Journal of Structural Biology: X最新文献

Salt bridge disruption in colicin Ib channel-forming domain enhances membrane translocation and bactericidal activity 大肠杆菌素Ib通道形成区域的盐桥破坏增强了膜易位和杀菌活性

IF 5.1

Journal of Structural Biology: X Pub Date : 2026-06-01 Epub Date: 2026-02-04 DOI: 10.1016/j.yjsbx.2026.100144

Jie Yang , Pei-Fen Liu , Wei-Jie Wang , Shih-Chun Yang , Chia-Liang Lin , Yung-Chuan Liu , Che-An Tsai , Jiann-Hwa Chen , Nien-Jen Hu

{"title":"Salt bridge disruption in colicin Ib channel-forming domain enhances membrane translocation and bactericidal activity","authors":"Jie Yang , Pei-Fen Liu , Wei-Jie Wang , Shih-Chun Yang , Chia-Liang Lin , Yung-Chuan Liu , Che-An Tsai , Jiann-Hwa Chen , Nien-Jen Hu","doi":"10.1016/j.yjsbx.2026.100144","DOIUrl":"10.1016/j.yjsbx.2026.100144","url":null,"abstract":"<div><div>Pore-forming colicins are bacteriocins produced by <em>Escherichia coli</em> to kill competing bacterial strains by forming ion-permeable channels in the inner membrane of target cells, leading to membrane depolarization, ion leakage, and ultimately cell death. While the crystal structures of their soluble form and membrane-perforating activities have been intensively studied, the structural rearrangements enabling outer membrane translocation and inner membrane pore formation remain puzzling. Here, we present the crystal structure of the channel-forming domain of colicin Ib (ColIb) and identify interhelical salt bridge networks that stabilize its tertiary structure. Comparative analysis shows that electrostatic interactions between helices H3–H7 and H4–H6 are conserved in E1-type but not A-type colicins. Disrupting these electrostatic interactions—either through alanine substitutions or acidic pH—produced a less compact structure with increased membrane association. Salt bridge mutations enhanced the bactericidal activity of full-length ColIb by at least an order of magnitude, and notably, introducing these mutations into the isolated C-domain conferred CirA-dependent cytotoxicity in the absence of the T- and R-domains. Protonation of the C-domain at pH 4.5 further amplified its killing capacity. Our findings reveal that destabilization of interhelical contacts facilitates unfolding and membrane association, providing a structural mechanism for CirA-mediated translocation and amplified killing efficiency.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"13 ","pages":"Article 100144"},"PeriodicalIF":5.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146169971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural insights of the coronavirus main protease in complex with the non-covalent inhibitor CCF0058981 冠状病毒主要蛋白酶与非共价抑制剂CCF0058981复合物的结构分析

IF 5.1

Journal of Structural Biology: X Pub Date : 2026-06-01 Epub Date: 2026-01-06 DOI: 10.1016/j.yjsbx.2026.100143

Pei Zeng , Xuelan Zhou , Li Guo , Wenwen Li , Jian Li

{"title":"Structural insights of the coronavirus main protease in complex with the non-covalent inhibitor CCF0058981","authors":"Pei Zeng , Xuelan Zhou , Li Guo , Wenwen Li , Jian Li","doi":"10.1016/j.yjsbx.2026.100143","DOIUrl":"10.1016/j.yjsbx.2026.100143","url":null,"abstract":"<div><div>The highly pathogenic SARS-CoV-2 causes COVID-19, which threatens global public health and socio-economic stability through persistent transmission and mutation. Effective therapeutics against SARS-CoV-2 and its variants are urgently needed. The main protease (M<sup>pro</sup>), highly conserved among coronaviruses and lacking human homologs, is pivotal for viral replication, making it an attractive antiviral target. CCF0058981, a novel non-covalent inhibitor developed based on the ML300 scaffold, demonstrates potent low-nanomolar inhibitory activity against SARS-CoV-2 M<sup>pro</sup> and sub-micromolar antiviral efficacy against SARS-CoV-2. Its non-covalent binding mechanism effectively mitigates the off-target risks commonly associated with traditional covalent inhibitors, thereby providing a versatile scaffold for the development of highly safe and effective anti-coronavirus therapeutics. However, the structural basis underlying CCF0058981′s inhibitory mechanism against SARS-CoV-2 M<sup>pro</sup> remains to be elucidated. Here, we report for the first time two crystal structures of M<sup>pro</sup> from SARS-CoV-2 and SARS-CoV in complex with the inhibitor CCF0058981. Detailed crystal structure analysis reveals that CCF0058981 occupies the catalytic pocket of M<sup>pro</sup> via conserved hydrogen bonds and hydrophobic interactions. The superimposition analysis of the reported crystal structures also reveals that CCF0058981 maintains stable binding to the M<sup>pro</sup> mutants (M49I and V186F), demonstrating its potential to combat drug resistance, demonstrating its potential to counteract drug resistance. Molecular dynamics simulations further validate the stability of the inhibitor-protease complex. These findings provide mechanistic insights into CCF0058981′s inhibition and support developing broad-spectrum coronavirus therapeutics.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"13 ","pages":"Article 100143"},"PeriodicalIF":5.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alanine scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure 酵母杀手毒素K2的丙氨酸扫描揭示了活性，功能获得变体的关键残基，并支持前体加工和3D结构的预测

