Circadian rhythms and the cell cycle are two fundamental biological oscillators. They are linked through molecular mechanisms creating coupled oscillators where the outcomes of this coupling depend on numerous factors, such as the directionality of coupling (i.e., unidirectional vs. bidirectional), periods of the two oscillators, and the number and strength of connections. In this review, we provide a general overview of the links between circadian rhythms and the cell cycle and discuss potential implications of this connection in stem cell proliferation and differentiation of mammalian cells.

SLC transporters are the entry gates of nutrients required by intracellular enzymes to accomplish cell metabolism. SLCs include many amino acid transporters, which belong to different families and are characterized by redundancy, cross-specificity, and diverse transport mechanisms. Amino acid transporters are critical, as demonstrated by the onset of diseases caused by their altered expression, function, or localization. Despite their crucial roles, a systematic description of structure/function relationships of amino acid transporters is still far from being obtained. Among many SLCs specific toward amino acids, the heterodimeric transporters (HATs) of the SLC7 family, paired to proteins of the SLC3 family via a conserved disulfide, have emerged. Members A5 (LAT1), A6 (y[+]LAT2), A7 (y[+]LAT1), A8 (LAT2), A10 (ASC1), and A11 (xCT) are combined with SLC3A2; the members A9 (b[0,+]AT1) and A13 (AGT1) are combined with SLC3A1. Even though the members of the SLC3 family are classified as solute carriers (SLCs), they do not display transport capacity but are mainly involved in assisting the trafficking of the transport SLC7 subunits. An update of the structure/function relationships and relation to pathologies is reported.

Nanobodies, the single-domain antigen-binding fragments derived from camelid heavy chain antibodies, have emerged as powerful tools in structural biology. Their small size, high stability, and ability to bind with exceptional specificity make them ideal for applications in nuclear magnetic resonance (NMR) spectroscopy. In protein NMR, nanobodies can serve as chaperones to stabilize flexible regions, reduce conformational heterogeneity, and enhance spectral quality. They facilitate the study of challenging targets such as membrane proteins, large complexes, and intrinsically disordered proteins by improving solubility and enabling selective labeling strategies. Furthermore, nanobody-assisted NMR spectroscopy provides unique opportunities for probing dynamic interactions and conformational states under near-physiological conditions. This review summarizes recent advances in nanobody engineering for NMR studies, including the synthetic nanobodies, highlights the nanobodies' role in overcoming size and stability limitations, and discusses future directions for integrating nanobodies into emerging NMR methodologies, with an emphasis on protein dynamics and protein-protein interactions in the context of drug discovery.

Biological membranes are more than structural boundaries: they are the thermodynamic interfaces that enable living systems to maintain a state far from equilibrium, continuously exchanging matter and energy with their environment. In this review, we explore three interconnected themes. First, we examine the biochemical composition of cell membranes, with particular focus on Escherichia coli, including lipid diversity, membrane asymmetry, and homeoviscous adaptation. Second, we reframe the membrane as the physical representation of the Markov blanket, the statistical boundary separating internal from external states, and discuss how biological systems minimize free energy to maintain homeostasis. Third, we evaluate synthetic cell research strategies for reconstructing life-like systems, highlighting how out-of-equilibrium approaches, based on selective membrane transport coupled to metabolic networks, may recapitulate the thermodynamic identity of living cells.

In metazoans, TGF-β signaling regulates essential cellular processes via the SMAD proteins. Many biophysical and cellular assays of SMAD-driven signaling require molecular tools that can recognize them in their native folded state. In this context, we report two nanobodies (Nbs), NbS4A1 and NbS4A7, which target the 3D structure of the human SMAD4-MH2 domain with high affinity and specificity. X-ray structures of the Nb-SMAD4 complexes reveal that each nanobody recognizes the SMAD4-MH2 domain through distinct but overlapping sites, precluding their simultaneous binding. Furthermore, NbS4A1 impedes SMAD4 binding with R-SMADs while NbS4A7 recognizes SMAD4 even when bound to R-SMADs. These distinct interaction modes will enable the study of folded SMAD complexes with cofactors and/or DNA in different experimental contexts.

