A5008124262- Lipid Membrane Structure and Behavior
- Protein Structure and Dynamics
- Bacteriophages and microbial interactions
- Cellular transport and secretion
- Advanced Fluorescence Microscopy Techniques
- DNA and Nucleic Acid Chemistry
- Bacterial Genetics and Biotechnology
- Microtubule and mitosis dynamics
- RNA and protein synthesis mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Force Microscopy Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Supramolecular Self-Assembly in Materials
- RNA Interference and Gene Delivery
- Glycosylation and Glycoproteins Research
- HIV Research and Treatment
- Spectroscopy and Quantum Chemical Studies
- Enzyme Structure and Function
- Advanced Proteomics Techniques and Applications
- Micro and Nano Robotics
- Cellular Mechanics and Interactions
- Genomics and Chromatin Dynamics
- Diffusion and Search Dynamics
- Membrane Separation Technologies
- Photosynthetic Processes and Mechanisms
South China University of Technology
2025
Johns Hopkins University
2019-2024
University of California, Merced
2023
Institute of Physics
2016-2019
Chinese Academy of Sciences
2016-2019
University of Chinese Academy of Sciences
2017
G-quadruplex (G4) can be formed by G-rich DNA sequences that are widely distributed throughout the human genome. Although G-triplex and G-hairpin have been proposed as G4 folding intermediates, their formation still requires further investigation experiments. Here, we employed single-molecule FRET to characterize dynamics of from telomeric sequence. First, observed four states during initially assigned anti-parallel G4, G-triplex, unfolded ssDNA. Then constructed putative intra-strand...
Helix-membrane interactions are key to membrane deformation and play significant biological roles. However, systematic studies on the mechanisms behind these limited. This study uses a continuum model investigate how shallowly inserted helices interact with membranes, focusing cooperative effects of multiple helices. Our findings show that even short (2 nm in length) can induce anisotropic deformation. Longer deeper insertions result more deformations, spatial arrangement affects nature...
Abstract Changes of affinity kinesin head to microtubule regulated by changes in the nucleotide state are essential processive movement on microtubule. Here, using all‐atom molecular dynamics simulations we show that besides state, large conformational microtubule‐tubulin heterodimers induced strong interaction with strongly binding also indispensable regulate tubulin. In high arises largely from mutual and specific between them via an induced‐fit mechanism. Moreover, ADP‐head has a much...
Cytoplasmic proteins must recruit to membranes function in processes such as endocytosis and cell division. Many of these recognize not only the chemical structure membrane lipids, but curvature surface, binding more strongly highly curved surfaces, or 'curvature sensing'. Curvature sensing by amphipathic helices is known vary with bending rigidity, changes lipid composition can simultaneously alter thickness, spontaneous curvature, leaflet symmetry, thus far preventing a systematic...
Localization of proteins to a membrane is an essential step in broad range biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength specificity binding depend on the lipid composition. Single-particle reaction-diffusion methods offer powerful tool for capturing lipid-specific surfaces by treating lipids explicitly individual diffusible sites. However, modeling particle populations expensive. Here, we present algorithm reversible continuum with...
Protein domains, such as ENTH (epsin N-terminal homology) and BAR (bin/amphiphysin/rvs), contain amphipathic helices that drive preferential binding to curved membranes.
Abstract For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature lattice has been structurally characterized and reconstituted in vitro , revealing sensitivity assembly multiple co-factors. Due this sensitivity, energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use reaction-diffusion model designed from cryo-ET structure map phase diagram outcomes...
ABSTRACT One of critical issues for RNA polymerase is how the enzyme translocates along DNA substrate during transcription elongation cycle. Comparisons structure II (Pol II) with that bacterial have suggested transition bridge helix (BH) from straight to flipped‐out conformations facilitates translocation upstream DNA‐RNA hybrid. However, conformation BH in Pol has not been observed up now and detailed mechanism facilitating hybrid still remains obscure. Here we use all‐atom molecular...
ABSTRACT The elasticity of polypeptide chains is usually characterized by the worm‐like chain model that was proposed first to describe double‐stranded DNA. However, molecular dynamics simulation data on are deviated significantly away from theoretical obtained based model. Here, we provide a revised considering entropic, enthalpic, and hydrophobic effects effect compressing force applied chains. in good agreement with data. Additionally, reveal that, besides positive‐force regime chains,...
Abstract DNA polymerase I (PolI), T7 primase and IV (Dpo4) have a common feature in their structures that the two main domains are connected by an unstructured polypeptide linker. To perform specific enzymatic activities, enzymes required to rearrange position orientation of one domain relative other into active mode. Here, we show three share same mechanism transition from inert modes use minimum numbers residues linkers achieve most efficient transitions. The time finally mode is...
To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) DNA nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D bare rapidly slides back-and-forth between naturally clustered motifs seconds before escape. Multimeric, full-length also 1D-3D diffusion, but remains...
Abstract Localization of proteins to a membrane is an essential step in broad range biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength specificity binding depend on the lipid composition. Single-particle reaction-diffusion methods offer powerful tool for capturing lipid-specific surfaces by treating lipids explicitly individual diffusible sites. However, modeling particle populations expensive. Here we present algorithm reversible...
Abstract Currently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular cannot capture minutes-long cellular dynamics couple distinct components with active processes, while reaction-diffusion lack sufficient detail for capturing assembly structures. Here we introduce the Non-Equilibrium Reaction-Diffusion Self-assembly Simulator (NERDSS), which addresses this gap by integrating structure-resolved algorithm rule-based model...