Natl Sci Rev. 2024 Sep 25;11(11):nwae340. doi: 10.1093/nsr/nwae340. eCollection 2024 Nov.

NO ABSTRACT

PMID:39555105 | PMC:PMC11565237 | DOI:10.1093/nsr/nwae340

bioRxiv [Preprint]. 2024 Oct 28:2024.10.23.619908. doi: 10.1101/2024.10.23.619908.

ABSTRACT

Existing antibody language models (LMs) are pre-trained using a masked language modeling (MLM) objective with uniform masking probabilities. While these models excel at predicting germline residues, they often struggle with mutated and non-templated residues, which are crucial for antigen-binding specificity and concentrate in the complementarity-determining regions (CDRs). Here, we demonstrate that preferential masking of the non-templated CDR3 is a compute-efficient strategy to enhance model performance. We pre-trained two antibody LMs (AbLMs) using either uniform or preferential masking and observed that the latter improves residue prediction accuracy in the highly variable CDR3. Preferential masking also improves antibody classification by native chain pairing and binding specificity, suggesting improved CDR3 understanding and indicating that non-random, learnable patterns help govern antibody chain pairing. We further show that specificity classification is largely informed by residues in the CDRs, demonstrating that AbLMs learn meaningful patterns that align with immunological understanding.

PMID:39553994 | PMC:PMC11565838 | DOI:10.1101/2024.10.23.619908

Plant Direct. 2024 Nov 15;8(11):e70017. doi: 10.1002/pld3.70017. eCollection 2024 Nov.

ABSTRACT

RNA interference (RNAi) is a crucial mechanism in immunity against infectious microbes through the action of DICER-LIKE (DCL) and ARGONAUTE (AGO) proteins. In the case of the taxonomically diverse fungal pathogen Botrytis cinerea and the oomycete Hyaloperonospora arabidopsidis, plant DCL and AGO proteins have proven roles as negative regulators of immunity, suggesting functional specialization of these proteins. To address this aspect in a broader taxonomic context, we characterized the colonization pattern of an informative set of DCL and AGO loss-of-function mutants in Arabidopsis thaliana upon infection with a panel of pathogenic microbes with different lifestyles, and a fungal mutualist. Our results revealed that, depending on the interacting pathogen, AGO1 acts as a positive or negative regulator of immunity, while AGO4 functions as a positive regulator. Additionally, AGO2 and AGO10 positively modulated the colonization by a fungal mutualist. Therefore, analyzing the role of RNAi across a broader range of plant-microbe interactions has identified previously unknown functions for AGO proteins. For some pathogen interactions, however, all tested mutants exhibited wild-type-like infection phenotypes, suggesting that the roles of AGO and DCL proteins in these interactions may be more complex to elucidate.

PMID:39553386 | PMC:PMC11565445 | DOI:10.1002/pld3.70017

PeerJ. 2022 Oct 14;10:e14183. doi: 10.7717/peerj.14183. eCollection 2022.

ABSTRACT

The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.

PMID:39552792 | PMC:PMC11566503 | DOI:10.7717/peerj.14183

J Comp Neurol. 2024 Nov;532(11):e25680. doi: 10.1002/cne.25680.

ABSTRACT

In Batesian mimicry, mimetic traits are not always as convincing as predicted by theory-in fact, inaccurate mimicry with only a superficial model resemblance is common and taxonomically widespread. The "selection trade-offs hypothesis" proposes a life-history trade-off between accurate mimetic traits and one or more vital biological functions. Here, using an accurate myrmecomorphic (ant-mimicking) jumping spider species, Myrmarachne smaragdina, we investigate how myrmecomorphic modifications to the body shape impact the internal anatomy in a way that could be functionally limiting. Specifically, via x-ray micro-computed tomography (microCT), we quantify how the spider's constricted prosoma, which emulates the head and thorax of ants, impacts the size of the central nervous system (CNS) and the venom glands. Although, relative to their whole-body mass, we found no significant difference in venom gland volume, the CNS of the ant-mimicking jumping spider was significantly smaller when compared with a relatively closely related non-mimic jumping spider, indicating that some trade-off between mimic accuracy and size of neural anatomy, as articulated by the "selection trade-offs hypothesis," is a possibility. Our explorative evidence enables and encourages broader investigation of how variable mimic accuracy impacts the neuroanatomy in ant mimics as a direct test of the "selection trade-offs hypothesis."

