Pub Date : 2025-08-08DOI: 10.1016/j.jsb.2025.108236
Victor O. Gawriljuk , Rick Oerlemans , Eswar R. Reddem , Robin M. Gierse , Anna K.H. Hirsch , Matthew R. Groves
Isoprenoids represent one of the largest and functionally diverse class of natural products, playing essential roles in cellular processes across all domains of life. Unlike humans, many pathogenic organisms such as bacteria and protozoa produce their isoprenoid precursors through the 2-C-methylerythritol phosphate (MEP) pathway. 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of this pathway. Despite its biological importance and potential as a drug target, structural studies on DXPS were limited due to its intrinsic flexibility and difficulties in crystallisation. Recent advances, including the development of more crystallisation-friendly constructs and the application of single-particle cryo-electron microscopy (cryo-EM), have significantly expanded our structural understanding of DXPS. This review provides a comprehensive overview of the structural insights gained over the past decades, focusing on the overall architecture of DXPS, its catalytic mechanism, and emerging relevance in structure-based drug discovery.
类异戊二烯是最大的、功能多样的天然产物之一，在生命所有领域的细胞过程中发挥着重要作用。与人类不同，许多致病生物如细菌和原生动物通过2- c -甲基赤藓糖醇磷酸（MEP）途径产生类异戊二烯前体。1-脱氧-d -木糖5-磷酸合酶（DXPS）是该途径的第一酶和限速酶。尽管DXPS具有重要的生物学意义和作为药物靶点的潜力，但由于其固有的灵活性和结晶困难，对DXPS的结构研究受到限制。最近的进展，包括更多结晶友好结构的发展和单粒子冷冻电子显微镜（cryo-EM）的应用，极大地扩展了我们对DXPS的结构理解。这篇综述提供了一个全面的概述，在过去的几十年里获得的结构见解，重点是DXPS的整体结构，它的催化机制，并在基于结构的药物发现新兴的相关性。
{"title":"1-Deoxy-D-xylulose 5-phosphate synthase: structural perspectives on an essential enzyme in isoprenoid biosynthesis","authors":"Victor O. Gawriljuk , Rick Oerlemans , Eswar R. Reddem , Robin M. Gierse , Anna K.H. Hirsch , Matthew R. Groves","doi":"10.1016/j.jsb.2025.108236","DOIUrl":"10.1016/j.jsb.2025.108236","url":null,"abstract":"<div><div>Isoprenoids represent one of the largest and functionally diverse class of natural products, playing essential roles in cellular processes across all domains of life. Unlike humans, many pathogenic organisms such as bacteria and protozoa produce their isoprenoid precursors through the 2-<em>C</em>-methylerythritol phosphate (MEP) pathway. 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of this pathway. Despite its biological importance and potential as a drug target, structural studies on DXPS were limited due to its intrinsic flexibility and difficulties in crystallisation. Recent advances, including the development of more crystallisation-friendly constructs and the application of single-particle cryo-electron microscopy (cryo-EM), have significantly expanded our structural understanding of DXPS. This review provides a comprehensive overview of the structural insights gained over the past decades, focusing on the overall architecture of DXPS, its catalytic mechanism, and emerging relevance in structure-based drug discovery.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108236"},"PeriodicalIF":2.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817032","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}
Pub Date : 2025-07-22DOI: 10.1016/j.jsb.2025.108235
Qingrong Xie , Jiuyu Ding , Chunting Fu , Xi Chen , Ziyi Sun , Xiaoming Zhou
Being the second most abundant trace metal in cells, zinc plays critical roles in a variety of cellular activities, serving as a structural or enzymatic co-factor, or a signaling molecule. Dysregulation of cellular zinc has been implicated in many pathophysiological conditions including cancer, neurodegenerative diseases and immune system disorders. Therefore, the cellular zinc homeostasis is tightly controlled by various transport proteins. Two solute carrier protein families, ZnT and ZIP transporters, mediate zinc efflux and influx, respectively, and are important players in maintaining the cellular zinc homeostasis. Recent structural advancement of ZnTs and ZIPs has gained new insight into the transport mechanism of zinc by these transporters. In this review, we discuss ZnT and ZIP transporters from a structural perspective to understand the transport mechanism of zinc across biological membranes.
