Poudel P et al. · Jul 1, 2026
The creatine transporter (CRT/SLC6A8) plays a key role in cellular energy homeostasis, yet the molecular mechanism underlying creatine transport remains poorly understood. Here, we reconstruct the complete transport cycle of human CRT using a hybrid simulation strategy that combines constant-force steered molecular dynamics (cf-sMD) with targeted molecular dynamics (tMD). This approach captures continuous progression through the outward-open, outward-occluded, inward-occluded, and inward-open states and reveals a water-assisted, sequential intracellular release of Na2, creatine, and Na1. Hydration analysis shows that progressive water penetration into the binding pocket weakens protein-substrate and protein-ion interactions and destabilizes the bound state before release. Residue-level contact analysis identifies residues that interact with creatine along the transport pathway, while dynamic network analysis reveals a TM1-TM6 communication backbone that mediates long-range coupling during transport. Together, these results provide a molecular framework for creatine transport and establish an approach for investigating transport mechanisms across the broader solute carrier family.
Biochemistry, Genetics and Molecular Biology
Xu H et al. · Jul 1, 2026
Arterial aging is a major risk factor for cardiovascular disease and is associated with progressive changes in vascular structure and function, including arterial stiffening, reduced elasticity, extracellular matrix remodeling, chronic low-grade inflammation, and accumulation of senescence-associated cell states. Recent advances in single-cell RNA sequencing (scRNA-seq) have provided new opportunities to resolve the cellular heterogeneity underlying these age-related alterations in the arterial wall. In this review, we summarize current single-cell studies of arterial aging by focusing first on key phenotypic programs, including cellular senescence, extracellular matrix remodeling, inflammaging, and altered intercellular communication, and then discuss how these programs are reflected in endothelial cells, smooth muscle cells, fibroblasts, and immune cells. Across studies, aging is recurrently associated with endothelial dysfunction, smooth muscle cell phenotypic modulation, fibroblast-related matrix remodeling, and immune activation, although the degree of conservation varies depending on species, vascular bed, sex, and disease context. We further discuss emerging evidence that vascular aging involves not only cell-intrinsic transcriptional changes but also alterations in communication networks across the arterial wall. Although current single-cell studies have substantially improved our understanding of arterial aging, important limitations remain, including inconsistent cell-state annotation across studies, incomplete functional validation, and limited spatial and epigenetic resolution. Future integration of cross-species analyses with spatial transcriptomics, single-cell epigenomic approaches, and functional studies will help refine the cellular framework of arterial aging and improve its translational relevance.
Biochemistry, Genetics and Molecular Biology
Chandler SF et al. · Jul 1, 2026
Almost all cellular processes are influenced by ubiquitination. A large family of enzymes known as E3 ligases provides the specificity for ubiquitination, with the largest class among them, the Really Interesting New Gene (RING) E3s, comprising over 600 members in humans. RING E3s facilitate transfer of ubiquitin (Ub) to substrates by constraining the highly dynamic E2-Ub thioester linkage to be primed for attack from the substrate nucleophile. We have established a workflow that uses an N-maleimido diazirine (NMD) photoactivatable cross-linker attached to ubiquitin that, once stably linked to the active site of an E2, creates an activity-based probe (ABP) to monitor interactions with E3 ligases. Cross-linking mass spectrometry using the NMD-Ub-E2 ABP identified regions of interaction between ubiquitin and a selection of different RING E3s, which not only agreed with existing crystal structures, but was also used to evaluate in silico structural models of complexes yet to be resolved by conventional means. The cross-linking data also provided insight into domains of conformational flexibility which likely adopt multiple configurations in solution and which are challenging to monitor by other methods. NMD-Ub-E2 ABPs offer great potential to explore the ensemble conformations of E2-E3 complexes in solution and have scope for applications beyond the ubiquitin system.