PMID:39552208 | DOI:10.1002/cne.25680

Biosystems. 2024 Nov 15:105363. doi: 10.1016/j.biosystems.2024.105363. Online ahead of print.

ABSTRACT

Understanding circadian clock mechanisms is fundamental in order to counteract the harmful effects of clock malfunctioning and associated diseases. Biochemical, genetic and systems biology approaches have provided invaluable information on the mechanisms of the circadian clock, from which many mathematical models have been developed to understand the dynamics and quantitative properties of the circadian oscillator. To better analyze and compare quantitatively all these circadian cycles, we propose a method based on a previously proposed circadian cycle segmentation into stages. We notably identify a sequence of eight stages that characterize the progress of the circadian cycle. Next, we apply our approach to an experimental dataset and to five different models, all built with ordinary differential equations. Our method permits to assess the agreement of mathematical model cycles with biological properties or to detect some inconsistencies. As another application of our method, we provide insights on how this segmentation into stages can help to analyze the effect of a clock gene loss of function on the dynamic of a genetic oscillator. The strength of our method is to provide a benchmark for characterization, comparison and improvement of new mathematical models of circadian oscillators in a wide variety of model systems.

PMID:39551427 | DOI:10.1016/j.biosystems.2024.105363

Clin Immunol. 2024 Nov 15:110398. doi: 10.1016/j.clim.2024.110398. Online ahead of print.

ABSTRACT

Multiple sclerosis (MS) is a chronic, multifactorial, inflammatory and demyelinating disease of the central nervous system (CNS), which involves an autoimmune response against components of the myelin sheaths. Anti-B cell therapies have been proven to be successful in reducing relapses. Therefore, the study of B cells in both phases of the disease (relapse and remission) is of great importance. Here, we analyzed peripheral blood-cell BCR repertoire from 11 MS patients during a relapse phase and during remission, 6 patients with other inflammatory neurological diseases (OIND) and 10 healthy subjects (HCs), using next generation sequencing. In addition, immunoglobulins G, M, A and D were quantified in the serum of patients and controls, using ELISA. BCR repertoire of relapsing MS patients showed lower diversity, as well as a higher rate of somatic hypermutation compared to the other study groups. Within this group, the highest percentage of shared clonotypes was observed. IGHV4-32 gene was identified as a potential differential biomarker between MS and OIND, as well as IGL3-21 gene as a potential MS biomarker. On the other hand, an elevation of IgG and IgD was found in the serum of MS patients during remission, and the serum IgG was also elevated in MS patients during relapse. In conclusion, these results show the important role of B cells in the pathogenesis of the MS relapses and a new panorama on the analysis of the peripheral blood BCR repertoire to obtain diagnostic tools for MS. Furthermore, this work highlights the need of studies in diverse populations, since results reported in Caucasian populations may not coincide with the immunological course of MS patients in other latitudes, due to differences in genetic background and environmental exposures.

PMID:39551364 | DOI:10.1016/j.clim.2024.110398

NPJ Biofilms Microbiomes. 2024 Nov 16;10(1):128. doi: 10.1038/s41522-024-00588-4.

ABSTRACT

Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.

PMID:39550371 | DOI:10.1038/s41522-024-00588-4

Nat Commun. 2024 Nov 16;15(1):9946. doi: 10.1038/s41467-024-54147-8.

ABSTRACT

Activities of ATP binding cassette (ABC) proteins are regulated by multiple mechanisms, including protein interactions, phosphorylation, proteolytic processing, and/or oligomerization of the ABC protein itself. Here we present the structure of yeast cadmium factor 1 (Ycf1p) in its mature form following cleavage by Pep4p protease. Ycf1p, a C subfamily ABC protein (ABCC), is homologue of human multidrug resistance protein 1. Remarkably, a portion of cleaved Ycf1p forms a well-ordered dimer, alongside monomeric particles also present in solution. While numerous other ABC proteins have been proposed to dimerize, no high-resolution structures have been reported. Both phosphorylation of the regulatory (R) region and ATPase activity are lower in the Ycf1p dimer compared to the monomer, indicating that dimerization affects Ycf1p function. The interface between Ycf1p protomers features protein-protein interactions and contains bound lipids, suggesting that lipids stabilize the dimer. The Ycf1p dimer structure may inform the dimerization interfaces of other ABCC dimers.