{"title":"A structural perspective of transmembrane transport of zinc by ZnT and ZIP transporters","authors":"Qingrong Xie , Jiuyu Ding , Chunting Fu , Xi Chen , Ziyi Sun , Xiaoming Zhou","doi":"10.1016/j.jsb.2025.108235","DOIUrl":"10.1016/j.jsb.2025.108235","url":null,"abstract":"<div><div>Being the second most abundant trace metal in cells, zinc plays critical roles in a variety of cellular activities, serving as a structural or enzymatic co-factor, or a signaling molecule. Dysregulation of cellular zinc has been implicated in many pathophysiological conditions including cancer, neurodegenerative diseases and immune system disorders. Therefore, the cellular zinc homeostasis is tightly controlled by various transport proteins. Two solute carrier protein families, ZnT and ZIP transporters, mediate zinc efflux and influx, respectively, and are important players in maintaining the cellular zinc homeostasis. Recent structural advancement of ZnTs and ZIPs has gained new insight into the transport mechanism of zinc by these transporters. In this review, we discuss ZnT and ZIP transporters from a structural perspective to understand the transport mechanism of zinc across biological membranes.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108235"},"PeriodicalIF":3.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144703772","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}
Pub Date : 2025-07-17DOI: 10.1016/j.jsb.2025.108231
Soheil Mojiri , Joseph M. Dobbs , Niko Faul , Thomas P. Burg , Julia Mahamid , Jonas Ries
Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.
{"title":"Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy","authors":"Soheil Mojiri , Joseph M. Dobbs , Niko Faul , Thomas P. Burg , Julia Mahamid , Jonas Ries","doi":"10.1016/j.jsb.2025.108231","DOIUrl":"10.1016/j.jsb.2025.108231","url":null,"abstract":"<div><div>Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at <span><math><mrow><mn>640</mn><mspace></mspace><mi>nm</mi></mrow></math></span> exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108231"},"PeriodicalIF":3.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144665781","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}
Pub Date : 2025-07-14DOI: 10.1016/j.jsb.2025.108233
Ritika Kukreja, Michael P. Latham
Emerging evidence highlights the importance of the interactions between amyloidogenic proteins and nucleic acids in both pathological and functional amyloid systems. Here, we review the current knowledge on the mechanisms by which nucleic acids modulate amyloid assembly and structure, highlighting conserved paradigms that govern these interactions. Drawing from studies of prion protein, amyloid-β, α-synuclein, and functional bacterial amyloids, we describe how nucleic acids act as cofactors in amyloidogenesis and influence the biological roles of these systems. Despite these studies, key questions remain regarding the structural specificity, sequence dependence, and biophysical principles underlying these interactions. Biophysical and structural tools such as NMR spectroscopy and cryo-EM offer exciting opportunities to resolve these gaps and deepen our understanding of how nucleic acids shape amyloid formation, function, and pathology.
{"title":"Molecular recognition and structural plasticity in amyloid–nucleic acid complexes","authors":"Ritika Kukreja, Michael P. Latham","doi":"10.1016/j.jsb.2025.108233","DOIUrl":"10.1016/j.jsb.2025.108233","url":null,"abstract":"<div><div>Emerging evidence highlights the importance of the interactions between amyloidogenic proteins and nucleic acids in both pathological and functional amyloid systems. Here, we review the current knowledge on the mechanisms by which nucleic acids modulate amyloid assembly and structure, highlighting conserved paradigms that govern these interactions. Drawing from studies of prion protein, amyloid-β, α-synuclein, and functional bacterial amyloids, we describe how nucleic acids act as cofactors in amyloidogenesis and influence the biological roles of these systems. Despite these studies, key questions remain regarding the structural specificity, sequence dependence, and biophysical principles underlying these interactions. Biophysical and structural tools such as NMR spectroscopy and cryo-EM offer exciting opportunities to resolve these gaps and deepen our understanding of how nucleic acids shape amyloid formation, function, and pathology.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108233"},"PeriodicalIF":3.0,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633415","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}
Pub Date : 2025-07-13DOI: 10.1016/j.jsb.2025.108234
Xiaodong Wang, Siqi Yang , Penghui Yang , Ziyi Sun, Xiaoming Zhou
The interaction between the membrane (M) protein and the nucleocapsid (N) protein of coronaviruses plays a crucial role in virus assembly and morphogenesis. Previous studies indicate that one M−N interaction occurs between M protein and the carboxy-terminus of N protein. However, the mechanistic details of M−N interactions remain unclear. Here, we present a complex structure of an N protein carboxy-terminal peptide bound to M protein from Pipistrellus bat coronavirus HKU5. The structure shows that the M−N peptide binding site includes a “horizontal” groove located between the carboxy-terminal domain and the transmembrane domain of M protein. Combined with molecular docking and binding analysis, our results provide structural insight into the binding mechanism between M and N proteins of a coronavirus.
