Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells

Bo Wang, Zhong Ru Xie, Jiawen Chen, Yinghao Wu

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The information of how two proteins interact is embedded in the atomic details of their binding interfaces. These interactions, spatial-temporally coordinating each other as a network in a variable cytoplasmic environment, dominate almost all biological functions. A feasible and reliable computational model is highly demanded to realistically simulate these cellular processes and unravel the complexities beneath them. We therefore present a multiscale framework that integrates simulations on two different scales. The higher-resolution model incorporates structural information of proteins and energetics of their binding, while the lower-resolution model uses a highly simplified representation of proteins to capture the long-time-scale dynamics of a system with multiple proteins. Through a systematic benchmark test and two practical applications of biomolecular systems with specific cellular functions, we demonstrated that this method could be a powerful approach to understand molecular mechanisms of dynamic interactions between biomolecules and their functional impacts with high computational efficiency. Wang et al. developed a multiscale modeling framework that is able to realistically simulate the complicated dynamics of a protein network. They demonstrated that this multiscale framework serves as a powerful approach to understand the molecular mechanisms of protein-protein interactions and their functional impacts with high computational efficiency.

Original languageEnglish (US)
Pages (from-to)1414-1424.e3
JournalStructure
Volume26
Issue number10
DOIs
StatePublished - Oct 2 2018

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Cell Communication
Proteins
Benchmarking
Structural Models
Molecular Dynamics Simulation

Keywords

  • multiscale modeling
  • protein-protein interactions

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells. / Wang, Bo; Xie, Zhong Ru; Chen, Jiawen; Wu, Yinghao.

In: Structure, Vol. 26, No. 10, 02.10.2018, p. 1414-1424.e3.

Research output: Contribution to journalArticle

Wang, Bo ; Xie, Zhong Ru ; Chen, Jiawen ; Wu, Yinghao. / Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells. In: Structure. 2018 ; Vol. 26, No. 10. pp. 1414-1424.e3.
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