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In-vivo chemical cross-linking combined with mass spectrometry analysis (XL-MS) enables the direct capture of protein-protein interactions (PPIs) within their native cellular environment. This platform provides a unique capability to capture weak or transient interactions in near-native contexts, complementing other large-scale methods that may lose these associations during cell lysis or purification. The workflow involves selection of suitable chemical cross-linkers to stabilize PPIs in biological samples, ranging from organelles and cells to whole tissues.

Fluorescent proteins (FPs) have revolutionized cell imaging by visualizing protein localizations in the cellular native environment and in real time. Recently, FPs have been widely used for investigating protein liquid-liquid phase separation. Nevertheless, given that small charged biomolecules are a main driver in protein condensation, the charge state of FPs would affect to protein condensation in cells. Many of current studies have overlooked that the electrostatic properties of fluorescent proteins can perturb delicate intermolecular interactions.

A short ( < 150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as the poloidal orientation. Despite theoretical and computational predictions, experimental evidence for this phenomenon has been lacking. In this study, we introduce a single-molecule approach to visualize the poloidal orientation of DNA minicircles. We constructed a set of DNA minicircles, each containing a single biotin located at a different position along one helical turn of the dsDNA, and imaged the location of biotin-bound NeutrAvidin relative to the DNA minicircle using atomic force microscopy (AFM).

Lamin A/C proteins, integral to the nuclear lamina and present throughout the nucleoplasm, contribute to the mechanical stability of the nucleus and influence transcription as seen in laminopathies like certain lipodystrophies and progeria. By using light-sheet FCS, earlier we proved that lamin A is an important determinant of chromatin viscoelasticity in murine adult fibroblasts (MAFs). Here, by using MAF WT and lamin A KO cells, we aimed to clarify the role of lamin A in chromatin organization and the DNA-binding of PPARγ, a key transcription factor in adipogenesis also implicated in lipodystrophies.

Proteins contain small pockets that form due to imperfections in residue packing or the rotational and conformational movement of amino acids. In this work, we used the fluorescent probe 1-aminoanthracene (AMA) to detect a small ligand pocket in the hydrophobic core of human proliferating cell nuclear antigen (PCNA), which is a critical protein for DNA replication and repair. Fluorescence measurements of AMA reported that the core of PCNA had a dielectric constant (ε) of 4, which was very apolar and similar to cyclohexane (ε = 2).

Ions and temperature jointly regulate RNA structure, dynamics and phase behavior, yet their coupled effects remain poorly understood at the molecular level. Single-stranded RNA (ssRNA), a ubiquitous and functionally versatile class of RNA, presents a particularly challenging target due to its intrinsic flexibility and pronounced sensitivity to ionic and thermal perturbations. Here, we extend our previously validated coarse-grained RNA model by introducing temperature-dependent divalent ion-phosphate potentials along with revised stacking interactions to elucidate how electrostatics, stacking, and hydration collectively determine ssRNA behavior.

Cryopreservation and transplantation of ovarian tissue is an important fertility preservation strategy for patients at risk of premature ovarian failure due to gonadotoxic treatments such as chemotherapy or radiation therapy for cancer patients. It is currently the only option available for prepubertal girls and for patients who must begin treatment immediately and cannot undergo ovarian stimulation. However, the precise microscopic mechanisms of the processes that occur in the preservation and transplantation of ovarian tissue are not yet understood.

Programmed Ribosomal Frameshifting (PRF) is a specialized controlled-slippage genetic mechanism that viruses like SARS-CoV-2 and HIV-1 use to shift the reading frame during translation. This process is used in compact viral genomes to enhance their protein repertoire, maintain a precise balance of viral proteins necessary for successful replication, and enhance survival within a host. Because this mechanism is vital to the viral life cycle and remains consistent across strains, frameshifting has emerged as a promising therapeutic target for new antiviral therapeutic strategies.

Bifurcating electron transfer flavoproteins (bETFs) accept a pair of modestly reducing electrons and produce a more potent electron carrier based on energy derived from favorable transfer of the other electron. A domain-scale conformational change is believed to gate electron transfer within the bETF, allowing only one electron to use the favorable path. 80° rotation of the so-called head domain carries the electron-transfer FAD (ET-FAD) from near the bifurcating FAD in bETF's closed conformation, to a position > 35 Å away in bETF's open conformation.

Investigating the dynamics of chromatin loci and the factors that influence them provides valuable insights into the organization and functionality of the genome within the cell nucleus. We control the expression of Lamin-A, an important organizer of chromatin and nuclear structure. By simultaneously tracking hundreds of telomeres in Lamin-A knocked-out (KO) and wild-type (WT) nuclei, we find that telomere motion in Lamin-A depleted cells is both faster and more directed on micrometer scales, comparable to the size of chromosome territories.

Biological membranes are compositionally asymmetric, with distinct lipid mixtures in each leaflet, yet how this asymmetry influences lateral membrane organization remains poorly understood. Here, we use calcium-induced hemifusion to generate asymmetric giant unilamellar vesicles (aGUVs) and investigate how lipid composition modulates interleaflet coupling of liquid-liquid phase separation. Symmetric GUVs composed of cholesterol, the high-melting lipid DPPC, and a low-melting phosphatidylcholine (either 14:1-PC or 16:1-PC) were prepared at compositions exhibiting coexisting liquid-ordered (Lo) and liquid-disordered (Ld) phases.

Understanding how chromatin folds in three dimensions remains challenging because most experimental assays capture low-dimensional projections of an underlying, highly heterogeneous polymer. Here we present an ensemble-based interpretive framework built on the previously introduced Self-Returning Excluded Volume (SR-EV) model, a minimal generator of chromatin conformations using a nucleosome-indexed coarse-grained representation based on stochastic return rules and excluded-volume geometry. Despite its simplicity, SR-EV recapitulates key experimental signatures across scales: heterogeneous nanoscale packing domains resembling ChromEMT and ChromSTEM observations, sparse and highly variable single-configuration contact patterns analogous to single-cell chromosome conformation capture (Hi-C), and robust ensemble-level contact enrichment consistent with topologically associating domains (TADs).