A prominent bacterial family in the human gut is Bacteroidetes, for which cobalamin (vitamin B12) is an essential micronutrient. Here, we characterized the structural-function relationships underlying the role of three BtuG family proteins, BtuG1, BtuG2, and BtuG3, in cobalamin acquisition. We solved crystal structures (resolution between 2 and 1.5 Å) of these homologs bound to different cobalamin forms and the precursor cobinamide, and measured the binding affinities by grating coupled interferometry. We observed high binding affinities, with KD values in the low picomolar range, underlining their role in cobalamin scavenging. Mutations based on the structures resulted in altered binding affinities for cobalamin and its precursor. This study provides structural and quantitative insights into the B12 scavenging mechanism of BtuG proteins.

Transcriptional regulation of key target genes by BRCA1 is crucial for its diverse functions. Here, we report fatty acid-binding protein 3 (FABP3) as a novel BRCA1-repressible target gene. Functional BRCA1 represses FABP3 promoter activity while mutant BRCA1 breast cancer cell lines show higher endogenous FABP3 expression which was reduced upon introducing wild-type protein. Furthermore, using deletion constructs we identified a critical minimal responsive FABP3 promoter region and confirmed BRCA1 recruitment to this site by ChIP. FABP3 overexpression promoted proliferation, clonogenicity, and migration in breast cancer cells while conferring sensitivity to chemotherapeutic drugs. TCGA analysis correlated high FABP3/BRCA1 expression with reduced overall survival. These findings implicate FABP3 de-repression as a mechanism linking BRCA1 loss to tumor aggressiveness and chemosensitivity.

Intrinsically disordered proteins (IDPs) are often readily characterized as soluble monomers, whereas their biological and pathological roles frequently involve transient, heterogeneous, or sparsely populated oligomers. Such assemblies are often described as 'invisible' but invisibility is method-dependent: Oligomers that escape direct detection by one technique may remain accessible through indirect or complementary measurements. Solution NMR is uniquely positioned to exploit exchange between observable monomers and NMR-invisible oligomers, providing residue-specific information on populations, kinetics, and intermolecular contacts. Other methods report on mass, stoichiometry, dimensions, morphology, or site-specific distance distributions. Here, we discuss how integrating orthogonal measurements can overcome method-specific blind spots and yield a self-consistent model that simultaneously accounts for structure, populations, exchange kinetics, and morphology, something no single method can provide.

Acquired resistance to vemurafenib, a BRAF[V600E]-targeted therapy, remains a major challenge in melanoma. The translation initiation factor eIF6 has been implicated in cancer; however, its role in vemurafenib resistance is poorly understood. We investigated eIF6 using melanoma cell lines with distinct mutational backgrounds. RNA sequencing of a resistant cell line revealed dysregulation of MAPK, PI3K-AKT, metabolic, and ribosome biogenesis pathways together with increased eIF6 expression and alterations in translation-related signaling. Silencing of eIF6 led to reduced proliferation and partially restored vemurafenib sensitivity, while its overexpression increased sensitivity irrespective of BRAF status via mTOR and MAPK modulation. These findings reveal a context-dependent role for eIF6, linking translation regulation to therapeutic response in melanoma.

Metastasis is responsible for the vast majority of cancer-related deaths, yet organ selectivity and the fate of disseminated cancer cells remain incompletely understood. While tumor-intrinsic programs have been extensively characterized, increasing evidence indicates that host-related extrinsic factors critically modulate the molecular and cellular landscape of metastatic niches. Aging, dietary habits, microbiome, physical activity, smoking, air pollution, and chronic stress may reshape systemic inflammation, immune surveillance, vascular permeability, stromal composition, extracellular matrix remodeling, and metabolic signaling in organs commonly targeted by metastasis, including bone, lung, liver, and brain. These host-dependent alterations influence disseminated cancer cell homing, extravasation, dormancy, and proliferative outgrowth by reprogramming tissue-resident and recruited cell populations, as well as niche-derived soluble and mechanical cues. In this review, we describe a framework in which metastasis is dynamically codetermined by tumor cell plasticity and host systemic state, contextualized by recent mechanistic insights into how lifestyle and physiological states rewire organ microenvironments to become either permissive or restrictive to metastatic colonization. Understanding these interactions may reveal actionable targets for metastasis prevention and highlight modifiable behaviors as biological determinants of organ susceptibility to metastatic disease.

