Paper Info
Title
A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction.
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 model predictions against a wide range of selection of time step sizes.
Year
DOI
Venue
2017
10.1089/cmb.2017.0178
JOURNAL OF COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
Brownian dynamics,multiscale modeling,receptor aggregation,multivalent assembly,signal transduction
Graph,Protein–protein interaction,Algorithm,Brownian dynamics,Multiscale modeling,Protein molecules,Bioinformatics,Modular design,Simulation algorithm,Mathematics,Computation
Journal
Volume
Issue
ISSN
24.0
12
1066-5277
Citations 
PageRank 
References 
0
0.34
2
Authors
2
Name
Order
Citations
PageRank
M D Shahinuzzaman100.68
Dipak Barua2293.16