A5024861014- Protein Structure and Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Enzyme Structure and Function
- Cellular Mechanics and Interactions
- Lipid Membrane Structure and Behavior
- Force Microscopy Techniques and Applications
- Cell Adhesion Molecules Research
- Immune Response and Inflammation
- RNA Research and Splicing
- Phagocytosis and Immune Regulation
- Pancreatic function and diabetes
- Computational Drug Discovery Methods
- vaccines and immunoinformatics approaches
- Immunotherapy and Immune Responses
- Adversarial Robustness in Machine Learning
- RNA and protein synthesis mechanisms
- T-cell and B-cell Immunology
- Erythrocyte Function and Pathophysiology
- Wnt/β-catenin signaling in development and cancer
- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- Viral Infectious Diseases and Gene Expression in Insects
- Complement system in diseases
- Glycosylation and Glycoproteins Research
- Cardiomyopathy and Myosin Studies
Albert Einstein College of Medicine
2016-2025
Shanghai Sixth People's Hospital
2024
Shanghai Jiao Tong University
2024
Nanjing University of Aeronautics and Astronautics
2021-2023
Central South University
2023
Shaanxi University of Science and Technology
2023
Central South University of Forestry and Technology
2023
Xi'an Jiaotong University
2022
Yeshiva University
2014-2020
The Bronx Defenders
2015-2019
Intercellullar junctions formed by cadherins, including desmosomes and adherens junctions, comprise two dimensional arrays of “ trans ” dimers between monomers emanating from opposing cell surfaces. Lateral cis interfaces cadherins the same surface have been proposed to play a role in cadherin clustering. Although molecular details interactions remain uncertain, they must define an anisotropic arrangement where binding is favorable only certain orientations. Here we report Monte Carlo...
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa . single-stranded RNA (ssRNA) phage PP7 binds to T4P and brought cell surface through retraction. Using fluorescence microscopy, we discovered that detaches T4P, which impairs motility restricts pathogen’s virulence. cryo–electron mutagenesis, optical trapping, Langevin dynamics simulation, resolved structure PP7, PP7/T4P complex showed detachment driven by affinity...
In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Calpha positions as input. The contributions from other atomic were established pseudo-positions artificially built trace for auxiliary purposes. function is formed based on seven major representative molecular interactions in proteins: distance-dependent pairwise energy with orientational preference, hydrogen bonding energy, short-range packing tri-peptide three-body and solvation...
The interactions between membrane receptors and extracellular ligands control cell-cell cell-substrate adhesion, environmental responsiveness by representing the initial steps of cell signaling pathways. These can be spatial-temporally regulated when different are tethered. detailed mechanisms this spatial-temporal regulation, including competition distinct with overlapping binding sites conformational flexibility in multi-specific ligand assemblies have not been quantitatively evaluated. We...
Polyamidoamine (PAMAM) dendrimers, a class of polymeric nanoparticles (NPs) with highly controllable sizes and surface chemistry, are promising candidates for many biomedical applications, including drug gene delivery, imaging, inhibition amyloid aggregation. In circulation, binding serum proteins dendritic NPs renders the formation protein corona alters biological identity NP core, which may subsequently elicit immunoresponse cytotoxicity. Understanding effects PAMAM size chemistry on is,...
We demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, (cis) E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using combination dynamic single-molecule Förster Resonance Energy Transfer (FRET) kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts...
The interactions of bio-molecules constitute the key steps cellular functions. However, in vivo binding properties differ significantly from their vitro measurements due to heterogeneity environments. Here we introduce a coarse-grained model based on rigid-body representation study how factors such as crowding and membrane confinement affect molecular binding. macroscopic parameters equilibrium constant kinetic rate are calibrated by adjusting microscopic coefficients used numerical...
Abstract Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. tested our method on previously used large benchmark set 49 complexes. The predicted rate was overestimated test compared experimental results for group hypothesized that this resulted from molecular flexibility at interface regions interacting proteins. After applying machine...
Abstract Membrane proteins are among the most functionally important in cells. Unlike soluble proteins, they only possess two translational degrees of freedom on cell surfaces, and experience significant constraints their rotations. As a result, it is currently challenging to characterize situ binding membrane proteins. Using receptors CD2 CD58 as testing system, we developed multiscale simulation framework study differences protein kinetics between 3D 2D environments. The association...
Abstract The interaction between TNFα and TNFR1 is essential in maintaining tissue development immune responses. While a cell surface receptor, exists both soluble membrane-bound forms. Interestingly, it was found that the activation of TNFR1-mediated signaling pathways preferentially through form TNFα, which can also induce clustering on plasma membrane living cells. We developed multiscale simulation framework to compare receptor induced by ligands. Comparing with freely diffusive ligands,...
This paper reports a computational method for describing the conformational flexibility of very large biomolecular complexes using reduced number degrees freedom. It is called substructure synthesis method, and basic concept to treat motions given structure as collection those an assemblage substructures. The choice substructures arbitrary sometimes quite natural, such domains, subunits, or even segments complexes. To start, group low-frequency modes determined, instance by normal mode...
Wnt signaling and cadherin-mediated adhesion have been implicated in both processes of embryonic development the progression carcinomas. Recent experimental studies revealed that cell close crosstalk with each other. A comprehensive model investigates dynamic balance β-catenins will improve our understanding to We constructed a network evaluate interplay between signaling. The is decomposed into three interdependent modules: adhesion, degradation circle transcriptional regulation. In module,...
Domains that belong to an immunoglobulin (Ig) fold are extremely abundant in cell surface receptors, which play significant roles cell-cell adhesion and signaling. Although the structures of domains Ig share common topology β-barrels, functions receptors signaling regulated by very heterogeneous binding between these domains. Additionally, only a small number directly involved two multidomain receptors. It is challenging time consuming experimentally detect partners given receptor further...
A coarse-grained simulation method and a knowledge-based potential were developed to explore the dissociation mechanisms of protein complexes.