Front Oncol. 2025 Jul 17;15:1652368. doi: 10.3389/fonc.2025.1652368. eCollection 2025.

NO ABSTRACT

PMID:40746608 | PMC:PMC12310605 | DOI:10.3389/fonc.2025.1652368

Front Mol Biosci. 2025 Jul 17;12:1593810. doi: 10.3389/fmolb.2025.1593810. eCollection 2025.

ABSTRACT

INTRODUCTION: Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia across various organs, leading to recurrent respiratory infections, subfertility, and laterality defects. While several diagnostic tools exist-such as high-speed video microscopy, immunofluorescence staining, electron microscopy, and genetic screening-the relationship between different pathogenic variants within a single PCD gene and their effects on ciliary composition, structure, and clinical phenotype remains poorly understood.

METHODS: To investigate this, we analyzed cilia from PCD patients with different mutations in axonemal dynein heavy chain dnah5 using mass spectrometry and cryo-electron tomography. These methods allowed us to examine both the protein composition and ultrastructural organization of motile cilia in affected individuals.

RESULTS: Though all analyzed patients present similarly in traditional diagnostic methods, we observed differences in axonemal composition among patients carrying different dnah5 mutations. Specific reductions in ciliary components varied between individuals, indicating a mutation-specific impact. Notably, proteins such as VWA3B, KIAA1430/CFAP97, and DTHD1-not previously identified as components of human respiratory motile cilia-were detected in wild type cilia, but not in patient cilia. Lastly, we confirmed some changes in protein abundance in the 96-nm repeated unit of the axoneme between wild-type and PCD samples.

DISCUSSION: These findings suggest that mutations in dnah5 result in varied and specific alterations in axonemal composition, reflecting the heterogeneity of the disease at the molecular level. The discovery of novel ciliary proteins and mutation-specific differences enhances our understanding of the complexity of PCD pathogenesis and may inform future diagnostic and therapeutic strategies.

PMID:40746421 | PMC:PMC12310455 | DOI:10.3389/fmolb.2025.1593810

Gut Microbes. 2025 Dec;17(1):2539452. doi: 10.1080/19490976.2025.2539452. Epub 2025 Aug 1.

ABSTRACT

The upper gastrointestinal (uGI) microbiota has been implicated in infectious, metabolic, and immunological conditions, yet remains poorly characterized due to invasive sampling and low microbial biomass. We developed and validated a contamination-controlled 16S rRNA gene and transcript-based protocol to profile the murine and human uGI microbiota from low-biomass samples. We applied this protocol to murine esophageal, gastric, and duodenal tissues, and to human saliva, gastric, and duodenal aspirates from patients undergoing endoscopy for suspected food-related, mild GI symptoms. Our objective was to identify conserved compositional and structural uGI microbiota patterns and assess their clinical relevance in relation to pathogen burden and inflammation. In mice, we found evidence for transcriptionally inactive and active intestinal taxa along the uGI tract, supporting horizontal microbiota transfer. In humans, we identified two distinct, inversely correlated salivary microbiota types - one dominated by the Prevotella 7 genus - which were conserved in the duodenum. The Prevotella 7-dominated uGI microbiota type was associated with lower relative abundances of gastrointestinal and extraintestinal opportunistic pathogens. These patterns were reproducible in an independent cohort and associated with lower systemic TNF-α levels. Our findings suggest that noninvasive salivary microbiota profiling can stratify individuals based on uGI microbiota composition and inflammation-associated risk traits, offering new opportunities for clinical applications and translational studies.

PMID:40746257 | DOI:10.1080/19490976.2025.2539452

Disabil Rehabil. 2025 Jul 31:1-17. doi: 10.1080/09638288.2025.2536722. Online ahead of print.

ABSTRACT

PURPOSE: The present study aimed to summarize the current evidence on the impact of exercise in patients at risk or with breast cancer-related lymphedema (BCRL) through an umbrella review of existing meta-analysis and a systematic review and meta-analysis of randomized controlled trials (RCTs).

MATERIAL AND METHODS: A search was conducted in PubMed and Web of Science up to June 2025 to identify meta-analyses and RCTs that included exercise interventions in patients at risk or with BCRL.

