Pub Date : 2025-02-06DOI: 10.1016/j.str.2025.01.013
Philipp Schönnenbeck, Benedikt Junglas, Carsten Sachse
Imaging of lipid structures and associated protein complexes using cryoelectron microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in particular when large amounts of data are involved. Here, we introduce the automated image-processing software cryo-vesicle image analyzer (CryoVIA) that parametrizes lipid structures of large datasets from cryo-EM images. This toolkit combines segmentation, structure identification with methods to automatically perform a large-scale data analysis of local and global membrane properties such as bilayer thickness, size, and curvature including membrane shape classifications. We included analyses of exemplary datasets of different lipid compositions and protein-induced lipid changes through an endosomal sorting complexes required for transport III (ESCRT-III) membrane remodeling protein. The toolkit opens new possibilities to systematically study structural properties of membrane structures and their modifications from cryo-EM images.
{"title":"CryoVIA: An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs","authors":"Philipp Schönnenbeck, Benedikt Junglas, Carsten Sachse","doi":"10.1016/j.str.2025.01.013","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.013","url":null,"abstract":"Imaging of lipid structures and associated protein complexes using cryoelectron microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in particular when large amounts of data are involved. Here, we introduce the automated image-processing software <em>cryo-vesicle image analyzer</em> (CryoVIA) that parametrizes lipid structures of large datasets from cryo-EM images. This toolkit combines segmentation, structure identification with methods to automatically perform a large-scale data analysis of local and global membrane properties such as bilayer thickness, size, and curvature including membrane shape classifications. We included analyses of exemplary datasets of different lipid compositions and protein-induced lipid changes through an endosomal sorting complexes required for transport III (ESCRT-III) membrane remodeling protein. The toolkit opens new possibilities to systematically study structural properties of membrane structures and their modifications from cryo-EM images.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"42 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-06DOI: 10.1016/j.str.2025.01.006
Haitao Yang, Lu Zhang, Quan Wang, Jun Li, Xiuna Yang, Yan Gao, Bing Zhang
In this Voices article, we introduce seven group leaders from the Anti-TB Structure Center (ATSC) in Shanghai, which was opened in 2020. The scientists at ATSC closely collaborate with the goal of identifying new drug targets and developing novel therapeutics against tuberculosis, COVID-19, and other infectious diseases.
{"title":"The Anti-TB Structural Center at ShanghaiTech University","authors":"Haitao Yang, Lu Zhang, Quan Wang, Jun Li, Xiuna Yang, Yan Gao, Bing Zhang","doi":"10.1016/j.str.2025.01.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.006","url":null,"abstract":"In this Voices article, we introduce seven group leaders from the Anti-TB Structure Center (ATSC) in Shanghai, which was opened in 2020. The scientists at ATSC closely collaborate with the goal of identifying new drug targets and developing novel therapeutics against tuberculosis, COVID-19, and other infectious diseases.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"137 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-06DOI: 10.1016/j.str.2025.01.015
Sarah Pellizzari, Erhu Cao
In this issue of Structure, Houser et al.1 report cryoelectron microscopy (cryo-EM) structures of two atypical forms of the heterotrimeric epithelial sodium channel (ENaC) in which either a δ or a β subunit assembles with one β and one γ subunit. These structures shed light on the molecular principles that govern the assembly of distinct ENaC trimers.
{"title":"Epithelial sodium channels assemble in an orderly manner: Biology does not play dice","authors":"Sarah Pellizzari, Erhu Cao","doi":"10.1016/j.str.2025.01.015","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.015","url":null,"abstract":"In this issue of <em>Structure</em>, Houser et al.<span><span><sup>1</sup></span></span> report cryoelectron microscopy (cryo-EM) structures of two atypical forms of the heterotrimeric epithelial sodium channel (ENaC) in which either a δ or a β subunit assembles with one β and one γ subunit. These structures shed light on the molecular principles that govern the assembly of distinct ENaC trimers.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"31 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-06DOI: 10.1016/j.str.2025.01.014
Benjamin J. Lane, Mariangela Dionysopoulou, Nana Yan, Jonathan D. Lippiat, Stephen P. Muench, Christos Pliotas
Bacterial mechanosensitive channels are divided into large (MscL) and small (MscS-like) conductance families. The function of MscS and MscL is to protect cells against osmotic shock by acting as pressure safety valves. Within the MscS-like family, E. coli encodes much larger channels, such as YbiO, MscK, and MscM, but their physiological role remains unclear. Compared to MscL their conductances are reported as 3–10 times lower. We show that YbiO can achieve a conductance of ∼3 nS, and an equivalent pore opening of > 25 Å in diameter, equaling the known largest gated pore, MscL. We determine a cryoelectron microscopy (cryo-EM) structure of YbiO in a sub-open conformation, demonstrating the existence of multiple substates. One substate is consistent with the pore opening extent of our structure and the other matches states previously thought to resemble full openings. Our findings demonstrate surprising capabilities, hinting at new physiological roles for YbiO and potentially other MscS-like channels.