IF 5.1

Journal of Structural Biology: X Pub Date : 2026-06-01 Epub Date: 2025-12-18 DOI: 10.1016/j.yjsbx.2025.100142

Rianne C. Prins , Tycho Marinus , Eyal Dafni , Iftach Yacoby , Sonja Billerbeck

{"title":"Alanine scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure","authors":"Rianne C. Prins , Tycho Marinus , Eyal Dafni , Iftach Yacoby , Sonja Billerbeck","doi":"10.1016/j.yjsbx.2025.100142","DOIUrl":"10.1016/j.yjsbx.2025.100142","url":null,"abstract":"<div><div>Yeast killer toxins (YKTs) are antimicrobial proteins secreted by yeast with potential applications ranging from food preservation to therapeutic agents in human health. However, the practical use of many YKTs is limited by specific pH requirements, low temperature stability, low production yields, and narrow target specificity. While protein engineering could potentially overcome these challenges, progress is hindered by a lack of detailed knowledge about sequence-function relationships and structural data for these often multi-step processed proteins. In this study, we focused on the YKT K2, encoded by the M2 satellite dsRNA in <em>Saccharomyces cerevisiae</em>. Using alanine scanning mutagenesis of the full open reading frame and structure predictions combined with molecular dynamics simulations, we generated a comprehensive sequence-structure–function map, refined the model for the proteolytic processing of the K2 precursor, and predicted the mature toxin structure. Our findings also demonstrate that K2 can be engineered toward enhanced toxicity and altered target specificity through single-site mutations. Furthermore, we identified structural homology between K2 and other killer toxins, including the SMK toxin from the yeast <em>Millerozyma farinosa</em>. Our cost-effective workflow provides a platform to broadly map YKT sequence-structure–function relationships.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"13 ","pages":"Article 100142"},"PeriodicalIF":5.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hemoglobin receptor redundancy in Staphylococcus aureus: molecular flexibility as a determinant of divergent hemophore activity 金黄色葡萄球菌的血红蛋白受体冗余：分子柔韧性作为发散性血红蛋白活性的决定因素

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-11-05 DOI: 10.1016/j.yjsbx.2025.100138

Valeria Buoli Comani , Omar De Bei , Francesca Pancrazi , Marcos Gragera , Giulia Paris , Marialaura Marchetti , Barbara Campanini , Luca Ronda , Ben F. Luisi , Serena Faggiano , Anna Rita Bizzarri , Stefano Bettati

