ArticleStructure (London, England : 1993)2018
Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells.
Article in Structure (London, England : 1993), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study.Journal of cell communication and signaling · 2023Article
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- Understanding the functional role of membrane confinements in TNF-mediated signaling by multiscale simulations.Communications biology · 2022Article
- Article
- A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells.PLoS computational biology · 2021Article
- Understanding the impacts of cellular environments on ligand binding of membrane receptors by computational simulations.The Journal of chemical physics · 2021Article
- A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces.Computational and structural biotechnology journal · 2021Article
- Understand the Functions of Scaffold Proteins in Cell Signaling by a Mesoscopic Simulation Method.Biophysical journal · 2020Article
- Cadherin clusters stabilized by a combination of specific and nonspecific cis-interactions.eLife · 2020Article
- Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.Journal of chemical theory and computation · 2020Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- A Systematic Test of Receptor Binding Kinetics for Ligands in Tumor Necrosis Factor Superfamily by Computational Simulations.International journal of molecular sciences · 2020Article
- Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly.Biochimica et biophysica acta. Molecular cell research · 2020Article
- A computational model for understanding the oligomerization mechanisms of TNF receptor superfamily.Computational and structural biotechnology journal · 2020Article
- Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays.Journal of the American Chemical Society · 2019Article
- A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2.Journal of chemical information and modeling · 2019Article
- Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteins.Physical chemistry chemical physics : PCCP · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.