{"title":"The mechanosensitive channel YbiO has a conductance equivalent to the largest gated-pore","authors":"Benjamin J. Lane, Mariangela Dionysopoulou, Nana Yan, Jonathan D. Lippiat, Stephen P. Muench, Christos Pliotas","doi":"10.1016/j.str.2025.01.014","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.014","url":null,"abstract":"Bacterial mechanosensitive channels are divided into large (MscL) and small (MscS-like) conductance families. The function of MscS and MscL is to protect cells against osmotic shock by acting as pressure safety valves. Within the MscS-like family, <em>E</em>. <em>coli</em> encodes much larger channels, such as YbiO, MscK, and MscM, but their physiological role remains unclear. Compared to MscL their conductances are reported as 3–10 times lower. We show that YbiO can achieve a conductance of ∼3 nS, and an equivalent pore opening of > 25 Å in diameter, equaling the known largest gated pore, MscL. We determine a cryoelectron microscopy (cryo-EM) structure of YbiO in a sub-open conformation, demonstrating the existence of multiple substates. One substate is consistent with the pore opening extent of our structure and the other matches states previously thought to resemble full openings. Our findings demonstrate surprising capabilities, hinting at new physiological roles for YbiO and potentially other MscS-like channels.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"62 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.
{"title":"Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage","authors":"Can Cai, Yueting Wang, Yunshu Liu, Qianqian Shao, Aohan Wang, Lin Li, Yaqi Zheng, Tianyi Zhang, Ziwen Luo, Chongguang Yang, Qianglin Fang","doi":"10.1016/j.str.2025.01.012","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.012","url":null,"abstract":"Bacteriophage T1, a member of Siphoviruses, infects <em>Escherichia coli</em> with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"50 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The microenvironment of membrane receptors controls their mobility, structure, interactions, and dynamics, but a systematic understanding of how it modulates receptor function is often lacking. Using single-molecule Förster resonance energy transfer (smFRET), we characterized how detergents and cholesterol modulate the conformational dynamics of metabotropic glutamate receptor 2 (mGluR2), a class C G protein-coupled receptor (GPCR). We found that, within the resolution of our measurements, all tested detergents stabilize the same overall active and inactive structure of different domains of mGluR2. However, the degree of stabilization and the equilibrium between active and inactive conformations depended on the detergent. Detergents with a single hydrophobic tail increased the active state occupancy compared to those with long, branched tails. Adding cholesterol to micelles with branched hydrophobic tails shifted the equilibrium toward the inactive state. Mutagenesis identified residues potentially involved in cholesterol interaction with mGluR2. Targeting the cholesterol-binding site with synthetic molecules could be a viable therapeutic approach.
{"title":"Direct effect of membrane environment on the activation of mGluR2 revealed by single-molecule FRET","authors":"Chiranjib Banerjee, Brandon Wey-Hung Liauw, Reza Vafabakhsh","doi":"10.1016/j.str.2025.01.011","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.011","url":null,"abstract":"The microenvironment of membrane receptors controls their mobility, structure, interactions, and dynamics, but a systematic understanding of how it modulates receptor function is often lacking. Using single-molecule Förster resonance energy transfer (smFRET), we characterized how detergents and cholesterol modulate the conformational dynamics of metabotropic glutamate receptor 2 (mGluR2), a class C G protein-coupled receptor (GPCR). We found that, within the resolution of our measurements, all tested detergents stabilize the same overall active and inactive structure of different domains of mGluR2. However, the degree of stabilization and the equilibrium between active and inactive conformations depended on the detergent. Detergents with a single hydrophobic tail increased the active state occupancy compared to those with long, branched tails. Adding cholesterol to micelles with branched hydrophobic tails shifted the equilibrium toward the inactive state. Mutagenesis identified residues potentially involved in cholesterol interaction with mGluR2. Targeting the cholesterol-binding site with synthetic molecules could be a viable therapeutic approach.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"6 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-04DOI: 10.1016/j.str.2025.01.010
Amy E. Kennedy, Adam H. Barczewski, Christina R. Arnoldy, J. Pepper Pennington, Kelly A. Tiernan, M. Beatriz Hidalgo, Caroline C. Reilly, Tanyawan Wongsri, Michael J. Ragusa, Gevorg Grigoryan, Dale F. Mierke, Maria Pellegrini
NEMO is an essential component in the activation of the canonical nuclear factor κB (NF-κB) pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the design and characterization of novel engineered constructs of the IKK-binding domain of NEMO, programmed to render this difficult protein domain amenable to NMR measurements and crystallization, while preserving its biological function. ZipNEMO binds IKKβ with nanomolar affinity, is amenable to heteronuclear nuclear magnetic resonance (NMR) techniques and structure determination by X-ray crystallography. We show that NMR spectra of zipNEMO allow to detect inhibitor binding in solution and resonance assignment. The crystal structure of zipNEMO reveals a novel ligand binding motif and the adaptability of the binding pocket and inspired the design of new peptide inhibitors.