{"title":"Hemoglobin receptor redundancy in Staphylococcus aureus: molecular flexibility as a determinant of divergent hemophore activity","authors":"Valeria Buoli Comani , Omar De Bei , Francesca Pancrazi , Marcos Gragera , Giulia Paris , Marialaura Marchetti , Barbara Campanini , Luca Ronda , Ben F. Luisi , Serena Faggiano , Anna Rita Bizzarri , Stefano Bettati","doi":"10.1016/j.yjsbx.2025.100138","DOIUrl":"10.1016/j.yjsbx.2025.100138","url":null,"abstract":"<div><div>To overcome iron limitation in the host, <em>Staphylococcus aureus</em> exploits sophisticated mechanisms to acquire this essential nutrient, particularly from hemoglobin (Hb). The bacterial hemophores IsdH and IsdB play key roles in binding Hb and extracting heme, but the structural and mechanistic differences underlying their individual contributions remain poorly defined. In this study, we dissected the molecular mechanisms by which IsdH engages Hb and mediates heme extraction, using cryo-electron microscopy, biochemical assays, and single-molecule force spectroscopy. Our structural analyses revealed pronounced conformational heterogeneity within IsdH:Hb complexes, highlighting marked flexibility in the heme-binding domain of IsdH, likely underlying its distinct functional behavior. This plasticity contrasts with the more rigid architecture of IsdB. The flexibility observed in IsdH correlates with our biochemical and biophysical findings, supporting its functional relevance. Unlike IsdB, IsdH does not display selectivity for α- or β-Hb chains and shows reduced involvement of the heme-binding domain in Hb recognition. It also follows a distinct kinetic mechanism for heme capture, which begins upon binding but proceeds more slowly than in IsdB. Finally, IsdH does not exhibit the catch bond-like behavior characteristic of IsdB, suggesting it may act in different physiological niches or conditions. Collectively, these findings highlight a distinct mode of Hb engagement by IsdH, shaped by its dynamic and flexible architecture, and provide mechanistic insight into the diversity of iron acquisition strategies employed by <em>S. aureus</em>.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100138"},"PeriodicalIF":5.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145516635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The J-shape of β2GPI reveals a cryptic discontinuous epitope across domains I and II β2GPI呈j形，在结构域I和II之间有一个隐隐约约的不连续表位

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-08-20 DOI: 10.1016/j.yjsbx.2025.100135

C.J. Lalaurie , M. Kulke , N. Geist , M. Delcea , P.A. Dalby , T.C.R. McDonnell

{"title":"The J-shape of β2GPI reveals a cryptic discontinuous epitope across domains I and II","authors":"C.J. Lalaurie , M. Kulke , N. Geist , M. Delcea , P.A. Dalby , T.C.R. McDonnell","doi":"10.1016/j.yjsbx.2025.100135","DOIUrl":"10.1016/j.yjsbx.2025.100135","url":null,"abstract":"<div><div>Beta-2-Glycoprotein I is the main target for pathogenic antiphospholipid syndrome autoantibodies. It can adopt several conformations, including an O-shape and two more linear J- and S-shapes. The <em>in vivo</em> existence of the O-shape is debated, and doubt remains pertaining to the pathogenic impact of each shape. Studies have shown that APS antibodies react weakly with the O-shape and bind to the linear shapes due to the exposure of a cryptic epitope in the 1st domain. How the protein transitions from O-shape to the linear shapes remains unknown. While the main epitope is widely recognised as the R39-R43 peptide, there is evidence pointing to a discontinuous epitope across domains I and II (DI & DII). We used molecular dynamics simulations to examine the potential pathways of conformational shift from the O-shape to the open forms, and the impact of plasmin clipping on these pathways. Through these studies, starting in a theorised O-shape, we identified that peptides R39-R43, T50-N56 and R63-F67 become more exposed and have increased stability in the J- and S-shapes relative to the O-shape. These changes are likely due to a shift in DII of the T106-G109 loop, which twists to form contacts with the DI K33-Y36 loop. The R39-R43 peptide is brought closer to R63-F67 suggesting a more complex DI epitope than previously theorised. These effects were observed in the wild type and plasmin clipped model, with the effect being larger in the latter. These results are in good agreement with the increased antibody binding observed experimentally for the clipped protein. We therefore suggest that we have been able to identify the structural mechanism at the residue level which results in increased antibody binding in the J-Shape, and specifically in the clipped protein.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100135"},"PeriodicalIF":5.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144885800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DiameTR: A cryo-EM tool for diameter sorting of tubular samples DiameTR：用于管状样品直径分选的低温电镜工具

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-09-02 DOI: 10.1016/j.yjsbx.2025.100136

