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

Structure
Bo WangYinghao Wu

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.

Citations

Feb 6, 2020·Computational and Structural Biotechnology Journal·Zhaoqian Su, Yinghao Wu
Apr 20, 2021·Computational and Structural Biotechnology Journal·Zhaoqian SuYinghao Wu
Aug 15, 2019·Journal of Chemical Information and Modeling·Bo WangYinghao Wu

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