RESULTS: Three systematic reviews including 14 individual meta-analyses were included in the umbrella review. Two of these met the criteria of strong evidence, reporting beneficial effects of exercise on upper- and lower-body strength. A total of 46 RCTs were included in the systematic review, of which 11 could be meta-analyzed. Strong evidence was found for a beneficial effect of exercise on upper- and lower-body strength and upper-limb disability.

CONCLUSION: Strong evidence supports the beneficial effects of exercise on upper- and lower-body strength and upper-limb disability in patients at risk or with BCRL.

PMID:40745968 | DOI:10.1080/09638288.2025.2536722

Nat Rev Gastroenterol Hepatol. 2025 Jul 31. doi: 10.1038/s41575-025-01100-9. Online ahead of print.

ABSTRACT

The microbiome has critical roles in human health and disease. Advances in high-throughput sequencing and metabolomics have revolutionized our understanding of human gut microbial communities and identified plausible associations with a variety of disorders. However, microbiome research remains constrained by challenges in establishing causality, an over-reliance on correlative studies, and methodological and analytical limitations. Artificial intelligence (AI) has emerged as a powerful tool to address these challenges; however, the seamless integration of preclinical models and clinical trials is crucial to maximizing the translational impact of microbiome studies. This manuscript critically evaluates best methodological practices and limitations in the field, focusing on how emerging AI tools can bridge the gap between microbial insights and clinical applications. Specifically, we emphasize the necessity of rigorous, reproducible methodologies that integrate multiomics approaches, preclinical models and clinical trials in the AI-driven era. We propose a practical framework for applying AI to microbiome studies, alongside strategic recommendations for clinical trial design, regulatory pathways, and best practices for microbiome-based informed diagnostics, AI training and clinical interventions. By establishing these guidelines, we aim to accelerate the translation of microbiome research into clinical practice, enabling precision medicine approaches informed by the human microbiome.

PMID:40745489 | DOI:10.1038/s41575-025-01100-9

NPJ Syst Biol Appl. 2025 Jul 31;11(1):84. doi: 10.1038/s41540-025-00570-6.

ABSTRACT

Universal differential equations (UDEs) are an emerging approach in biomedical systems biology, integrating physiology-driven mathematical models with machine learning for data-driven model discovery in areas where knowledge of the underlying physiology is limited. However, current approaches to training UDEs do not directly accommodate heterogeneity in the underlying data. As a data-driven approach, UDEs are also vulnerable to overfitting and consequently cannot sufficiently generalize to heterogeneous populations. We propose a conditional UDE (cUDE) where we assume that the structure and weights of the embedded neural network are common across individuals, and introduce a conditioning parameter that is allowed to vary between individuals. In this way, the cUDE architecture can accommodate inter-individual variation in data while learning a generalizable network representation. We demonstrate the effectiveness of the cUDE as an extension of the UDE framework by training a cUDE model of c-peptide production. We show that our cUDE model can accurately describe postprandial c-peptide levels in individuals with normal glucose tolerance, impaired glucose tolerance, and type 2 diabetes mellitus. Furthermore, we show that the conditional parameter captures relevant inter-individual variation. Subsequently, we use symbolic regression to derive a generalizable analytical expression for c-peptide production.

PMID:40744933 | DOI:10.1038/s41540-025-00570-6

Nucleic Acids Res. 2025 Jul 19;53(14):gkaf739. doi: 10.1093/nar/gkaf739.

ABSTRACT

Yeast ribosomal protein gene RPL7B is autoregulated by inhibition of splicing. The first intron has a "zipper stem" that brings the 5' splice site near the branch point (BP) and serves as an enhancer of splicing that is required for efficient splicing because the intron has a nonconsensus BP sequence of UGCUAAC. The intron also contains an alternative, and mutually exclusive, structure that is conserved across many yeast species. That conserved structure is a binding site for the Rpl7 protein so that when the protein is in excess over what is required for ribosomes, the protein binds to the conserved structure which eliminates the enhancer structure and represses splicing and gene expression.

