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Clathrin-mediated endocytosis is an essential cellular process that facilitates nutrient uptake, cell signaling, and recycling of membrane proteins. Many membrane proteins that are internalized by endocytosis are glycosylated. Interestingly, glycosylation of transmembrane receptors has been shown to work against receptor uptake by clathrin-mediated endocytosis. This observation suggests that cells may use glycosylation to tune the residence time of individual transmembrane proteins at the cell surface.

The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex mediates physical communication between the cytoskeleton to the nucleus, thereby influencing nuclear positioning, transcriptional responses, and cell migration. While prior studies have examined LINC’s role in single-cell migration, its impact on collective migration of epithelial cells on surfaces of varying stiffness remains unclear. Here, we disrupted LINC function in MCF10A mammary epithelial cells using an inducible dominant-negative SUN1 construct (SUN1L) that sequesters nesprins.

We describe a straightforward method for purifying and optimizing human green cone opsin (GCO), which we then used for biophysical and structural studies of a GCO mutant, GCOE129Q. Our results show that in dark-state (DS) GCO, residue E129 enables long-wavelength light absorption, presumably by acting as the counterion for the protonated retinal Schiff base. Notably, the Schiff-base pKa in DS GCOE129Q appears to be markedly lower (pKa ≈ 4) than in the rhodopsin equivalent, RhoE113Q (pKa ≈ 7), indicating distinct electrostatic environments at the retinal attachment site.

The proline-rich domain (PRD) of the tumour suppressor p53 plays a central role in modulating conformational dynamics and molecular interactions, yet its intrinsic structural behaviour remains incompletely understood. Here, we combine extensive all-atom molecular dynamics (MD) simulations with biophysical validation to characterise the conformational ensemble of the p53 PRD. The domain behaves as an intrinsically disordered region (IDR), sampling a highly heterogeneous ensemble with average end-to-end distance and radius of gyration of 52.5 Å and 21.8 Å, respectively.

Lipids in all biological membranes are distributed heterogeneously across the bilayer. A particularly striking example of this asymmetry is the yeast plasma membrane (PM), which exhibits a high concentration of very long-chain tail-asymmetric sphingolipids (SL) in its outer leaflet. Experimental observations indicate the existence of highly ordered gel-like PM domains that are enriched in SL but depleted of the major yeast sterol ergosterol. For a better mechanistic understanding of these unusual domains we have performed coarse-grained molecular dynamics simulations with membranes containing varying concentrations of very long-chain tail-asymmetric lipids.

Human skin wound healing is a complex process of tissue pattern formation driven by massive cell migration and regeneration, coordinated through intercellular communication. A multi-scale tissue modeling framework, the Dynamic Cellular Finite-Element Method (DyCelFEM), was developed to more realistically study the wound healing process in silico with detailed cellular mechanical interactions and geometric changes. Cells produce and release signaling cytokines that diffuse through the extracellular matrix (ECM) to mediate cell communication.

Compositional asymmetry is a defining feature of cellular membranes, controlling permeability, protein activity, cholesterol dynamics, and shape remodeling. This asymmetry can create a stress imbalance, with the two leaflets experiencing opposing tensions, though direct experimental measurement of leaflet stress remains challenging. Such a stress imbalance can compress one leaflet and trigger a fluid-to-gel phase transition, which reduces membrane fluidity and markedly increases bending rigidity.

Nitric oxide synthase (NOS) catalyzes the formation of nitric oxide through the transfer of electrons from FAD to FMN in the reductase domain of the enzyme and then from FMN to a heme in the oxygenase domain of the partner enzyme in a homodimeric complex. The calcium signaling protein calmodulin (CaM) binds to a CaM-binding domain located between the reductase and oxygenase domains to enable efficient NO synthase activity. Directed electron transfer in NOS occurs through the formation of conformational states of the enzyme that sequentially place electron donor and acceptor domains nearby, suggesting that the electron transfers are conformationally gated.

We investigate the conformational stability and binding of the inhibitor bestatin to Xenopus laevis LTA4H (xlLTA4H) in both monomeric and dimeric states using all-atom molecular dynamics (MD) simulations. Despite the crystallographic observation of a homodimer, our simulations suggest that dimerization does not significantly enhance conformational stability compared to the monomeric form. Bestatin binding induces modest stabilization at the active site, with notable suppression of C-terminal domain dynamics in monomers.

Protein S (PS) is an important anticoagulant implicated in both bleeding and thrombotic disorders, making it a promising drug target. The anticoagulant function of PS arises in part because PS enhances the anticoagulant function of tissue factor pathway inhibitor alpha (TFPIα). PS has been proposed to circulate in the bloodstream together with TFPIα and a truncated form of factor V (fV-short) in the trimolecular complex, TFPIα-PS-fV-short, which we call protein S complex (PSC). PSC has been proposed to strongly inhibit thrombin production by enhancing the ability of TFPIα to inhibit clotting factor Xa up to 100-fold and by localizing to platelet membranes, limiting fXa activity shortly after coagulation starts.

Cell surface-dependent biochemical reactions play a critical role in many biological processes. These include interactions between macromolecules in a 3D bulk solution, macromolecules confined to a 2D membrane surface, and/or lipids that comprise the membrane. In blood coagulation, for instance, biochemical reactions that generate the key enzyme thrombin occur predominantly on the membrane surfaces of activated platelets. However, how the spatial distribution of the membrane binding sites affects enzymatic activity and reaction efficiency remains poorly understood.

DNAmethylation is a widely studied epigenetic mark, a!ecting gene expression and cellular function at multiple levels. DNA methylation in the mammalian genome occurs primarily at cytosine-phosphate-guanine (CpG) dinucleotides, and patterning of the methylation landscape (i.e., the presence or absence of CpG methylation at a given genomic location) exhibits a generally bimodal distribution. Although much is known about the enzymatic writers and erasers of CpG methylation, it is not fully understood how these enzymes, along with genetic, chromatin, and regulatory factors, control the genome wide methylation landscape.