PMID:39550367 | DOI:10.1038/s41467-024-54147-8

Cell Signal. 2024 Nov 14:111505. doi: 10.1016/j.cellsig.2024.111505. Online ahead of print.

ABSTRACT

The DLC (Deleted in Liver Cancer) family of RhoGAP (Rho GTPase-activating) proteins has been extensively studied since the identification of the first family member nearly 30 years ago. Rho GTPase signaling is essential for various cellular processes, including cytoskeletal dynamics, cell migration, and proliferation. Members of the DLC family are key regulators of this signaling pathway, with well-established roles in development and carcinogenesis. Here, we provide a comprehensive review of research into DLC regulation and cellular functions over the last three decades. In particular, we summarize control mechanisms of DLC gene expression at both the transcriptional and post-transcriptional level. Additionally, recent advances in understanding the post-translational regulation of DLC proteins that allow for tuning of protein activity and localization are highlighted. This detailed overview will serve as resource for future studies aimed at further elucidating the complex regulatory mechanisms of DLC family proteins and exploring their potential as targets for therapeutic applications.

PMID:39549821 | DOI:10.1016/j.cellsig.2024.111505

Cell. 2024 Nov 12:S0092-8674(24)01216-9. doi: 10.1016/j.cell.2024.10.034. Online ahead of print.

ABSTRACT

Stress induces aversive memory overgeneralization, a hallmark of many psychiatric disorders. Memories are encoded by a sparse ensemble of neurons active during an event (an engram ensemble). We examined the molecular and circuit processes mediating stress-induced threat memory overgeneralization in mice. Stress, acting via corticosterone, increased the density of engram ensembles supporting a threat memory in lateral amygdala, and this engram ensemble was reactivated by both specific and non-specific retrieval cues (generalized threat memory). Furthermore, we identified a critical role for endocannabinoids, acting retrogradely on parvalbumin-positive (PV+) lateral amygdala interneurons in the formation of a less-sparse engram and memory generalization induced by stress. Glucocorticoid receptor antagonists, endocannabinoid synthesis inhibitors, increasing PV+ neuronal activity, and knocking down cannabinoid receptors in lateral amygdala PV+ neurons restored threat memory specificity and a sparse engram in stressed mice. These findings offer insights into stress-induced memory alterations, providing potential therapeutic avenues for stress-related disorders.

PMID:39549697 | DOI:10.1016/j.cell.2024.10.034

Ecotoxicol Environ Saf. 2024 Nov 15;288:117344. doi: 10.1016/j.ecoenv.2024.117344. Online ahead of print.

ABSTRACT

Endosulfan, recognized as an endocrine disruptor, has emerged as an important risk factor for human breast cancer. The chemokine ligand 5 (CCL5) and its receptor CCR5 constitute a biological axis, that is implicated in tumorigenesis and cancer progression. However, the role of the CCL5/CCR5 axis in breast cancer when exposure to endosulfan remains unclear. The present study aimed to determine the significance of the CCL5/CCR5 axis in the carcinogenic effects of endosulfan in human breast cancer MCF-7 cells. The results showed that endosulfan significantly promoted cell proliferation, increased the rate of colony formation, and enhanced cell migration ability in a dose-dependent manner by activating the PI3K/AKT signaling pathway, which were rescued by the specific inhibitor (LY-294002) for PI3K/AKT signaling pathway. We utilized Cytoscape software to construct protein-protein interaction (PPI) network when exposure to endosulfan, and identified 47 highly connected genes in the network diagram centered on CCL5. Endosulfan significantly increased the secretion of CCL5 and the expression levels of CCL5/CCR5, which were reversed by CCR5 inhibitor (HY-13004). HY-13004 significantly counteracted the effects of endosulfan on colony formation, cell migration and the activation of PI3K/AKT signaling pathway. Endosulfan markedly altered the expression levels of epithelial-mesenchymal transition (EMT) biomarkers and enhanced transwell migration and invasion capabilities of MCF-7 cells, which were inhibited by HY-13004, similar to the effects observed with LY-294002. Collectively, our findings suggest that endosulfan activates the PI3K/AKT signaling pathway to promote cell growth, and induces EMT, thereby enhancing cell migration and invasion via the CCL5/CCR5 axis in MCF-7 cells.

