Archives of biochemistry and biophysics最新文献

{"title":"Protein misfolding, aggregation and other factors determining the amyloidogenic landscape of human leucocyte chemotaxin-2: A review","authors":"Akhilesh Kumar ,&nbsp;Sudarshan Singh Lakhawat ,&nbsp;Naveen Malik ,&nbsp;Vinay Sharma ,&nbsp;Yashdeep Singh ,&nbsp;Ananya Jain ,&nbsp;Vinod Sharma ,&nbsp;Sandeep Singh ,&nbsp;Pushpender Kumar Sharma","doi":"10.1016/j.abb.2025.110500","DOIUrl":"10.1016/j.abb.2025.110500","url":null,"abstract":"<div><div>Amyloidosis refers to a group of diseases characterized by the deposition of insoluble protein fibrils in various tissues and organ systems. Several proteins are reported to form amyloid under varying conditions, some of them are well characterized, e.g. Alzheimer's and Parkinson's. Though amyloid depositions affect all body parts, the organs most affected by amyloid deposition are the brain, kidneys, and liver. This manuscript focuses on human leucocyte chemotaxin-2, a recently identified protein involved in amyloid formation. Leukocyte cell-derived chemotaxis-2 (LECT2), a secretory protein that mainly acts as a chemotactic factor. It regulates TNF signaling in macrophages and osteo lineage cells, influencing hematopoietic stems cells (HSC) expansion and mobilization. LECT2 misfolding and aggregation mostly causes the deposition of amyloids, primarily in the kidney and spleen. Amyloid form of LECT2 (ALECT2) has a strong racial bias being highly prevalent in the Hispanic population. The precise mechanism of LECT2's action in amyloidosis is mainly unknown and thus hinders the development of therapeutic intervention, kidney transplant remains therefore the most effective treatment for ALECT2. This review shall foster insights about structure, function and the key factors responsible for the LECT2 amyloidosis. LECT2 transcript encodes four different splice variants in humans and one among these four transcripts shows' expression specifically in liver, testes and prostate. LECT2 protein sequence is highly conserved in higher vertebrates indicating its functional importance across species and genera. Specifically, the amyloid forming region is highly conserved except its slight variation in birds indicating difference in amyloid forming capabilities in this group. A single SNP variation causing substitution of isoleucine in place of valine is particularly documented to be important for amyloid formation.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110500"},"PeriodicalIF":3.8,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and functional insights into β-glucosidase derived from Thermoproteus sp. AZ2","authors":"Anke Chen ,&nbsp;Kelin Liu ,&nbsp;Yanchao Guo ,&nbsp;Cheng Wang ,&nbsp;Chaoneng Ji","doi":"10.1016/j.abb.2025.110478","DOIUrl":"10.1016/j.abb.2025.110478","url":null,"abstract":"<div><div>β-glucosidase (BGL) is a pivotal enzyme with broad implications across diverse industrial sectors, demonstrating robust proficiency in catalyzing glycosidic bond hydrolysis, particularly critical in lignocellulosic biomass conversion. This study explored the structural features and enzymatic activity of <em>Thermoproteus</em> sp. AZ2-derived BGL (TsBGL2). The optimum temperature and pH for TsBGL2 were 95 °C and 5.0, respectively. TsBGL2 exhibited strong thermal stability, retaining &gt;95 % of its activity after incubation at 99 °C for 10 h. Three high-resolution crystal structures of TsBGL2 revealed a canonical (α/β)8-barrel catalytic domain and thermostabilization mechanism. Based on the structure of TsBGL2, Δ(473–495) TsBGL2 was constructed, revealing a significant decrease in thermal stability. Collectively, this study provides enzymatic properties and structural analyses of TsBGL2, laying the groundwork for further studies of β-glucosidase.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110478"},"PeriodicalIF":3.