Cell Reports Physical Science最新文献

Approved by the US Food and Drug Administration in 2006, varenicline was the first nicotinic-based therapy for smoking cessation, targeting the α4β2 nicotinic acetylcholine receptor (nAChR). While inspired by cytisine, varenicline has distinct effects at both target and off-target receptors; however, despite being widely used clinically, the precise molecular interactions underpinning varenicline's mode of action remain unclear. Using a multidisciplinary approach, the interactions that set varenicline apart from related compounds such as nicotine and cytisine have been identified. In particular, the binding-site residues α4T139, α4T183, and especially β2S133 were shown to be key modulators for varenicline's function. Substituting β2S133 with valine significantly reduced efficacy, pinpointing it as a crucial determinant. Additionally, a set of novel varenicline variants showed that the positioning of the quinoxaline moiety in varenicline is essential for receptor activation. These insights reveal a unique interaction network at α4β2 that underlies varenicline's function, offering a deeper understanding of the ligand's working mechanism.

D-Tagatose is a low-calorie rare sugar with health benefits as a low-glycemic sweetener. Current production methods are limited, often relying on galactose isomerization, and remain inefficient and costly. Here, we report a whole-cell process in Escherichia coli that converts glucose directly to tagatose by reversing the Leloir pathway. Central to this approach is a galactose-1-phosphate-specific phosphatase that drives equilibrium toward galactose. Computational analyses reveal hydrogen-bond networks that underlie stringent substrate selectivity. By co-expressing this phosphatase with an L-arabinose isomerase in a metabolically engineered strain, we demonstrate direct glucose-to-tagatose conversion. Cultures produced ~10.5 g/L galactose from 30 g/L glucose (35% yield) and >1 g/L tagatose. While this is a proof-of-principle demonstration and further optimization is required to improve tagatose production, this strategy eliminates dependence on lactose-derived galactose and provides a framework for scalable, glucose-based biosynthesis of tagatose and other galactose-derived molecules, supporting sustainable rare-sugar production.

[This corrects the article DOI: 10.1016/j.xcrp.2025.102663.].

From a circular economy point of view, the valorization of gaseous alkanes into large-volume commodity chemicals is of the utmost importance. Such protocols would help reduce the current reliance on a petroleum-based economy and contribute to the challenge of reducing greenhouse gas emissions. In this regard, we hereby report a methodology based on dual photoredox/nickel catalysis that enables the direct coupling of gaseous alkanes with a range of acid chlorides. The protocol is operationally simple, proceeds under mild reaction conditions, and features high chemo- and regioselectivity and good functional group tolerance. Of note, this method serves as an efficient tool for the upscaling of feedstock gaseous alkanes into industrially relevant ketones, such as propiophenone, acetophenone, or isobutyrophenone derivatives.

Vitamin B₁₂ (cobalamin) is a high-value yet scarce cofactor critical for metabolic homeostasis, necessitating efficient handling mechanisms. ATP:cob(I)alamin adenosyltransferase (MMAB) plays a central role in synthesizing, delivering, and repairing 5'-deoxyadenosylcobalamin (AdoCbl), but the kinetic mechanisms regulating this process, including negative cooperativity, remain unclear. Using single-molecule relative fluorescence spectroscopy, we reveal that conformation-gated binding mechanism, involving a required structural rearrangement prior to the first cofactor association, dictates MMAB's interaction kinetics. This mechanism slows the association of a second AdoCbl, resulting in strong negative cooperativity, favoring the singly bound state, and optimizing AdoCbl handling. This gating mechanism, supported by direct observation of a kinetic intermediate, also contributes to MMAB's preferential handling of AdoCbl over hydroxocobalamin, highlighting MMAB's effective cofactor utilization, supporting bacterial survival in nutrient-limited environments. Furthermore, our approach offers a platform to study cofactor interactions, including cobalamin sensing and gene regulation, shedding light on bacterial adaptation to nutrient fluctuations.