PMID:39549571 | DOI:10.1016/j.ecoenv.2024.117344

Mutat Res. 2024 Nov 8;830:111886. doi: 10.1016/j.mrfmmm.2024.111886. Online ahead of print.

ABSTRACT

Formaldehyde and acetaldehyde are reactive, small compounds that humans are exposed to routinely, variously from endogenous and exogenous sources. Both small aldehydes are classified as human carcinogens. Investigation of the DNA damaging properties of these two compounds began some 50 years ago. In this review, we summarize progress in this field since its inception over half a century ago, distilling insights gained by the collective efforts of many research groups while highlighting areas for future directions. Over the decades, general consensus about aspects of the mutagenicity of formaldehyde and acetaldehyde has been reached. But other characteristics of formaldehyde and acetaldehyde remain incompletely understood and require additional investigation. These include crucial details about the mutational signature(s) induced and possible mechanistic role(s) during carcinogenesis.

PMID:39549522 | DOI:10.1016/j.mrfmmm.2024.111886

J Chromatogr A. 2024 Nov 9;1738:465513. doi: 10.1016/j.chroma.2024.465513. Online ahead of print.

ABSTRACT

Studies surrounding deamidation have relied on the chromatographic and mass spectrometric differentiation of Asn containing peptides and their isomeric Asp and isoAsp products. The development of mass spectrometry analytical techniques and characterization of isomer specific fragmentation patterns has permitted the investigation of some deamidation species but has struggled to remain effective when applied and on complex samples or in high throughput scenarios. On the other hand, chromatographic separations can provide additional information to facilitate detection of deamidation. In this work the retention characteristics of deamidation products have been reported in reversed-phase separations using formic acid as an ion-pairing modifier. We found three major elution patterns depending on primary and secondary structure of Asn-Gly containing tryptic peptides. Random coil, helical conformations, and N-terminal positioning of Asn usually result in Asn < isoAsp < Asp, isoAsp < Asn < Asp, and Asn < Asp < isoAsp elution order, respectively. These trends, found from the analyses of proteomic samples, were subsequently confirmed via analytical scale UV-HPLC. Additionally, we determined the retention shifts following deamidation for twenty various separation settings used as a first-dimension fractionation for high-throughput proteomic 2D LC-MS/MS analyses.

PMID:39549499 | DOI:10.1016/j.chroma.2024.465513

Oral Oncol. 2024 Nov 15;159:107107. doi: 10.1016/j.oraloncology.2024.107107. Online ahead of print.

ABSTRACT

INTRODUCTION: A substantial proportion of head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is associated with human papillomavirus (HPV), resulting in distinct molecular phenotypes. In this study, we investigated differential immune checkpoint molecule (ICM) expression by HPV status using RNA sequencing data to identify additional ICM targets that may complement anti-PD1 antibodies.

MATERIAL AND METHODS: RNA sequencing was performed on 51 OPSCC cases and validated using the TCGA HNSCC dataset. Unsupervised clustering and differential gene expression analyses in R were conducted based on HPV status. Additionally, a published single-cell RNA sequencing (scRNA) dataset of tumor-infiltrating lymphocytes (TIL) and peripheral immune cells (PBMC) (GSE139324) was analyzed with a Seurat pipeline grouped by HPV status.

RESULTS: Our study identified a significant upregulation of all examined ICM in HPV-positive OPSCC through bulk RNA sequencing, validated by the TCGA cohort. Unsupervised clustering revealed a strong association between HPV-positive/-negative and high/low ICM expression cases respectively, indicating overlap between ICM and HPV status. In scRNA analysis, CD27, PD-1, OX-40, and BTLA were significantly more highly expressed on TILs of HPV-positive OPSCC. Conversely, VSIR was increased in PBMC and TILs of HPV-negative OPSCC, while LAG3 expression on PBMC was reduced in HPV-negative OPSCC.