Ruizhi Peng , Heidy Elkhaligy , Timothy Grant , Scott M. Stagg

{"title":"DiameTR: A cryo-EM tool for diameter sorting of tubular samples","authors":"Ruizhi Peng , Heidy Elkhaligy , Timothy Grant , Scott M. Stagg","doi":"10.1016/j.yjsbx.2025.100136","DOIUrl":"10.1016/j.yjsbx.2025.100136","url":null,"abstract":"<div><div>Tubular structures are ubiquitous in biological systems and have been a focal point of cryo-electron microscopy (cryo-EM) structural analysis since the technique’s inception. A critical step in processing tubular cryo-EM data is particle classification by diameter, as uniformity in diameter is a prerequisite for high-resolution three-dimensional reconstructions. Conventional methods rely on cross-correlation-based algorithms, which require prior knowledge to generate reference images, or iterative two-dimensional (2D) classification, that align and cluster particles into a predefined number of classes—a process that is both time-consuming and subjective. To address these limitations, we developed diameTR, a computational tool that rapidly determines tubular diameters in a prior knowledge-free and reference-free manner using GPU-accelerated processing on a per-particle basis. When applied to homogeneous datasets, diameTR yields narrow diameter distributions aligning closely with published values. For heterogeneous samples, it enables the separation of subsets with distinct diameters, validated by 2D averaging. Notably, diameTR identified an unreported smaller diameter subset of particles with new helical symmetry parameters in the previously published KpFtsZ-Monobody dataset. Collectively, diameTR represents a robust, efficient solution for diameter determination in tubular cryo-EM samples, eliminating the need for extensive human intervention while significantly accelerating processing.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100136"},"PeriodicalIF":5.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA indel驱动的牛磺酸trna编辑去乙酰化酶CtdA的进化

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-06-18 DOI: 10.1016/j.yjsbx.2025.100132

Nino Tabagari , Franziskus Hauth , Jennifer R. Fleming , Jörg S. Hartig , Olga Mayans

{"title":"Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA","authors":"Nino Tabagari , Franziskus Hauth , Jennifer R. Fleming , Jörg S. Hartig , Olga Mayans","doi":"10.1016/j.yjsbx.2025.100132","DOIUrl":"10.1016/j.yjsbx.2025.100132","url":null,"abstract":"<div><div>Proteins are heteropolymers composed of twenty standard amino acids, but over 500 non-proteogenic amino acids exist in nature that can be misincorporated into proteins. Canavanine is an antimetabolite of the chemically similar L-arginine. It can be utilized by bacteria such as <em>Pseudomonas canavaninivorans</em> in the legume rhizome as a sole source of carbon and nitrogen. However, canavanine misincorporates in proteins of this bacterium as its arginyl-tRNA synthetase loads tRNA<sup>Arg</sup> with both canavanine and arginine. Canavanyl-tRNA<sup>Arg</sup> deacetylase (CtdA) removes canavanine from misloaded tRNA<sup>Arg</sup>, preventing its protein toxicity, being the first enzyme known to edit tRNA mischarged with a non-proteinogenic amino acid. We have elucidated CtdA’s crystal structure and studied its active site using site-directed mutagenesis. We found that CtdA is a small monomeric enzyme with a central, deep cavity that predictably is the canavanine binding site and a positively charged surface area that likely coordinates the CCA-3′ tRNA attachment sequence. CtdA is distantly related to the B3/B4 <em>cis</em>-editing domains of the multi-subunit enzyme Phenylalanine-tRNA-Synthetase (PheRS). CdtA and B3/B4 domains from bacterial and archaeal/eukaryotic origin are three subclasses of a conserved 3D-fold that differ in type-specific indels, which shape the substrate binding site. We propose a class-unifying nomenclature of secondary structure for this fold. In CtdA, residues Y104, N105, E118 and E191 are relevant for catalysis, of which N105 is conserved in bacterial B3/B4 domains. Residue N105 is in proximity of the canavanyl-ribose junction and might coordinate the nucleophilic water molecule that attacks the substrate, possibly sharing a mechanistic role in CtdA and bacterial B3/B4 editing enzymes.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100132"},"PeriodicalIF":3.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The structure of the bacterial outer membrane transporter FusA enabled by addition of the native lipid lipopolysaccharide 细菌外膜转运蛋白FusA的结构通过添加天然脂质脂多糖实现

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-11-18 DOI: 10.1016/j.yjsbx.2025.100141

Jonathan M. Machin , Khedidja Mosbahi , Dheeraj Prakaash , Sheena E. Radford , Daniel Walker , Antreas C. Kalli , Neil A. Ranson