Biochemistry, Genetics and Molecular Biology
Tzuri N et al. · Jul 1, 2026
Protein-protein interactions (PPIs) are shaped by evolutionary pressures that fine-tune binding affinities and drive the epistatic relationships that support functional outcomes. Here, we used the complex of bovine pancreatic trypsin inhibitor (BPTI) and chymotrypsin as a model system to study how mutations at one or two positions affect binding affinity and epistasis. To predict the binding affinity landscape of the BPTI-chymotrypsin complex, we combined deep sequencing data, obtained from a saturation scanning mutagenesis BPTI library, with a machine-learning (ML) model. Using this ML model, which was trained on a subset of experimental binding data, we predicted the binding affinities and epistatic interactions across thousands of single and double BPTI mutants, including those not observed in the library. Our predictive approach completed missing data points and enabled us to reveal global trends in affinity changes and mutation couplings within specific binding interface positions. Our analysis revealed that different mutations in the same position may have different effects on affinity, with most double mutations leading to increased epistasis, particularly at hotspot positions, thereby indicating a cooperative binding effect. In most cases, affinity and epistasis were inversely correlated, with affinity enhancement of double-mutant variants being associated with negative epistasis. Our approach can be readily generalized to predict mutation effects in larger combinatorial libraries and in proteins for which structural information is lacking.
Biochemistry, Genetics and Molecular Biology
Hasberg L et al. · Jul 1, 2026
Mitochondrial protein import is essential for organelle biogenesis and cellular homeostasis. It operates in an environment that is intrinsically shaped by redox chemistry. Mitochondria are major sources of reactive oxygen species (ROS), which arise as by-products of oxidative phosphorylation. Cells therefore maintain sophisticated ROS-handling systems, including compartmentalized antioxidant networks, to balance redox signaling with protection from oxidative stress. Increasing evidence indicates that these redox conditions directly influence mitochondrial protein import at multiple levels. In this review, we provide an overview of ROS production, ROS signaling, and oxidative stress in relation to mitochondrial protein import. We outline the major mitochondrial protein import pathways, and discuss how their activity is modulated by redox-dependent mechanisms. A particular focus is placed on the mitochondrial disulfide relay system of the intermembrane space, which directly couples protein import to redox chemistry through oxidative folding, and how it is influenced by the local redox environment. Collectively, we propose that mitochondrial protein import is partially governed by redox-dependent mechanisms, enabling integration of metabolic state, stress responses, and signaling pathways.
Biochemistry, Genetics and Molecular Biology
Soendenbroe C. · Jul 1, 2026
Muscle fibre denervation describes the loss of effective neural input from a motor neuron to one or more muscle fibres. In ageing, denervation is increasingly recognised as an important contributor to progressive declines in muscle strength and functional capacity, yet it remains heterogeneous and difficult to define in humans. This ambiguity reflects both biological complexity and current methodological limitations. The purpose of the present review is to synthesise current human evidence for muscle fibre denervation in ageing, clarify key conceptual distinctions, and evaluate methodological approaches used to assess denervation in humans. Muscle fibre denervation can occur through structural disconnection of the motor neuron from the fibre or through functional impairment of neuromuscular transmission. Evidence for denervation in ageing is derived from histological, molecular, electrophysiological, and circulating biomarker approaches, each capturing distinct and only partially overlapping aspects of neuromuscular integrity. Importantly, no single measure provides a comprehensive assessment of denervation. Experimental models of disuse in humans reveal a functional denervation phenotype, characterised by molecular and electrophysiological changes that partially resemble those observed with ageing. Physical activity appears to mitigate against aspects of muscle fibre denervation; however, the mechanisms underlying these effects remain incompletely understood. Collectively, the available evidence indicates that denervation in ageing is a multifaceted and dynamic process that requires multimodal, longitudinal approaches to define, detect, and ultimately target denervation-related mechanisms to preserve neuromuscular function across the human lifespan.
Biochemistry, Genetics and Molecular Biology
Cruz BOD et al. · Jul 1, 2026
Introduction The transcription factor BTB and CNC homology 1 (Bach1) represses the nuclear factor erythroid 2-related factor 2 (Nrf2), which controls antioxidant gene expression, and its role in chronic kidney disease (CKD) remains unclear. Methods CKD was induced by 5/6 nephrectomy in rats. Kidney fibrosis and oxidative stress markers were measured. The gene expression of Nrf2, Bach1, and nuclear factor kappa B (NF-κB) was assessed. Results CKD increased oxidative stress markers in plasma, kidney, and heart, as well as promoted kidney fibrosis. Moreover, CKD reduced cardiac Nrf2 expression. However, Bach1, Nrf2, and NF-κB remained unchanged in the kidney. Conclusion CKD did not modulate Bach1 mRNA levels in the kidneys of 5/6 nephrectomized rats.