CONCLUSION: Our study unveils the intricate interplay of ICMs in OPSCC, emphasizing the necessity for personalized therapeutic approaches based on HPV status and immune profiles. The identified ICMs, including PD1, CD27, and CTLA4, are promising candidates for further investigation and may enhance immunotherapeutic interventions in the HPV-dependent treatment strategies for OPSCC.

PMID:39549431 | DOI:10.1016/j.oraloncology.2024.107107

Aquat Toxicol. 2024 Nov 14;277:107165. doi: 10.1016/j.aquatox.2024.107165. Online ahead of print.

ABSTRACT

As an emerging contaminant, microplastics (MPs) are widely distributed in freshwater ecosystems and pose potential threats to aquatic organisms, attracting significant attention from both the scientific community and the general public. However, there is still uncertainty regarding the mechanisms of MPs transfer within aquatic biota and how particle size and food availability influence their transport patterns. In this study, zebrafish (Danio rerio) were selected as a model organism to investigate the uptake and elimination of fluorescent polyethylene (PE) MPs under different exposure scenarios (waterborne or trophic transfer, with or without food) and varying particle sizes (ranging from 10-300 μm at concentrations of 0.1, 2, and 300 mg/L). Additionally, water fleas (Daphnia magna) were provided as prey for the fish. The dynamic accumulation of PE-MPs sized between 10-20 μm at a concentration of 25 mg/L by daphnia was also determined along with its impact on animal feeding behavior. The results demonstrated that both organisms were capable of ingesting PE-MPs during exposures lasting up to 24 hours for daphnia and up to 72 hours for zebrafish. Furthermore, rapid elimination rates were observed within just 30 minutes for daphnia and between 6-12 hours for zebrafish. The presence of food reduced MPs uptake and removal by daphnia but significantly increased MP elimination by fish. Zebrafish showed a preference for ingesting larger-sized MPs that they could easily recognize; however, trophic transfer from daphnia to fish was found to be the primary route of ingestion specifically for PE-MPs sized between 10-20 μm. The findings suggest that while fish directly ingest fewer invisible MPs from the water column, they still accumulate these particles through predation on contaminated prey organisms. Therefore, it is imperative to prioritize the ecological risks associated with the transfer of MPs from zooplankton to fish.

PMID:39549359 | DOI:10.1016/j.aquatox.2024.107165

Iran J Allergy Asthma Immunol. 2024 Jul 27;23(4):393-402. doi: 10.18502/ijaai.v23i4.16213.

ABSTRACT

The coronavirus disease 2019 (CVOID-19) has varied clinical manifestations including mild to severe acute respiratory symptoms. Inflammasome complex and mitochondria play an important role in initiating inflammatory responses and could potentially be affected by this infection. To study the inflammasome and mitochondrial fission and fusion gene expression levels in COVID-19 patients, we designed this experiment. The inflammasome and mitochondrial gene expression profiles were determined by real-time polymerase chain reaction in the peripheral blood of 70 hospitalized CVOID-19 patients with mild to moderate symptoms (HOSP) and 30 ICU patients with severe symptoms (ICU) compared to 20 healthy controls (HC). The results indicated that the expression of the dynamin-related protein-1 was extremely suppressed in HOSP while it came back to the normal range in the ICU group. However, the expression of fission 1 protein had a non-significant increase in HOSP and a decrease in the ICU group. The mitofusin-1 and dominant optic atrophy genes showed high expression levels (10-fold) and (70-fold), respectively, in the HOSP group. However, mitofusin-2 significantly decreased in both groups. Although leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) and apoptosis-associated speck-like protein containing a caspase activating and recruitment domain genes dramatically increased in both groups (10 and 4-fold), other inflammasome genes declined in both groups. Finally, Nuclear factor kappa-light-chain-enhancer of activate d B cells (NF-κB) extremely decreased, and Intreleukine-1 showed high expression in ICU patients (3-fold). CVOID-19 infection suppresses the fission genes and elevates the fusion gene expression in mitochondria, and it can cause activation of the inflammasome via the NLRP3 pathway.