PMID:40744491 | DOI:10.1093/nar/gkaf739

Biochem Pharmacol. 2025 Jul 29:117201. doi: 10.1016/j.bcp.2025.117201. Online ahead of print.

ABSTRACT

Alzheimer's disease is a severe neurological disorder and the most prevalent form of dementia, characterized by cognitive impairment and hypomnesia. The accumulation and aggregation of Amyloid-β peptides are central to AD pathology, triggering neuroinflammation and neuronal cell death. This study aims to investigate the molecular mechanisms underlying Aβ aggregation and its impact on neuronal function, and to explore potential therapeutic strategies, including peptide-based small molecules, for AD. We analyzed the role of Aβ in neuroinflammation and mitochondrial dysfunction using various in vitro and in vivo models. Structural characterization of the Aβ-TTR complex was performed using cryo-electron microscopy to understand the molecular interactions involved. The study reveals that Aβ aggregation leads to the activation of microglia, increased production of reactive oxygen species, and mitochondrial dysfunction, which contribute to neurodegeneration. Peptide-based small molecules demonstrated high specificity in binding to Aβ, inhibiting its aggregation, and reducing cytotoxicity in neuroblastoma cell lines. The TTR peptide (P2) effectively prevented Aβ-induced cytotoxicity and apoptosis by modulating oxidative stress and mitochondrial dynamics. Structural analysis using cryo-electron microscopy identified key interactions between Aβ and TTR, providing insights into their biological activity. The findings highlight the critical role of Aβ aggregation in AD pathogenesis and underscore the potential of peptide-based small molecules as therapeutic candidates. Understanding the structural mechanisms of Aβ and TTR interactions offers new avenues for developing strategies to prevent neurodegeneration and manage AD more effectively.

PMID:40744232 | DOI:10.1016/j.bcp.2025.117201

Microb Pathog. 2025 Jul 29:107933. doi: 10.1016/j.micpath.2025.107933. Online ahead of print.

ABSTRACT

BACKGROUND: Pseudomonas aeruginosa is one of the common bacterial agents in keratitis and is resistant to drugs. Due to the difference in the mechanism of action of antibacterial compounds, phage therapy can be a therapeutic candidate to deal with drug-resistant infections. The purpose of this study is to isolate, identify, and investigate the antimicrobial ability of a phage sample to treat keratitis caused by P. aeruginosa.

MATERIALS AND METHODS: The Bacteriophage (phage) MIZ-Pa99 isolated from hospital wastewater in Tehran, Iran was identified by TEM imaging. The presence of phage was confirmed by the spot technique and its titration was evaluated using the double-layer agar culture method. Phage lytic activity was evaluated through host range determination against P. aeruginosa, S. aureus, and E. coli, and biofilm destruction assays. Phage's novelty was determined through whole-genome sequencing. Phage safety was assessed using in vitro cytotoxicity assays and in vivo Draize eye irritation tests in rabbit eyes. Therapeutic efficacy was investigated in a mouse model using phage eye drops, with bacterial load quantified by CFU counts and tissue damage assessed by histopathology. Also, the antibiotic resistance pattern of Pseudomonas clinical isolates was investigated.

RESULTS: MIZ-Pa99 belongs to the Straboviridae family and the Caudoviricetes order. Whole genome analysis of MIZ-Pa99 phage showed that it belongs to Elvirus genus, and has linear and double-stranded DNA with a length 209,183 bp and a GC content of 49.30%. The anti-biofilm effect of phage was observed on clinical isolates. IC50 of phage (HCE-2) was determined as 10-1 dilution (9.93 × 1011 PFU/mL). The synergistic effect of ciprofloxacin and phage in the form of eye drops was observed in the improvement of keratitis caused by P. aeruginosa.

CONCLUSION: The results obtained in this study indicated that MIZ-Pa99 can be effective in controlling bacterial keratitis infection. However, combined antibiotic and phage treatment has a synergistic effect.

PMID:40744162 | DOI:10.1016/j.micpath.2025.107933

Annu Rev Cell Dev Biol. 2025 Jul 31. doi: 10.1146/annurev-cellbio-101123-051723. Online ahead of print.