{"title":"Binding of an N protein peptide to M protein of a bat coronavirus","authors":"Xiaodong Wang, Siqi Yang , Penghui Yang , Ziyi Sun, Xiaoming Zhou","doi":"10.1016/j.jsb.2025.108234","DOIUrl":"10.1016/j.jsb.2025.108234","url":null,"abstract":"<div><div>The interaction between the membrane (M) protein and the nucleocapsid (N) protein of coronaviruses plays a crucial role in virus assembly and morphogenesis. Previous studies indicate that one M−N interaction occurs between M protein and the carboxy-terminus of N protein. However, the mechanistic details of M−N interactions remain unclear. Here, we present a complex structure of an N protein carboxy-terminal peptide bound to M protein from <em>Pipistrellus</em> bat coronavirus HKU5. The structure shows that the M−N peptide binding site includes a “horizontal” groove located between the carboxy-terminal domain and the transmembrane domain of M protein. Combined with molecular docking and binding analysis, our results provide structural insight into the binding mechanism between M and N proteins of a coronavirus.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108234"},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633414","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}
Pub Date : 2025-07-05DOI: 10.1016/j.jsb.2025.108228
Claudie Carron , Sarah Danché , Valdir Gomes Neto , Mickaël Lelek , Nana Kadidia Maiga , Isabelle Léger-Silvestre , Thomas Mangeat , Stéphanie Balor , Carla C. Oliveira , Christophe Zimmer , Frédéric Beckouët , Christian Rouvière , Benjamin Albert , Sylvain Cantaloube , Olivier Gadal
Spatial organization of chromosomes is crucial for genome stability, transcription, and proper mitotic segregation. By employing a range of imaging technologies, including random illumination microscopy and single molecule localization microscopy (SMLM), we conducted an in-depth exploration of the chromatin organization in budding yeast, with optical resolutions ranging from 250 nm to 50 nm. In silico models based on passively moving polymer chains and local tethering to nuclear landmarks explained much of the experimental data in yeast chromatin. We compared these models with our new imaging data of the nucleoplasmic and nucleolar chromatin. Chromatin fibers observed in the nucleoplasm showed some similarity with model prediction with a resolution of 150 nm. However, we visualized local clustering of chromatin in both the nucleoplasm and nucleolus, rather than the tube-like appearance predicted by polymer chain models. In the nucleolus, local clustering of ribosomal DNA (rDNA) chromatin is consistently observed from 150 nm resolution down to 50 nm. We also observed that actively transcribed rDNA spatially segregates from bulk nucleolar chromatin. Using correlative light and electron microscopy (CLEM), we found that local rDNA clustering is forming a specific nucleolar subdomain visible in transmission electron microscopy, the yeast equivalent of metazoan fibrillar center. We conclude that nucleolar chromatin forms a distinct sub-nucleolar compartment in yeast, supporting the model of a tripartite structural organization of the yeast nucleolus.
