Yiben Fu
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View article: Membrane Remodeling Driven by Shallow Helix Insertions via a Cooperative Mechanism
Membrane Remodeling Driven by Shallow Helix Insertions via a Cooperative Mechanism Open
Helix-membrane interactions are key to membrane deformation and play significant biological roles. However, systematic studies on the mechanisms behind these interactions are limited. This study uses a continuum membrane model to investiga…
View article: Predicting protein curvature sensing across membrane compositions with a bilayer continuum model
Predicting protein curvature sensing across membrane compositions with a bilayer continuum model Open
Cytoplasmic proteins must recruit to membranes to function in processes such as endocytosis and cell division. Many of these proteins recognize not only the chemical structure of the membrane lipids, but the curvature of the surface, bindi…
View article: GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion
GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion Open
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) on DNA a…
View article: Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly
Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly Open
For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro , revealing the…
View article: Correction: A continuum membrane model can predict curvature sensing by helix insertion
Correction: A continuum membrane model can predict curvature sensing by helix insertion Open
Correction for ‘A continuum membrane model can predict curvature sensing by helix insertion’ by Yiben Fu et al. , Soft Matter , 2021, 17 , 10649–10663, DOI: 10.1039/D1SM01333E.
View article: A continuum membrane model predicts curvature sensing by helix insertion
A continuum membrane model predicts curvature sensing by helix insertion Open
Protein domains, such as ENTH (Epsin N-terminal homology) and BAR (bin/amphiphysin/rvs), contain amphipathic helices that drive preferential binding to curved membranes. However, predicting how the physical parameters of these domains cont…
View article: A continuum membrane model can predict curvature sensing by helix insertion
A continuum membrane model can predict curvature sensing by helix insertion Open
Protein domains, such as ENTH (epsin N-terminal homology) and BAR (bin/amphiphysin/rvs), contain amphipathic helices that drive preferential binding to curved membranes.
View article: NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale
NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale Open
Currently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular models cannot capture minutes-long cellular dynamics that couple distinct components with active processes, while reacti…
View article: An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology
An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology Open
Localization of proteins to a membrane is an essential step in a broad range of biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength and specificity of proteins binding to a membrane dep…
View article: An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology
An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology Open
Localization of proteins to a membrane is an essential step in a broad range of biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength and specificity of proteins binding to a membrane dep…
View article: Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex
Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex Open
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 invest…