PMID:39549292 | DOI:10.18502/ijaai.v23i4.16213

STAR Protoc. 2024 Nov 15;5(4):103446. doi: 10.1016/j.xpro.2024.103446. Online ahead of print.

ABSTRACT

An in vitro cell model mimicking human 8C blastomeres would be invaluable to understanding the mechanisms regulating major zygote genome activation (ZGA) in humans. Here, we present a protocol for deriving human preimplantation epiblast stem cells and 8-cell embryo-like cells. We describe steps for developing an 8C-specific GFP reporter (8C::GFP) and capturing the rare human 8C-like cells (8CLCs) from human preimplantation epiblast-like stem cells (prEpiSCs). We then detail procedures for optimizing the culture condition to extend 8CLC culturing. For complete details on the use and execution of this protocol, please refer to Yu et al.1.

PMID:39549238 | DOI:10.1016/j.xpro.2024.103446

Adv Mater. 2024 Nov 16:e2410368. doi: 10.1002/adma.202410368. Online ahead of print.

ABSTRACT

Orofacial muscles are particularly prone to refractory fibrosis after injury, leading to a negative effect on the patient's quality of life and limited therapeutic options. Gaining insights into innate inflammatory response-fibrogenesis homeostasis can aid in the development of new therapeutic strategies for muscle fibrosis. In this study, the crucial role of macrophages is identified in the regulation of orofacial muscle fibrogenesis after injury. Hypothesizing that orchestrating macrophage polarization and functions will be beneficial for fibrosis treatment, nanomaterials are engineered with polyethylenimine functionalization to regulate the macrophage phenotype by capturing negatively charged cell-free nucleic acids (cfNAs). This cationic nanomaterial reduces macrophage-related inflammation in vitr and demonstrates excellent efficacy in preventing orofacial muscle fibrosis in vivo. Single-cell RNA sequencing reveals that the cationic nanomaterial reduces the proportion of profibrotic Gal3+ macrophages through the cfNA-mediated TLR7/9-NF-κB signaling pathway, resulting in a shift in profibrotic fibro-adipogenic progenitors (FAPs) from the matrix-producing Fabp4+ subcluster to the matrix-degrading Igf1+ subcluster. The study highlights a strategy to target innate inflammatory response-fibrogenesis homeostasis and suggests that cationic nanomaterials can be exploited for treating refractory fibrosis.

PMID:39548911 | DOI:10.1002/adma.202410368

Protein Sci. 2024 Dec;33(12):e5206. doi: 10.1002/pro.5206.

ABSTRACT

We earlier showed that Torpedo californica acetylcholinesterase (AChE) contains a cluster of four conserved aspartates that can strongly bind divalent cations, which we named the 4D motif. Binding of the divalent metal cations greatly increases its thermal stability. Here we systematically examined all available crystallographic structures of T. californica AChE. Two additional metal-binding sites were identified, both composed of acidic and histidine residues. Relative binding to the 4D and additional sites was studied using metadynamics simulations. It was observed that in crystal structures devoid of metal ions in the 4D site, the conformation of T. californica AChE is almost identical to that in structures in which it is occupied by a divalent metal ion. Closer examination of the 4D motif reveals that three of the four acidic residues form ion pairs with conserved basic residues surrounding them. We named this new motif the 4A/3B motif. Molecular dynamics with quantum potential simulations was used to quantify the 4D motif's binding strength compared with that of the metal-binding site in the protein fXIIIa, which consists of four aspartates, but is devoid of adjacent cationic residues. Whereas fXIIIa's 4D site, in the absence of a metal cation, expanded significantly in the simulation, that of Torpedo AChE displayed only minor periodic changes in size. Furthermore, the energy of metal ion unbinding from the two sites differs by ca. 10 kcal/mol. We identified several other proteins in the PDB that contain the 4A/3B motif, whose conformations are identical in the presence or absence of a metal ion. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:Protein_Science:4.

PMID:39548604 | DOI:10.1002/pro.5206