{"title":"The structure of the bacterial outer membrane transporter FusA enabled by addition of the native lipid lipopolysaccharide","authors":"Jonathan M. Machin , Khedidja Mosbahi , Dheeraj Prakaash , Sheena E. Radford , Daniel Walker , Antreas C. Kalli , Neil A. Ranson","doi":"10.1016/j.yjsbx.2025.100141","DOIUrl":"10.1016/j.yjsbx.2025.100141","url":null,"abstract":"<div><div>Lipopolysaccharide (LPS) is a glycolipid found uniquely in the outer membrane of diderm bacteria, formed of 4–7 acyl chains covalently linked to an extended polysaccharide chain. While a few examples of the interaction between LPS and outer membrane proteins (OMPs) have been structurally characterised, either experimentally or computationally, the precise nature of LPS-OMP interactions and their functional consequences remains unclear. Here, we show that the addition of LPS facilitated cryoEM structure determination of FusA, a 100 kDa TonB-dependent outer membrane transporter from <em>P. atrosepticum</em>. A 2.8 Å structure combined with molecular dynamics of FusA with different LPS models reveals LPS binding sites with a strong LPS interaction site located adjacent to the β-seam region of the FusA β-barrel. The requirement of lipid binding for successful structure determination indicates a stabilisation of the protein, which in turn suggests a potential method for solving other, small OMPs and membrane proteins. Further, it hints at how LPS may mediate protein conformation and thus how LPS and OMPs can work in concert to maintain a structural and functional OM.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100141"},"PeriodicalIF":5.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure reveals the hydrophilic R1 group impairs NDM-1–ligand binding via water penetration at L3 晶体结构显示亲水性R1基团通过水渗透在L3破坏ndm -1配体的结合

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-07-01 DOI: 10.1016/j.yjsbx.2025.100133

Xiangrui Shi , Huijuan Yang , Yujie Dai , Hui Zhao , Yuhang Li , Yanxi Li , Xin Zhou , Hailong Yan , Qinghua Zhang , Wei Liu

{"title":"Crystal structure reveals the hydrophilic R1 group impairs NDM-1–ligand binding via water penetration at L3","authors":"Xiangrui Shi , Huijuan Yang , Yujie Dai , Hui Zhao , Yuhang Li , Yanxi Li , Xin Zhou , Hailong Yan , Qinghua Zhang , Wei Liu","doi":"10.1016/j.yjsbx.2025.100133","DOIUrl":"10.1016/j.yjsbx.2025.100133","url":null,"abstract":"<div><div>The global spread of New Delhi metallo-β-lactamases (NDMs) has exacerbated the antimicrobial resistance crisis. This study resolved the crystal structure of NDM-1 hydrolyzing amoxicillin for the first time, revealed that the hydroxyl group in the R1 moiety of amoxicillin anchors a key water molecule (Wat1) via hydrogen bond, inducing a conformational shift in Met67 (average displacement of 3.8 Å compared to its position in complexes with ampicillin, penicillin G, and penicillin V) and impairing the hydrophobic interaction between the loop 3 and the substrate. Molecular dynamics simulations confirmed that the π-π stacking contact time between amoxicillin and the L3 critical residue Phe70 decreased to 4.3 % (ampicillin: 12.3 %), with a binding energy reduction of 10.5 kcal/mol. Steady-state kinetics showed that amoxicillin exhibited a 2.2-fold higher <em>K</em><sub>m</sub> and a 5.2-fold higher <em>k</em><sub>cat</sub> compared to ampicillin, demonstrating that hydrophilic R1 groups impair enzyme-substrate binding. This work demonstrates the essential role of hydrophobic interactions in L3-mediated substrate binding and provides a novel strategy for designing L3-targeted NDM-1 inhibitors: maximize hydrophobicity and minimize polar surface area in the L3 contact region to block water penetration, thereby stabilizing the inhibitor-L3 interaction.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100133"},"PeriodicalIF":3.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144523258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automated removal of corrupted tilts in cryo-electron tomography 冷冻电子断层扫描中损坏倾斜的自动去除

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-12-01 Epub Date: 2025-07-17 DOI: 10.1016/j.yjsbx.2025.100130

Tomáš Majtner, Beata Turoňová

引用次数: 0