{"title":"The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition","authors":"Amy E. Kennedy, Adam H. Barczewski, Christina R. Arnoldy, J. Pepper Pennington, Kelly A. Tiernan, M. Beatriz Hidalgo, Caroline C. Reilly, Tanyawan Wongsri, Michael J. Ragusa, Gevorg Grigoryan, Dale F. Mierke, Maria Pellegrini","doi":"10.1016/j.str.2025.01.010","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.010","url":null,"abstract":"NEMO is an essential component in the activation of the canonical nuclear factor κB (NF-κB) pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the design and characterization of novel engineered constructs of the IKK-binding domain of NEMO, programmed to render this difficult protein domain amenable to NMR measurements and crystallization, while preserving its biological function. ZipNEMO binds IKKβ with nanomolar affinity, is amenable to heteronuclear nuclear magnetic resonance (NMR) techniques and structure determination by X-ray crystallography. We show that NMR spectra of zipNEMO allow to detect inhibitor binding in solution and resonance assignment. The crystal structure of zipNEMO reveals a novel ligand binding motif and the adaptability of the binding pocket and inspired the design of new peptide inhibitors.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"61 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1016/j.str.2024.12.022
Yuri Rafael de Oliveira Silva, Carlos Contreras-Martel, Ricardo Rodrigues de Melo, Letícia Maria Zanphorlin, Daniel Maragno Trindade, Andréa Dessen
Acinetobacter baumannii is a major human pathogen responsible for a growing number of multi-antibiotic-resistant infections, and of critical priority for the World Health Organization (WHO). A. baumannii employs a type II secretion system (T2SS) to secrete toxins extracellularly to enable cytotoxicity and colonization. Lipase LipA, secreted by the A. baumannii T2SS, is required for virulence and fitness, and in the periplasm is maintained in an active state by its essential foldase, LipB. Here we report that LipA is able to recognize lipids of different chain lengths at extremes of pH and temperature, thanks to its stabilization by LipB through an extended, highly helical “embrace.” A vast bioinformatic analysis indicates that LipB-like foldases are widespread over numerous proteobacteria, and thus the extended foldase architecture shown here could be widespread. These results provide new insight into A. baumannii’s adaptability as a pathogen in different environments and could facilitate the development of novel antibacterials.