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Knockdown of OPTN modulates miRNA-125b-5p expression via NF-κB pathways in amyotrophic lateral sclerosis","authors":"Jian Qin ,&nbsp;Ye He ,&nbsp;Weiyi Yu ,&nbsp;Zhaoyong Zhang ,&nbsp;Xiaodan Chen ,&nbsp;Yafang Hu ,&nbsp;Haishan Jiang","doi":"10.1016/j.abb.2025.110499","DOIUrl":"10.1016/j.abb.2025.110499","url":null,"abstract":"<div><div>Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease characterized by severe dysfunction in upper and lower motor neurons. Previous studies have reported that the optineurin gene (<em>OPTN</em>) downregulation is one of the causative genetic factors for ALS, leading to the dysfunction of optineurin (OPTN), a multifunctional protein implicated in several cellular processes. Herein, we found that conditional knockout of the <em>O</em><em>ptn</em> gene in mouse microglia leads to activation of microglia. In subsequent studies, we also found that <em>OPTN</em> knockdown in BV2 cells leads to the activation of BV2 cells and promotes the apoptosis of co-cultured NSC34 cells via exosomes derived from BV2 cells in vitro. In contrast, <em>OPTN</em> knockdown in NSC34 cells did not cause apoptosis of the NSC34 cells themselves. It was suggested that microglia activation is involved in ALS initiation and development, but the nature of microglial-neuronal interactions remained elusive, requiring further exploration. Exosomes have been proven to be essential mediators. Notably, increased miRNA-125b-5p expression was uncovered in BV2 cells with the <em>OPTN</em> gene silenced, their derived exosomes, as well as the cocultured NSC34 cells. Interestingly, we proved that increased miRNA-125b-5p enhanced the apoptosis of NSC34 cells. We further noted that the overexpression of miRNA-125b-5p in BV2 cells can be regulated by an NF-κB activator (LPS) or inhibitor (withaferin A). Altogether, this study showed that silencing the <em>OPTN</em> gene may overexpress miRNA-125b-5p levels via the classical NF-κB pathway in BV2 cells. Up-regulated miRNA-125b-5p might be transmitted from exosomes to NSC34 cells, resulting in NSC34 cells apoptosis. Microglial-neuronal interactions mediated by exosomes were the crucial mechanism of <em>OPTN</em> gene downregulation leading to ALS, and this conclusion had been verified in cell models.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110499"},"PeriodicalIF":3.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure, biophysical characterisation, modeling and docking studies of bL12 ribosomal protein from Mycobacterium tuberculosis","authors":"Preeti Tripathi,&nbsp;Lata Panicker","doi":"10.1016/j.abb.2025.110489","DOIUrl":"10.1016/j.abb.2025.110489","url":null,"abstract":"<div><div>Tuberculosis (TB) is a fatal infectious disease caused by <em>Mycobacterium tuberculosis</em> (Mtb), with high rates of relapse and mortality worldwide. The Mtb stalk protein bL7/bL12 is a component of 50S ribosomal subunit, and plays a crucial role in the translation process during protein synthesis. The bL7 differs from bL12 by the presence of an acetyl group at its N-terminal region. In this study, the bL12 gene from Mtb was cloned into prokaryotic expression vector pET-28a(+), then expressed, purified, characterised and crystallised using the vapour diffusion method. Rod-shaped crystals of bL12 were obtained, which diffracted to 1.5 Å resolution at 100 K, with an R_merge of 0.025. The bL12 crystallised in the <em>P22</em>_<em>1</em><em>2</em>_<em>1</em> space group with unit cell dimensions a = 25.86 Å, b = 47.27 Å, c = 61.07 Å, and α = β = γ = 90°. The compact, globular C-terminal domain consists of β1-α1-α2-β2-α3-β3 fold. The bL12 protein was further characterised using various biophysical techniques: CD, SEC, DLS, DSC, DSF and fluorescence spectroscopy. Structural modeling and docking of bL12 protein with its interacting partners in the ribosome were performed using HDOCK and AlphaFold3. The resulting data were analysed to gain insights into its functional role. This structural information on the Mtb bL12 protein enhances our understanding of translational biology and contributes to structure-based drug design efforts targeting tuberculosis.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110489"},"PeriodicalIF":3.