ABSTRACT

Biomolecular condensates provide a way to compartmentalize subcellular components with high temporal and spatial resolution, enabling rapid responses to signals and environmental changes. While the formation, components, and function of some condensates are well-characterized, their presence across organisms, their evolutionary history, and their origin are less well-understood. Here, we review the diversity of condensate components and highlight that not only disordered but also fully structured proteins are capable of driving condensate formation. We compare how proteomes of condensates overlap within and across species, and we present functionally analogous condensates across organisms. Additionally, we discuss the potential role of condensation in early life, suggesting that phase separation could have facilitated the selection and concentration of prebiotic molecules, promoting essential biochemical processes. We conclude that condensate-related organization principles are ubiquitously used across organisms from bacteria to mammals, and they potentially played a key role in prebiotic evolution, serving as primitive compartments for early biochemical processes.

PMID:40744081 | DOI:10.1146/annurev-cellbio-101123-051723

Cell Stem Cell. 2025 Jul 28:S1934-5909(25)00261-9. doi: 10.1016/j.stem.2025.07.004. Online ahead of print.

ABSTRACT

White adipose tissue supports essential physiological functions through adipocyte precursor cells (APCs), comprising progenitors and preadipocytes, which generate mature adipocytes during depot expansion. Using single-cell RNA sequencing-based lineage tracing, we characterize APCs in skin adipose tissue-a depot uniquely capable of rapid adipogenesis compared with other sites, such as inguinal adipose. We identify a previously uncharacterized population of immature preadipocytes and reveal distinct differentiation potentials among APCs. Contrary to traditional stepwise differentiation models, progenitors predominantly generate committed preadipocytes, whereas preexisting preadipocytes accumulate in immature states with divergent potential. Leveraging this refined APC hierarchy, we uncover Sox9 as a crucial regulator of progenitor proliferation and adipogenic differentiation. Cross-depot transplantation further demonstrates how intrinsic and extrinsic factors differentially regulate skin progenitor behavior, highlighting distinct adipogenic dynamics between skin and inguinal depots. Together, these insights redefine the cellular hierarchy and molecular mechanisms underpinning rapid adipogenesis in skin adipose tissue.

PMID:40744015 | DOI:10.1016/j.stem.2025.07.004

J Proteome Res. 2025 Jul 31. doi: 10.1021/acs.jproteome.5c00390. Online ahead of print.

ABSTRACT

IgG4-related disease (IgG4-RD) is a rare disease characterized by lymphoplasmatic infiltration and fibrosis in multiple organs, often accompanied by elevated serum levels of IgG4. Considerable efforts have been devoted to the diagnosis of IgG4-related diseases, but its etiology and pathogenesis remain poorly understood. The total serum N-glycome profile can reflect disease phenotypes with specific serum N-glycans serving as potential biomarkers for diagnosis and prognosis. However, the serum N-glycome profile in IgG4-RD has yet to be characterized. In this study, two high-throughput orthogonal strategies, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and lectin-based enzyme-linked immunosorbent assay (ELISA), were employed to analyze serum N-glycome in IgG4-RD and patients undergoing different therapeutic treatments. It was observed that IgG4-RD is associated with a decreased level of galactosylation and an increased level of sialylation. These alterations were further validated through an independent validation set and a lectin-based ELISA assay. Importantly, longitudinal analysis showed a good response of total galactosylation and monosialylated N-glycan (H4N3S1) to drug therapy. Additionally, altered serum N-glycosylation was associated with the routine prognostic indicators for IgG4-RD, including response index (RI), and the levels of IgG4 and IgE. Our study demonstrated the crucial role of N-glycosylation in IgG4-RD, providing new insight into its etiology and pathogenesis.

PMID:40742384 | DOI:10.1021/acs.jproteome.5c00390

J Cell Biol. 2025 Sep 1;224(9):e202507106. doi: 10.1083/jcb.202507106. Epub 2025 Jul 31.

ABSTRACT

In this issue, Kim et al. (https://doi.org/10.1083/jcb.202409078) report that the scaffold protein Arc acts through Crumbs to spatially restrict where actomyosin-based apical constriction occurs across the invaginating Drosophila salivary gland. This restriction is needed for a long, thin tube to form.