ALKBH5 is one of only two known human non-heme Fe(II)/2-oxoglutarate-dependent oxygenases that catalyze the demethylation of N⁶-methyladenine (m⁶A) in single-stranded mRNA, underscoring its role in diverse cancers. Unlike its homolog, the fat mass and obesity-associated protein (FTO), which oxidizes m⁶A to a stable N⁶-hydroxymethyladenine (hm⁶A) intermediate, ALKBH5 demethylates m⁶A, yielding adenine and formaldehyde as products. Here, we integrate molecular dynamics simulations and quantum mechanics/molecular mechanics methods to elucidate ALKBH5's complete catalytic mechanism. Two post-hydroxylation pathways were evaluated: a proton transfer pathway and a Schiff base formation pathway, with the former emerging as the favored mechanism. We identify second-sphere residues Lys132 and Tyr139 as essential contributors to catalysis and demonstrate how Val191 and Tyr133 modulate activity. Dynamic analyses reveal that correlated motions of structural elements such as nucleotide recognition lids NRL1 and NRL2 and increased flexibility of the NRL2 loop in the hm⁶A intermediate may be critical for efficient demethylation.

Triple-negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC) are aggressive solid tumors with limited treatment options. Nectin cell adhesion molecule 4 (Nectin4) is a tumor-associated antigen frequently overexpressed in these cancers, making it a promising therapeutic and imaging target. Here, we report the development and evaluation of [⁸⁹Zr]Zr-desferrioxamine (DFO)-Padcev, a radiolabeled antibody-drug conjugate targeting Nectin4, for immuno-positron emission tomography (ImmunoPET) imaging. [⁸⁹Zr]Zr-DFO-Padcev is synthesized with a radiochemical yield of 88.87% ± 2.59% and a radiochemical purity above 99%. ImmunoPET imaging successfully visualizes Nectin4-positive tumors in TNBC (MDA-MB-468) and NSCLC (H1975) models as early as 6 h post-injection, with uptake progressively increasing and peaking at 48 h (14.57 ± 1.94 and 9.50 ± 0.76 %ID/g, respectively). Minimal tumor uptake is observed in blocking and Nectin4-negative controls, confirming specificity. Complementary fluorescence imaging further reveals the in vivo distribution of Padcev, providing valuable insights into optimal therapeutic time windows.

About 1.9 gigatons of steel is produced every year, emitting 8% (3.6 gigatons) of global CO₂ in the process. More than 50% of the CO₂ emissions come from a single step of steel production, known as ironmaking. Hydrogen-based direct reduction (HyDR) of iron oxide to iron has emerged as an emission-free ironmaking alternative. However, multiple physical and chemical phenomena ranging from nanometers to meters inside HyDR reactors alter the microstructure and pore networks in iron oxide pellets, in ways that resist gaseous transport of H₂/H₂O, slow reaction rates, and disrupt continuous reactor operation. Using synchrotron nano X-ray computed tomography and percolation theory, we quantify the evolution of pores in iron oxide pellets and demonstrate how nanoscale pore connectivity influences micro- and macroscale flow properties such as permeability, diffusivity, and tortuosity. Our modeling framework connects disparate scales and offers opportunities to accelerate HyDR.

Self-sufficient heterogeneous biocatalysts (ssHBs), in which enzymes and cofactors are coimmobilized on the same support, provide in situ cofactor regeneration and reduce operating costs. However, the underlying mechanisms remain poorly understood. Here, we present a theoretical model for ssHBs consisting of NAD(P)H-dependent dehydrogenases immobilized on porous agarose-based materials with cofactors coimmobilized through electrostatic interactions via a cationic polymer coating. This model links enzyme activity to cofactor-polymer binding thermodynamics and demonstrates that ssHBs obey the Sabatier principle, where maximum catalytic efficiency is achieved at an intermediate binding strength. Adjustment of pH and ionic strength modulates this interaction, and the resulting activity exhibits the predicted volcano plot. Depending on the reaction conditions, electrostatic complexation is influenced, resulting in the formation of a dense, liquid-like phase inside the particles. Our study directly confirms the Sabatier principle in ssHBs and highlights the crucial role of cofactor binding thermodynamics in optimizing biocatalysis for chemical applications.

The SARS-CoV-2 nucleocapsid (N) drives the compaction and packaging of the viral genome. Here, we focused on quantifying the mechanisms that control dimer formation utilizing single-molecule Förster resonance energy transfer to investigate the conformations and energetics of the dimerization domain in the context of the full-length protein. Under monomeric conditions, we observed significantly expanded configurations of the dimerization domain (compared to the folded dimer structure), which is consistent with a dynamic conformational ensemble. The addition of unlabeled protein stabilizes a folded dimer configuration with a high mean transfer efficiency, which is in agreement with predictions based on known structures. Dimerization is characterized by a dissociation constant of ~12 nM at 23°C and is driven by strong enthalpic interactions between the two protein subunits, which originate from the coupled folding and binding. We propose that the retained flexibility of the dimer can affect its interaction with RNA and phase separation propensity.