{"title":"Multiscale visualization of nucleolar chromatin in yeast Saccharomyces cerevisiae","authors":"Claudie Carron , Sarah Danché , Valdir Gomes Neto , Mickaël Lelek , Nana Kadidia Maiga , Isabelle Léger-Silvestre , Thomas Mangeat , Stéphanie Balor , Carla C. Oliveira , Christophe Zimmer , Frédéric Beckouët , Christian Rouvière , Benjamin Albert , Sylvain Cantaloube , Olivier Gadal","doi":"10.1016/j.jsb.2025.108228","DOIUrl":"10.1016/j.jsb.2025.108228","url":null,"abstract":"<div><div>Spatial organization of chromosomes is crucial for genome stability, transcription, and proper mitotic segregation. By employing a range of imaging technologies, including random illumination microscopy and single molecule localization microscopy (SMLM), we conducted an in-depth exploration of the chromatin organization in budding yeast, with optical resolutions ranging from 250 nm to 50 nm. <em>In silico</em> models based on passively moving polymer chains and local tethering to nuclear landmarks explained much of the experimental data in yeast chromatin. We compared these models with our new imaging data of the nucleoplasmic and nucleolar chromatin. Chromatin fibers observed in the nucleoplasm showed some similarity with model prediction with a resolution of 150 nm. However, we visualized local clustering of chromatin in both the nucleoplasm and nucleolus, rather than the tube-like appearance predicted by polymer chain models. In the nucleolus, local clustering of ribosomal DNA (rDNA) chromatin is consistently observed from 150 nm resolution down to 50 nm. We also observed that actively transcribed rDNA spatially segregates from bulk nucleolar chromatin. Using correlative light and electron microscopy (CLEM), we found that local rDNA clustering is forming a specific nucleolar subdomain visible in transmission electron microscopy, the yeast equivalent of metazoan fibrillar center. We conclude that nucleolar chromatin forms a distinct sub-nucleolar compartment in yeast, supporting the model of a tripartite structural organization of the yeast nucleolus.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108228"},"PeriodicalIF":2.7,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584210","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}
Pub Date : 2025-07-04DOI: 10.1016/j.jsb.2025.108232
Priyanka Garg , Xiangsong Feng , Swastik De , Joachim Frank
This study examines the validity of an assay that is used to report on the retainment of functional competence by ribosomes as they pass a microsprayer. We find a reproducible increase, rather than the expected decrease in GFP production as monitored by fluorescence, which may suggest heterogeneity or partial aggregation of ribosomes in solution. An even larger increase in functional activity is observed when sonication is used, pointing to mechanical agitation as the decisive factor in both scenarios. The results have a bearing on the design and interpretation of validation experiments in time-resolved cryo-EM based on microfluidic chips.
{"title":"Passage of ribosomes through microsprayer increases functional activity – Implications for activity assays in time-resolved cryo-EM","authors":"Priyanka Garg , Xiangsong Feng , Swastik De , Joachim Frank","doi":"10.1016/j.jsb.2025.108232","DOIUrl":"10.1016/j.jsb.2025.108232","url":null,"abstract":"<div><div>This study examines the validity of an assay that is used to report on the retainment of functional competence by ribosomes as they pass a microsprayer. We find a reproducible <em>increase</em>, rather than the expected <em>decrease</em> in GFP production as monitored by fluorescence, which may suggest heterogeneity or partial aggregation of ribosomes in solution. An even larger increase in functional activity is observed when sonication is used, pointing to mechanical agitation as the decisive factor in both scenarios. The results have a bearing on the design and interpretation of validation experiments in time-resolved cryo-EM based on microfluidic chips.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108232"},"PeriodicalIF":3.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575723","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}
Pub Date : 2025-06-26DOI: 10.1016/j.jsb.2025.108230
Sebastian Dorawa , Katarzyna Biniek-Antosiak , Magdalena Bejger , Anna-Karina Kaczorowska , Karol Ciuchcinski , Agnieszka Godlewska , Magdalena Płotka , Gudmundur O. Hreggvidsson , Lukasz Dziewit , Tadeusz Kaczorowski , Wojciech Rypniewski
We presents the discovery and molecular characterization of a novel lytic enzyme from the extremophilic Thermus thermophilus MAT72 phage vB_Tt72. The protein of 346-aa (MW = 39,705) functions as phage vB_Tt72 endolysin and shows low sequence identity (<37 %) to members of M23 family of peptidoglycan hydrolases, except for two uncharacterized endopeptidases of T. thermophilus phages: φYS40 (87 %) and φTMA (88 %). The enzyme exhibits lytic activity mainly against bacteria of the genus Thermus and, to a lesser extent, against other Gram-negative and Gram-positive bacteria. The protein is monomeric in solution and is highly thermostable (Tm = 98.3 °C). It retains ∼ 50 % of its lytic activity after 90 min of incubation at 99 °C. Crystallographic analysis, at 2.2 Å resolution, revealed a fold characteristic of M23 metallopeptidases, accounting for 40 % of the structure. The remaining parts of the molecule are folded in a manner that was previously undescribed. The M23 fold contains a Zn2+ ion coordinated by a conserved His-Asp-His triad, and two conserved His residues essential for catalysis. The active site is occupied by a phosphate or a sulfate anion, while the substrate-binding groove contains a ligand, which is a fragment of E. coli peptidoglycan. The common sequence-based criteria failed to identify the protein as (hyper)thermophilic. It is likely that the protein’s thermal stability is owed to peculiar features of its three-dimensional structure. Instead of trimmed surface loops, observed in many thermostable proteins, the catalytic domain contains two long loops that interlace and form an α-helical bundle with its own hydrophobic core.