PMID:40742383 | DOI:10.1083/jcb.202507106

Bioinformatics. 2025 Jul 31:btaf432. doi: 10.1093/bioinformatics/btaf432. Online ahead of print.

ABSTRACT

MOTIVATION: Accurate structures of protein complexes are essential for understanding biological pathway function. A previous study showed how downstream modifications to AlphaFold 2 could yield AF2Complex, a model better suited for protein complexes. Here, we introduce AF3Complex, a model equipped with both similar and novel improvements, built on AlphaFold 3.

RESULTS: Benchmarking AF3Complex and AlphaFold 3 on a large dataset of protein complexes, it was shown that AF3Complex outperforms AlphaFold 3. Moreover, by evaluating the structures generated by AF3Complex on datasets of protein-peptide complexes and antibody-antigen complexes, it was established that AF3Complex could create high-fidelity structures for these challenging complex types. Additionally, when deployed to generate structural predictions for protein complexes used in the recent CASP16 competition, AF3Complex yielded structures that would have placed it among the top models in the competition.

AVAILABILITY: The AF3Complex code is freely available at https://github.com/Jfeldman34/AF3Complex.git.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:40742329 | DOI:10.1093/bioinformatics/btaf432

mSystems. 2025 Jul 31:e0098425. doi: 10.1128/msystems.00984-25. Online ahead of print.

ABSTRACT

Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.

PMID:40742180 | DOI:10.1128/msystems.00984-25

mBio. 2025 Jul 31:e0060625. doi: 10.1128/mbio.00606-25. Online ahead of print.

ABSTRACT

The emergence of pandemic coronaviruses remains a global health concern, highlighting the need for broadly neutralizing antibodies (bnAbs) that can target multiple sarbecoviruses. In this study, we isolated and characterized a novel antibody, pT1679, that demonstrates exceptional neutralization breadth. The antibody prevented infection with SARS-CoV-2 variants of concern, such as Omicron BA.1, and effectively neutralized pseudotyped viruses displaying S proteins from many SARS-CoV-2 variants and various bat and pangolin sarbecoviruses, including both SARS-CoV-like and SARS-CoV-2-like viruses. In addition, pT1679 reduced the viral load in the lung of infected Syrian hamsters and prevented the severe lung pathology typical for SARS-CoV-2 infections. The cryo-electron microscopy structure of pT1679 in complex with SARS-CoV-2 S revealed that the antibody employs a YYDRxxG motif to recognize a highly conserved epitope on the RBD. Through detailed structural analysis, mutagenesis studies, and binding assays, we identified RBD residue 384 as a critical determinant of antibody recognition. Structure-function analyses of several related bnAbs, such as COVA1-16, allowed for the classification of YYDRxxG antibodies into two distinct groups that differ in neutralization breadth. Our findings provide crucial insights into the molecular basis of broad Sarbecovirus neutralization and offer strategic guidance for selecting therapeutic antibodies in preparation for future Sarbecovirus outbreaks.IMPORTANCEThe threat of emerging coronaviruses demands therapeutic strategies capable of targeting both current and future circulating viruses. We report the discovery and characterization of pT1679, a broadly neutralizing antibody that demonstrates cross-reactivity against diverse sarbecoviruses, including SARS-CoV, SARS-CoV-2 variants, and related viruses from bats and pangolins. pT1679 targets a highly conserved epitope via a YYDRxxG motif in the paratope, with RBD residue 384 serving as a critical determinant of recognition. Our analysis allows for a classification of YYDRxxG antibodies, providing a framework for predicting antibody effectiveness against emerging sarbecoviruses.

PMID:40742150 | DOI:10.1128/mbio.00606-25

J Microbiol Biol Educ. 2025 Jul 31:e0010425. doi: 10.1128/jmbe.00104-25. Online ahead of print.