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of indole-2,3-dione on radiosensitivity of U251 cells and zebrafish embryos","authors":"Ping-ping Li ,&nbsp;Jing-e Song ,&nbsp;Yu-lu Guo ,&nbsp;Si-jia Hao ,&nbsp;Jin-hua Zhang ,&nbsp;Xiao-yi Liu ,&nbsp;Yi Xie ,&nbsp;Lu Gan ,&nbsp;Bing Wang ,&nbsp;Dan Xu ,&nbsp;Hong Zhang ,&nbsp;Jing Si","doi":"10.1016/j.abb.2025.110498","DOIUrl":"10.1016/j.abb.2025.110498","url":null,"abstract":"<div><div>Radiotherapy is an effective treatment for gliomas, which are among the most malignant tumors in the central nervous system (CNS). A significant challenge in glioma radiotherapy is improving tumor control while minimizing damage to normal nervous tissue. In this study, we investigated the dual role of indole-2,3-dione (Isatin, ISA), a compound with diverse biological and pharmacological activities, including anticancer, antioxidant, and anti-inflammatory properties, in modulating radiosensitivity. The effects of ISA were examined in both human malignant glioblastoma U251 cells in vitro and zebrafish (Danio rerio) embryos in vivo. In U251 cells, irradiation significantly decreased cell viability and clonogenic capacity, while increasing reactive oxygen species (ROS) levels, inducing Cell cycle G2/M arrest, upregulating apoptotic gene expression, and inducing apoptosis. ISA pretreatment markedly enhanced these radiation-induced effects, potentiating clonogenic inhibition and proapoptotic activity. Moreover, combined ISA and irradiation treatment led to increased DNA damage and delayed DNA repair in U251 cells. In the in vivo zebrafish model, ISA pretreatment demonstrated significant radioprotective effects, reducing radiation-induced damage, including embryo mortality, behavioral alterations, ROS overproduction, and upregulation of proapoptotic genes. These findings suggest that ISA has dual functionality: acting as a radiosensitizer for glioblastoma cells and a radioprotector for normal CNS cells, primarily by modulating ROS production and apoptotic pathways. This study provides robust preclinical evidence supporting the potential clinical application of ISA in brain tumor radiotherapy, offering a promising approach to optimize therapeutic outcomes in glioma treatment.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110498"},"PeriodicalIF":3.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interaction of phage chaperonin OBP domains with amyloidogenic proteins","authors":"Evgeniia V. Leisi ,&nbsp;Darya V. Zyurkalova ,&nbsp;Uliana F. Dzhus ,&nbsp;Alexey D. Nikulin ,&nbsp;Sergei A. Golyshev ,&nbsp;Vladimir I. Muronetz ,&nbsp;Lidia P. Kurochkina","doi":"10.1016/j.abb.2025.110493","DOIUrl":"10.1016/j.abb.2025.110493","url":null,"abstract":"<div><div>GroEL-like chaperonins encoded by bacterial viruses have unique features compared to other group I and II chaperonins. Here, the properties of the single-ring chaperonin of the bacteriophage OBP <em>Pseudomonas fluorescens</em> were further studied. To understand the role of the chaperonin domains in its function, two deletion variants of the chaperonin OBP were obtained. One represented the isolated apical domain (AD) only and the other was a chaperonin without apical domains (OBPΔAD). It was shown that removal of the apical domains slightly destabilises the chaperonin structure, but does not affect its heptameric assembly. In addition, the chaperonin without the apical domains retains its ATPase activity and exhibits the properties that are characteristic of the full-length chaperonin OBP. In the presence of ATP, the mutant chaperonin OBPΔAD protects the phage endolysin from thermal aggregation and promotes the fibrillation of two amyloidogenic proteins, α-synuclein and the prion protein. In the absence of ATP, OBPΔAD is able to bind α-synuclein monomers in the same way as the full-length chaperonin OBP, thus preventing their spontaneous fibrillation. The recombinant chaperonin apical domain, lacking ATPase activity, binds α-synuclein monomers independently of ATP presence, preventing amyloid formation. The results obtained suggest that, in mutant OBP, which lacks apical domains, substrate proteins, including non-specific ones, are capable of binding to the internal cavity formed by the other two chaperonin domains. The possible role of chaperonin domains in regulating the pathological transformation of amyloidogenic proteins is discussed.