The ubiquitin system is a highly regulated cellular mechanism that plays a central role in germinal center (GC) B cells, essential for protective humoral immunity and the site of gammaherpesvirus latency establishment. GC B cells undergo extraordinary levels of proliferation, DNA damage, and apoptosis prior to differentiating to long-lived memory or plasma cells, and ubiquitin pathways underpin these activities. Oncogenic gammaherpesviruses infect B cells and drive them through a GC activation program. Viral programs exploit ubiquitin biology to establish latency in GC B cells and persist for life in long-lived memory B cells, poised to drive lymphomagenesis over time. Here, we will first define how ubiquitin regulates normal GC B cells. Within this framework, we will describe how gammaherpesviruses interact with these mechanisms to establish latency, highlighting common and divergent mechanisms of GC control in infected and normal B cells. Further understanding ubiquitin mechanisms in GC B cells will aid the discovery of highly specific molecular circuits that regulate B-cell fate and function, with broad relevance to antiviral immunity and cancer biology.

Fic enzymes mediate diverse post-translational modifications, including adenosine monophosphate (AMP) transfer and removal, referred to as AMPylation and deAMPylation, respectively. We identified the prokaryotic translation elongation factor Tu (EF-Tu) as an AMPylation target of the Fic enzyme SoFic. SoFic can constitutively reverse EF-Tu modification via deAMPylation whereas AMPylation depends on SoFic homodimerization. The complex crystal structure between SoFic and EF-Tu confirms a conserved target binding mode across evolutionarily distant Fic enzymes. AMPylation disrupts EF-Tu's regulatory switch-I region, causing translational inhibition. SoFic furthermore binds to its promoter DNA in vitro, suggesting a dual function as transcriptional and translational regulator in bacterial cells. Together, our structural and biochemical data provide valuable insights into the functional and regulatory diversity of Fic enzymes.

Generative AI has driven remarkable breakthroughs in protein design, enabling the rapid, computationally guided creation of high-affinity binders against diverse targets. While remarkable experimental success has been demonstrated, the confidence metrics used to filter and evaluate designs remain optimized for static protein interfaces and can fail when applied to underrepresented or conformationally complex targets. In this review, we outline the current landscape of deep learning-driven protein design pipelines, discuss tailored applications in peptide, small molecule, binder, vaccine, and antibody design, and argue that the integration of ensemble-based methods represents a promising avenue for improving design success rates. Beyond single target binder design, we further highlight emerging strategies that expand the functional scope of designed proteins, including fold-switching scaffolds and molecular glues realized through engineered cyclic peptides, which enable context-dependent control of protein-protein interaction networks. Together, these advances position de novo protein design as a broadly applicable technology platform at the intersection of structural biology, biophysics, and molecular medicine.

In Lgi1[-/-] mice, increased neuronal excitability is accompanied by a marked decrease in Kv1 channels, but the mechanism linking LGI1 loss to reduced ion channel expression remains unknown. We show that LGI1 contains multiple conserved canonical ganglioside-binding domains (GBDs) and that GT1b copurifies with LGI1 antibodies from native rat brain extracts. Recombinant LGI1 bound ganglioside-containing liposomes, and the ganglioside-binding capacity of surface-exposed GBD peptide sequences was confirmed experimentally. These findings suggest LGI1 interacts with gangliosides and may help organize lipid membrane platforms that accommodate functional protein complexes. We hypothesize that loss of LGI1 destabilizes these platforms, contributing to the reduced ion channel expression observed in Lgi1[-/-] mice.

Cyanobacteria are promising microbial hosts for production of succinate, a central metabolite of the tricarboxylic acid (TCA) cycle, which cyanobacteria can secrete during anoxic fermentation. To investigate the route for succinate formation, we generated strains of Synechocystis PCC6803 lacking subunits of the succinate dehydrogenase complex (SDH). During dark anaerobic fermentation, the deletion strains show higher succinate accumulation than the wild type, indicating succinate dehydrogenase activity of SDH rather than fumarate reduction. Another potential route for succinate formation from fumarate is as a byproduct of the L-aspartate oxidase (Laspo) reaction. Using purified SynLaspo, we show that in addition to L-aspartate oxidation, the enzyme exhibits L-aspartate-fumarate oxidoreductase activity, generating succinate. This work contributes to the understanding of the cyanobacterial TCA cycle.