ABSTRACT

Fate mapping is an essential technique in developmental biology that allows researchers to track the future identity or "fate" of embryonic cells in an organism. However, the experimental procedure for constructing fate maps is tedious, time-consuming, and technically challenging, making it difficult to incorporate as an undergraduate lab experience. Here, we describe a hands-on undergraduate laboratory activity that allows students to generate and examine model organisms' fate maps, employing a free, user-friendly web-based app, FatemapApp (http://fatemapapp.com/). Students used the app to construct the fate maps for the 32-cell stage Xenopus laevis frog embryo, the gastrula stage Danio rerio zebrafish embryo, and the 76-cell stage Holocynthia roretzi tunicate embryo. Individual analysis of the maps allows students to identify the potential of cells to contribute to one or multiple tissues and their probability of moving and mixing with the neighboring cells. Subsequently, cross-species comparative analysis allows students to infer tissue organization across chordate and vertebrate embryos that may be evolutionarily conserved. Surveys showed that the students found this activity engaging and valuable, reporting a deeper understanding of the rationale, methodology, and outcomes underlying the construction of fate maps. Furthermore, students reported increased comprehension of embryonic development and its processes.

PMID:40742142 | DOI:10.1128/jmbe.00104-25

J Cell Sci. 2025 Jul 31:jcs.263539. doi: 10.1242/jcs.263539. Online ahead of print.

ABSTRACT

During phagocytosis, a phagocytic cup grows via F-actin remodelling and localized secretion to entrap a particle within a phagosome, which then fuses with endosomes and lysosomes to digest the particle, followed by phagosome resolution. As spatially limited systems, phagocytes have a maximal phagocytic capacity, at which point further uptake must be blunted. However, the processes responsible for phagocytic appetite exhaustion as phagocytes reach their maximal phagocytic capacity are poorly defined. We found that macrophages at their capacity have lower surface levels of Fcg receptors but overexpression of these receptors did not increase their capacity, suggesting that receptor levels are not limiting. Instead, surface membrane in-folding, membrane tension, and cortical F-actin were all reduced in exhausted macrophages. While this might contribute to appetite suppression, we also found that "free" endosomes and lysosomes were severely depleted in exhausted macrophages. Consequently, focal exocytosis at sites of externally bound particles was blunted. In comparison, macrophages recovered their appetite if phagosome resolution was permitted. We propose that depletion of the endomembrane pools is a major determinant of phagocytic fatigue as macrophages reach their phagocytic capacity.

PMID:40741709 | DOI:10.1242/jcs.263539

Comput Struct Biotechnol J. 2025 Jul 16;27:3216-3228. doi: 10.1016/j.csbj.2025.07.014. eCollection 2025.

ABSTRACT

The activity of G protein-coupled receptors has been generally linked to dynamically interconverting structural and functional states and the process of activation was proposed to be controlled by an interconnecting network of conformational switches in the transmembrane domain. However, it is yet to be uncovered how ligands with different extent of functional effect exert their actions. According to our recent hypothesis, the transmission of the external stimulus is accompanied by the shift of macroscopic polarization in the transmembrane domain, furnished by concerted movements of conserved polar amino acids and the rearrangement of polar species. Previously, we have examined the μ-opioid, β2-adrenergic and type 1 cannabinoid receptors by performing molecular dynamics simulations. Results revealed correlated dynamics of a polar signaling channel connecting the orthosteric binding pocket and the intracellular G protein-binding surface in all three class A receptors. In the present study, the interplay of this polar signaling channel in the activation mechanism was evidenced by systematic mutation of the channel residues of the μ-opioid receptor. Mutant receptors were analyzed utilizing molecular dynamics simulations and characterized in vitro by means of radioligand receptor binding and G protein stimulation assays. Apart from one exception, all mutants failed to bind the endogenous agonist endomorphin-2 and to stimulate the Gi protein complex. Furthermore, mutation results confirmed allosteric connection between the binding pocket and the intracellular surface. The strong association and optimal bioactive orientation of the bound agonist was found to be crucial for the initiation of correlated motions and consequent signaling.

PMID:40741542 | PMC:PMC12309854 | DOI:10.1016/j.csbj.2025.07.014

J Pharm Anal. 2025 Jul;15(7):101180. doi: 10.1016/j.jpha.2024.101180. Epub 2024 Dec 31.

ABSTRACT

Image 1.

PMID:40741339 | PMC:PMC12310053 | DOI:10.1016/j.jpha.2024.101180