework integrated with a multiscale Brownian Dynamics (BD) simulation algorithm. The framework employs spatial graphs to describe multivalent molecules and complexes with their site-specific details. By implementing a time-adaptive feature, the BD algorithm enables efficient computation while capturing the site-specific interactions of the diffusing species at the sub-nanometer scale. We demonstrate these capabilities by modeling two multivalent molecules, one representing a ligand and the other a receptor, in a two-dimensional plane (cell membrane). Using the model, we show that the algorithm can accelerate computation by orders of magnitudes in both concentrated and dilute regimes. We also show that the algorithm enables robust...Continue Reading

References

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Citations

Jul 15, 2018·Chemistry : a European Journal·Hyeongjoo Choi, Yongwon Jung
Mar 7, 2019·Royal Society Open Science·Md ShahinuzzamanDipak Barua

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Software Mentioned

VirtualCell
MCell
DeclareMathSizes
SRSim

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