{"title":"Crystal structure, enzymatic and thermodynamic properties of the Thermus thermophilus phage Tt72 lytic endopeptidase with unique structural signatures of thermal adaptation","authors":"Sebastian Dorawa , Katarzyna Biniek-Antosiak , Magdalena Bejger , Anna-Karina Kaczorowska , Karol Ciuchcinski , Agnieszka Godlewska , Magdalena Płotka , Gudmundur O. Hreggvidsson , Lukasz Dziewit , Tadeusz Kaczorowski , Wojciech Rypniewski","doi":"10.1016/j.jsb.2025.108230","DOIUrl":"10.1016/j.jsb.2025.108230","url":null,"abstract":"<div><div>We presents the discovery and molecular characterization of a novel lytic enzyme from the extremophilic <em>Thermus thermophilus</em> MAT72 phage vB_Tt72. The protein of 346-aa (MW = 39,705) functions as phage vB_Tt72 endolysin and shows low sequence identity (<37 %) to members of M23 family of peptidoglycan hydrolases, except for two uncharacterized endopeptidases of <em>T. thermophilus</em> phages: φYS40 (87 %) and φTMA (88 %). The enzyme exhibits lytic activity mainly against bacteria of the genus <em>Thermus</em> and, to a lesser extent, against other Gram-negative and Gram-positive bacteria. The protein is monomeric in solution and is highly thermostable (T<sub>m</sub> = 98.3 °C). It retains ∼ 50 % of its lytic activity after 90 min of incubation at 99 °C. Crystallographic analysis, at 2.2 Å resolution, revealed a fold characteristic of M23 metallopeptidases, accounting for 40 % of the structure. The remaining parts of the molecule are folded in a manner that was previously undescribed. The M23 fold contains a Zn<sup>2+</sup> ion coordinated by a conserved His-Asp-His triad, and two conserved His residues essential for catalysis. The active site is occupied by a phosphate or a sulfate anion, while the substrate-binding groove contains a ligand, which is a fragment of <em>E. coli</em> peptidoglycan. The common sequence-based criteria failed to identify the protein as (hyper)thermophilic. It is likely that the protein’s thermal stability is owed to peculiar features of its three-dimensional structure. Instead of trimmed surface loops, observed in many thermostable proteins, the catalytic domain contains two long loops that interlace and form an α-helical bundle with its own hydrophobic core.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108230"},"PeriodicalIF":3.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522821","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}
Pub Date : 2025-06-23DOI: 10.1016/j.jsb.2025.108229
Mia Argyrou , Eleni Pitsillou , Andrew Hung , Assam El-Osta , Tom C. Karagiannis
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogenic agent responsible for the coronavirus disease 2019 (COVID-19) pandemic, uses the trimeric spike protein to gain entry into the host cell. Structural studies have revealed that the spike protein is comprised of the S1 and S2 subunits. The S1 subunit of the spike protein contains the receptor-binding domain (RBD), which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor. The interaction between the RBD and ACE2 facilitates membrane fusion and host cell infection. The SARS-CoV-2 spike protein also contains a unique insertion of four amino acids that results in the 682-RRAR↓S-686 polybasic furin cleavage motif at the boundary of the S1 and S2 subunits. The furin cleavage motif contributes to the high infectivity and transmissibility of SARS-CoV-2. This review provides a comprehensive analysis of the molecular interactions of the spike protein, with a specific focus on the RBD and furin cleavage site. In addition to examining the binding characteristics with ACE2, the interactions with alternative receptors, such as neuropilin-1 (NRP1) and the nicotinic acetylcholine receptors (nAChRs) are highlighted. The ability of the spike protein to bind alternative receptors and host factors has been linked to the pathophysiology of COVID-19 and the persistence of symptoms in the post COVID-19 condition. Furthermore, we examine the impact of spike protein mutations on receptor affinity and disease severity. SARS-CoV-2 continues to evolve, with variants remaining an ongoing threat to public health. Understanding these molecular interactions is critical for the development of novel therapeutic interventions.