{"title":"Architecture of an embracing lipase-foldase complex of the type II secretion system of Acinetobacter baumannii","authors":"Yuri Rafael de Oliveira Silva, Carlos Contreras-Martel, Ricardo Rodrigues de Melo, Letícia Maria Zanphorlin, Daniel Maragno Trindade, Andréa Dessen","doi":"10.1016/j.str.2024.12.022","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.022","url":null,"abstract":"<em>Acinetobacter baumannii</em> is a major human pathogen responsible for a growing number of multi-antibiotic-resistant infections, and of critical priority for the World Health Organization (WHO). <em>A. baumannii</em> employs a type II secretion system (T2SS) to secrete toxins extracellularly to enable cytotoxicity and colonization. Lipase LipA, secreted by the <em>A. baumannii</em> T2SS, is required for virulence and fitness, and in the periplasm is maintained in an active state by its essential foldase, LipB. Here we report that LipA is able to recognize lipids of different chain lengths at extremes of pH and temperature, thanks to its stabilization by LipB through an extended, highly helical “embrace.” A vast bioinformatic analysis indicates that LipB-like foldases are widespread over numerous proteobacteria, and thus the extended foldase architecture shown here could be widespread. These results provide new insight into <em>A. baumannii</em>’s adaptability as a pathogen in different environments and could facilitate the development of novel antibacterials.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"166 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1016/j.str.2025.01.008
Merve Demir, Laura Koepping, Ya Li, Lynn Fujimoto, Andrey Bobkov, Jianhua Zhao, Taro Hitosugi, Eduard Sergienko
Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The inhibition of breast cancer growth by cyclocreatine targeting CKs indicates dependence of cancer cells on the “energy shuttle” for cell growth and survival. Hence, understanding key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present mutational and structural investigations on understudied ubiquitous MtCK that showed closure of the loop comprising His61 is specific to and relies on creatine binding and mechanism of phosphoryl transfer depends on electrostatics of active site. We demonstrate that previously identified pan-CK covalent inhibitor CKi inhibit breast cancer cell proliferation; however, our biochemical and structural data indicated that inhibition by CKi is highly dependent on covalent link formation and conformational changes upon creatine binding are not observed.
{"title":"Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor","authors":"Merve Demir, Laura Koepping, Ya Li, Lynn Fujimoto, Andrey Bobkov, Jianhua Zhao, Taro Hitosugi, Eduard Sergienko","doi":"10.1016/j.str.2025.01.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.008","url":null,"abstract":"Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The inhibition of breast cancer growth by cyclocreatine targeting CKs indicates dependence of cancer cells on the “energy shuttle” for cell growth and survival. Hence, understanding key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present mutational and structural investigations on understudied ubiquitous MtCK that showed closure of the loop comprising His61 is specific to and relies on creatine binding and mechanism of phosphoryl transfer depends on electrostatics of active site. We demonstrate that previously identified pan-CK covalent inhibitor CKi inhibit breast cancer cell proliferation; however, our biochemical and structural data indicated that inhibition by CKi is highly dependent on covalent link formation and conformational changes upon creatine binding are not observed.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"63 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-31DOI: 10.1016/j.str.2025.01.004
Alexander Krah, Vandana Grover, Tuck Choy Fong, Peter J. Bond, Gerhard Grüber
The Acinetobacter baumannii F1FO-ATP synthase is essential for the opportunistic human pathogen. Its membrane-embedded FO domain consists of the c-ring and subunit a. The c-ring translocates protons via a conserved carboxylate across the membrane via two half-channels in subunit a, and its revolution enables the F1 domain to carry out ATP formation. Here, we used molecular dynamics simulations, free energy calculations, and in vivo mutational experiments to assess the likely existence of water molecules in the binding site of the A. baumannii c-ring. We first predicted its binding site structure in the ion-locked conformation and extrapolated the presence of two water molecules in the ion-binding site. Based on our predictions, amino acid point mutations confirmed the critical role of key residues involved in the water-binding site upon ATP synthesis ability and cell growth. We discuss the implications of our findings in the context of rational drug design to target the A. baumannii FO domain.
{"title":"Water occupancy in the Acinetobacter baumannii F-ATP synthase c-ring and its implications as a novel inhibitor target","authors":"Alexander Krah, Vandana Grover, Tuck Choy Fong, Peter J. Bond, Gerhard Grüber","doi":"10.1016/j.str.2025.01.004","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.004","url":null,"abstract":"The <em>Acinetobacter baumannii</em> F<sub>1</sub>F<sub>O</sub>-ATP synthase is essential for the opportunistic human pathogen. Its membrane-embedded F<sub>O</sub> domain consists of the <em>c</em>-ring and subunit <em>a</em>. The <em>c</em>-ring translocates protons via a conserved carboxylate across the membrane via two half-channels in subunit <em>a</em>, and its revolution enables the F<sub>1</sub> domain to carry out ATP formation. Here, we used molecular dynamics simulations, free energy calculations, and <em>in vivo</em> mutational experiments to assess the likely existence of water molecules in the binding site of the <em>A. baumannii c</em>-ring. We first predicted its binding site structure in the ion-locked conformation and extrapolated the presence of two water molecules in the ion-binding site. Based on our predictions, amino acid point mutations confirmed the critical role of key residues involved in the water-binding site upon ATP synthesis ability and cell growth. We discuss the implications of our findings in the context of rational drug design to target the <em>A. baumannii</em> F<sub>O</sub> domain.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"60 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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