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110493"},"PeriodicalIF":3.8,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new series of naphthyl-thiosemicarbazone and thio/carbohydrazone derivatives: Synthesis, spectroscopic elucidation, dual enzyme inhibition targeting carbonic anhydrase/ acetylcholinesterase and molecular docking studies","authors":"Hasan Yakan ,&nbsp;Halit Muğlu ,&nbsp;Musa Erdoğan ,&nbsp;Cüneyt Türkeş ,&nbsp;Yeliz Demir","doi":"10.1016/j.abb.2025.110491","DOIUrl":"10.1016/j.abb.2025.110491","url":null,"abstract":"<div><div>New naphthyl-thiosemicarbazone derivatives (<strong>1</strong>–<strong>9</strong>) were obtained from 1-naphthaldehyde and numerous thiosemicarbazides. New naphthyl-thio/carbohydrazones (<strong>10</strong>–<strong>12</strong>) were prepared from 1-naphthaldehyde and various thio/carbohydrazides. FT-IR, ¹H NMR, ¹³C NMR, and elemental analysis were used to elucidate the structures of the newly obtained compounds. The inhibitory effects of these compounds against human carbonic anhydrase isoforms I and II (<em>hCA</em> I and <em>hCA</em> II) and acetylcholinesterase (AChE) were systematically evaluated. Several compounds exhibited potent inhibition, particularly derivatives bearing halogenated and electron-donating aromatic substituents. Among them, compound <strong>11</strong> demonstrated the strongest inhibition for all three enzymes, with <em>K</em>_I values of 52.42 nM (<em>hCA</em> I), 59.23 nM (<em>hCA</em> II), and 40.16 nM (AChE), surpassing the reference standards acetazolamide and tacrine. Structure–activity relationship (SAR) analysis highlighted the critical influence of substituent type and position on enzymatic activity. In addition, molecular docking simulations were conducted to elucidate the binding interactions of the most potent compound with <em>hCA</em> I, <em>hCA</em> II, and AChE enzymes. The docking results supported the <em>in vitro</em> findings, revealing favorable binding energies and key interactions such as π–π stacking and hydrogen bonding, especially for compound <strong>11.</strong></div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110491"},"PeriodicalIF":3.8,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of glutamate 292 and lysine 331 in catalysis for the flavoenzyme (S)-6-hydroxynicotine oxidase from Shinella sp. HZN7","authors":"Zhiyao Zhang,&nbsp;Kaitrin Freeland,&nbsp;Frederick Stull","doi":"10.1016/j.abb.2025.110492","DOIUrl":"10.1016/j.abb.2025.110492","url":null,"abstract":"<div><div>The flavoenzyme NctB from <em>Shinella</em> sp. HZN7 catalyzes the oxidation of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine concomitant with dioxygen reduction, which is the same chemistry catalyzed by the well-studied flavoenzyme L-6-hydroxynicotine oxidase (LHNO) from <em>Paenarthrobacter nicotinovorans</em>. However, while both enzymes are members of the flavoprotein amine oxidoreductase (FAO) family, they share only 26 % sequence identity and are evolutionarily distant. Furthermore, nearly all FAOs (including LHNO) have a conserved lysine proximal to N5 of the flavin that is known to promote the reaction with O₂ in the oxidative half-reaction, yet NctB, unusually, has a glutamate (Glu292) at this position. We report here using transient kinetics that NctB reacts rapidly with dioxygen in the oxidative half-reaction despite lacking the conserved lysine associated with promoting the reaction with O₂ in FAO family enzymes. Mutagenesis reveals that a lysine derived from a different sequence position (Lys331) likely accelerates the reaction with dioxygen in NctB, as the K331M mutation results in a 1400-fold decrease in rate constant for reaction with O₂. Glu292 forms a salt bridge with Lys331 in the structure of NctB, and a E292T mutation results in a ∼80-fold decrease in rate constant for reaction with O₂, suggesting that Glu292 optimizes the positioning and/or properties of Lys331 to promote dioxygen activation. Analysis of pH-rate effects in NctB shows similar pH profiles as in LHNO despite having differences in active site structure. These results indicate that NctB and LHNO convergently evolved to have the same enzymatic function.