ArticleProtein science : a publication of the Protein Society2014
Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations.
Article in Protein science : a publication of the Protein Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.Biophysical journal · 2026Article
- VesicleVoyager: In Vivo Selection of Surface Displayed Proteins That Direct Extracellular Vesicles to Tissue-Specific Targets.Journal of extracellular vesicles · 2025Article
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.bioRxiv : the preprint server for biology · 2025Article
- Binding of Soluble Ligands to Membrane Receptors: A Molecular Dynamics Simulation Study.The journal of physical chemistry. B · 2025Article
- Solution-Phase Kinetics of Ranibizumab Binding VEGF Using Solid-Phase Surface Plasmon Resonance.Analytical chemistry · 2025Article
- Quantitative Analysis of Protein-Protein Equilibrium Constants in Cellular Environments Using Single-Molecule Localization Microscopy.Nano letters · 2024Article
- Computational and experimental approaches to quantify protein binding interactions under confinement.Biophysical journal · 2024Review
- How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study.Journal of cell communication and signaling · 2023Article
- Signaling via a CD28/CD40 chimeric costimulatory antigen receptor (CoStAR™), targeting folate receptor alpha, enhances T cell activity and augments tumor reactivity of tumor infiltrating lymphocytes.Frontiers in immunology · 2023Article
- Novel γ-sarcoglycan interactors in murine muscle membranes.Skeletal muscle · 2022Article
- Molecular motion and tridimensional nanoscale localization of kindlin control integrin activation in focal adhesions.Nature communications · 2021Article
- 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
- Cadherin clusters stabilized by a combination of specific and nonspecific cis-interactions.eLife · 2020Article
- Article
- A computational model for understanding the oligomerization mechanisms of TNF receptor superfamily.Computational and structural biotechnology journal · 2020Article
- Cadherin Extracellular Domain Clustering in the Absence ofThe journal of physical chemistry letters · 2019Article
- General principles of binding between cell surface receptors and multi-specific ligands: A computational study.PLoS computational biology · 2017Article
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
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3 authors.
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Abstract
Membrane proteins are among the most functionally important proteins in cells. Unlike soluble proteins, they only possess two translational degrees of freedom on cell surfaces, and experience significant constraints on their rotations. As a result, it is currently challenging to characterize the in situ binding of membrane proteins. Using the membrane receptors CD2 and CD58 as a testing system, we developed a multiscale simulation framework to study the differences of protein binding kinetics between 3D and 2D environments. The association and dissociation processes were implemented by a coarse-grained Monte-Carlo algorithm, while the dynamic properties of proteins diffusing on lipid bilayer were captured from all-atom molecular dynamic simulations. Our simulations show that molecular diffusion, linker flexibility and membrane fluctuations are important factors in adjusting binding kinetics. Moreover, by calibrating simulation parameters to the measurements of 3D binding, we derived the 2D binding constant which is quantitatively consistent with the experimental data, indicating that the method is able to capture the difference between 3D and 2D binding environments. Finally, we found that the 2D dissociation between CD2 and CD58 is about 100-fold slower than the 3D dissociation. In summary, our simulation framework offered a generic approach to study binding mechanisms of membrane proteins.
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