Biochemistry, Genetics and Molecular Biology
Bergdoll L et al. · Jul 1, 2026
Gating by voltage-dependent anion channels (VDAC) regulates mitochondrial metabolite flux, yet the structural mechanism underlying the open-to-closed transition remains unresolved. Here, we combine atomistic molecular dynamics (MD) simulations with double electron-electron resonance (DEER), using hydrostatic pressure as a reversible thermodynamic perturbation to shift conformational equilibria and stabilize low-population states. MD simulations reveal localized intrinsic flexibility within β-strands β1-β5 and β19, as well as in cytosolic loops connecting β6-β7 and β8-β9. High-pressure DEER measurements in lipid nanodiscs corroborate these predictions, identifying reversible, pressure-dependent distance changes within the pore lumen consistent with asymmetric deformation of the β-barrel. DEER-informed analysis of unbiased MD trajectories reveals an elliptical β-barrel conformation aligned parallel to the N-terminal helix that corresponds to the pressure-stabilized experimental state. ATP permeation simulations identify a free-energy barrier to metabolite translocation in this elliptical geometry, whereas diffusion through the circular open state is energetically favorable. These findings indicate that the elliptical conformation represents a transient gating-competent state rather than a fully closed channel. Together, our results support a gating mechanism driven by reversible β-barrel deformation and establish pressure-perturbed DEER integrated with MD as a general strategy for capturing transient, functionally relevant conformations of membrane channels.
Biochemistry, Genetics and Molecular Biology
Link SC et al. · Jul 1, 2026
Formal risk assessment considers characteristics such as proximity, dose, and vulnerability. However, public risk perception may also be influenced by other-possibly less relevant-factors such as visibility and novelty. The introduction of 5G and its associated infrastructure and radiofrequency electromagnetic fields (RF-EMF) may therefore change perceptions of RF-EMF from mobile communications in general. To explore this, we conducted an online survey in 10 European countries (n = 10,358) using a picture-based approach. Respondents perceived daily RF-EMF exposures as moderate but expected them to increase with 5G. A mobile phone at the ear was generally associated with higher perceived exposure than multiple base stations. Overall, distance to the RF-EMF source most strongly influenced perceived exposure, followed by the number of sources. 5G reception was linked to higher exposure perception than 4G or Wi-Fi reception. These patterns were consistent across most countries. We conclude that when assessing RF-EMF exposure, people rely on heuristics (e.g., more sources imply more exposure) that often guide them correctly. Understanding when and why people feel particularly exposed can help develop more effective communication about true levels of exposure and risk.
Biochemistry, Genetics and Molecular Biology
da Silva ARP et al. · Jul 1, 2026
The development of antifungal resistance is a complex process that involves the interaction between hosts, drugs, and microbial factors, all of which contribute to therapeutic ineffectiveness. For this reason, studies on natural products as possible therapeutic alternatives are increasingly necessary in order to gain a better understanding of plant compounds that may be more effective in treating infections caused by fungal pathogens. In this context, this study aimed to investigate the antifungal potential of the saponin-enriched fraction of the Sarcomphalus joazeiro species against the Candida albicans, Candida tropicalis, and Candida krusei strains. The selection of this species for study is due to its rich phytochemical composition and the vast traditional knowledge of its medicinal properties. The fraction obtained from the stem bark of S. joazeiro was analyzed by UPLC-QTOF-MS/MS, in which compounds such as triterpenoids, flavonoids, acids, and saponins were identified. Therefore, the results obtained in this study contribute to understanding the antifungal potential of the S. joazeiro species fraction against fungal infections, especially those caused by Candida spp.
Biochemistry, Genetics and Molecular Biology