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110492"},"PeriodicalIF":3.8,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eribulin's exclusive binding to microtubule plus ends results from discrimination between GTP and GDP forms of β-tubulin","authors":"Kishan Lal Agarwala ,&nbsp;Kenji Kubara ,&nbsp;Boris M. Seletsky ,&nbsp;Koji Sagane ,&nbsp;Bruce A. Littlefield","doi":"10.1016/j.abb.2025.110482","DOIUrl":"10.1016/j.abb.2025.110482","url":null,"abstract":"<div><div>The clinically approved anticancer agent eribulin (Halaven®) exerts cytotoxic antimitotic effects by binding to high affinity sites on exposed plus ends of growing microtubules (MT). Despite X-ray crystallographic mapping of eribulin's binding pocket within β-tubulin's vinca domain, the biophysical basis for eribulin's MT plus end binding exclusivity remains unknown. We performed surface plasmon resonance (SPR) studies of tubulin binding to biotinylated eribulin probes to ask if eribulin discriminates between GTP and GDP forms of β-tubulin, which characterize growing MT plus ends and MT sides, respectively. Tubulin binding to biotin-eribulin proceeded via a single state binding reaction, while binding to biotin-vinblastine occurred via a two-state reaction incorporating a conformational change. Biochemical approaches confirmed tubulin conformational changes induced by vinblastine but not eribulin. SPR competition studies using free eribulin and vinblastine confirmed tubulin binding specificity to cognate biotinylated probes, showing that eribulin binding within the β-tubulin vinca domain is physically and functionally distinct from vinblastine. SPR studies using tubulin containing only GTP or GDP forms of β-tubulin showed that while biotin-eribulin has only slightly higher overall affinity for GTP-tubulin, dissociation from GTP-tubulin was ∼7-fold slower than from GDP-tubulin, establishing that eribulin discriminates between GTP and GDP forms of β-tubulin. In contrast, vinblastine fails to discriminate between these two tubulin forms, consistent with its known binding to both MT ends and sides. Overall, our results establish, for the first time, the biophysical basis for eribulin's MT plus end binding exclusivity as resulting from the ability to discriminate between GTP and GDP forms of β-tubulin.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"771 ","pages":"Article 110482"},"PeriodicalIF":3.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative molecular dynamics reveal the conformational dynamics of the IrtAB-cMBT complex in mycobacterial iron uptake","authors":"Gauri Shankar,&nbsp;Yusuf Akhter","doi":"10.1016/j.abb.2025.110477","DOIUrl":"10.1016/j.abb.2025.110477","url":null,"abstract":"<div><div>The IrtAB transporter in <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>) is essential for iron acquisition through the import of iron-bound carboxymycobactin (cMBT), yet the molecular mechanisms governing substrate recognition and transport remain unresolved. Here, we employed 450-ns molecular dynamics simulations to elucidate the conformational dynamics of IrtAB in substrate-free (apo) and substrate-bound (holo) states, revealing key structural rearrangements and residue-specific interactions underpinning its transport cycle. Comparative analyses demonstrated enhanced conformational flexibility in the holo state, with asymmetric domain movements in IrtA and IrtB subunits facilitating cMBT translocation. Three histidine residues (His356, His402, His407) in IrtA undergone significant positional shifts (6–10 Å) upon substrate binding, forming a dynamic coordination network critical for cMBT recognition. The ligand exhibited complex behavior, including a 3.5–4.0 Å downward movement within the binding pocket and RMSD fluctuations (0.5–5.0 Å), indicative of multiple energetically favorable binding modes. Substrate-induced stabilization of the transmembrane domains correlates with progressive dehydration of the binding cavity, while RMSF profiles highlighted asymmetric flexibility in transmembrane helices during transport. These findings reveal how IrtAB's exporter-like architecture is repurposed for iron-siderophore import, balancing structural rigidity with conformational plasticity to enable efficient nutrient uptake. By delineating the mechanistic basis of IrtAB-mediated iron acquisition, this study provides a framework for targeting this pathway in <em>Mtb</em>, offering potential avenues for therapeutic intervention against tuberculosis.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"770 ","pages":"Article 110477"},"PeriodicalIF":3.8,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}