{"title":"Insights into the pathogenic mechanisms associated with the SARS-CoV-2 spike protein","authors":"Mia Argyrou , Eleni Pitsillou , Andrew Hung , Assam El-Osta , Tom C. Karagiannis","doi":"10.1016/j.jsb.2025.108229","DOIUrl":"10.1016/j.jsb.2025.108229","url":null,"abstract":"<div><div>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogenic agent responsible for the coronavirus disease 2019 (COVID-19) pandemic, uses the trimeric spike protein to gain entry into the host cell. Structural studies have revealed that the spike protein is comprised of the S1 and S2 subunits. The S1 subunit of the spike protein contains the receptor-binding domain (RBD), which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor. The interaction between the RBD and ACE2 facilitates membrane fusion and host cell infection. The SARS-CoV-2 spike protein also contains a unique insertion of four amino acids that results in the 682-RRAR↓S-686 polybasic furin cleavage motif at the boundary of the S1 and S2 subunits. The furin cleavage motif contributes to the high infectivity and transmissibility of SARS-CoV-2. This review provides a comprehensive analysis of the molecular interactions of the spike protein, with a specific focus on the RBD and furin cleavage site. In addition to examining the binding characteristics with ACE2, the interactions with alternative receptors, such as neuropilin-1 (NRP1) and the nicotinic acetylcholine receptors (nAChRs) are highlighted. The ability of the spike protein to bind alternative receptors and host factors has been linked to the pathophysiology of COVID-19 and the persistence of symptoms in the post COVID-19 condition. Furthermore, we examine the impact of spike protein mutations on receptor affinity and disease severity. SARS-CoV-2 continues to evolve, with variants remaining an ongoing threat to public health. Understanding these molecular interactions is critical for the development of novel therapeutic interventions.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108229"},"PeriodicalIF":3.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481082","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}
Pub Date : 2025-06-22DOI: 10.1016/j.jsb.2025.108226
Roman Ye. Brodskii , Olga V. Vashchenko
Lipid membranes are uniquely complex biological structures with large and still undisclosed regulatory potential in many living processes caused by versatile changes in their structure while adsorption of various guest molecules (dopants). This work is devoted to exploring spontaneous dopant-driven formation of lipid domains in a monolipid membrane observed experimentally for dopants with bimodal adsorption. The work offers the results obtained for a wide range of different cases exploiting our proposed original simulation method and numerical model. The central idea of the approach is dopant binding ‘like the surroundings’, i.e. preferential binding.
The value range of the preferential binding extent was determined, where stable domains are formed and their size distribution becomes steady. The density of domain size distribution is power-law, i.e. the domain patterns possesses self-similarity. Outside this range, only one phase dominates if the extent is too large, whereas if it is too small, great dispersion of membrane was observed, so the membrane is physically homogeneous. Various neighboring as well as different methods of calculation of dopant binding probabilities are considered. The results obtained differed quantitatively but not qualitatively. The suggested model and the domain definition are similar to those used in percolation theory. Thus, the results can be applicated to percolation problems.
Grounding on analysis of literature data on domain patterns formed in various lipid systems, we suggested that the preferential binding mechanism is in line with the mechanism of preferential neighboring which is implicitly assumed in such systems irrespective of their specific nature.
{"title":"Preferential binding as a driving mechanism of lipid domains formation","authors":"Roman Ye. Brodskii , Olga V. Vashchenko","doi":"10.1016/j.jsb.2025.108226","DOIUrl":"10.1016/j.jsb.2025.108226","url":null,"abstract":"<div><div>Lipid membranes are uniquely complex biological structures with large and still undisclosed regulatory potential in many living processes caused by versatile changes in their structure while adsorption of various guest molecules (dopants). This work is devoted to exploring spontaneous dopant-driven formation of lipid domains in a monolipid membrane observed experimentally for dopants with bimodal adsorption. The work offers the results obtained for a wide range of different cases exploiting our proposed original simulation method and numerical model. The central idea of the approach is dopant binding ‘like the surroundings’, i.e. preferential binding.</div><div>The value range of the preferential binding extent was determined, where stable domains are formed and their size distribution becomes steady. The density of domain size distribution is power-law, i.e. the domain patterns possesses self-similarity. Outside this range, only one phase dominates if the extent is too large, whereas if it is too small, great dispersion of membrane was observed, so the membrane is physically homogeneous. Various neighboring as well as different methods of calculation of dopant binding probabilities are considered. The results obtained differed quantitatively but not qualitatively. The suggested model and the domain definition are similar to those used in percolation theory. Thus, the results can be applicated to percolation problems.</div><div>Grounding on analysis of literature data on domain patterns formed in various lipid systems, we suggested that the preferential binding mechanism is in line with the mechanism of preferential neighboring which is implicitly assumed in such systems irrespective of their specific nature.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 3","pages":"Article 108226"},"PeriodicalIF":3.0,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484878","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号