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Nutrients and Their Role in Autophagy Regulation 营养物质及其在自噬调节中的作用
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-14 DOI: 10.1021/acs.biochem.6c00482
Niall Wilson, Gamze Kocak, Sovan Sarkar, Yoana Rabanal Ruiz, Viktor I. Korolchuk
{"title":"Nutrients and Their Role in Autophagy Regulation","authors":"Niall Wilson,&nbsp;Gamze Kocak,&nbsp;Sovan Sarkar,&nbsp;Yoana Rabanal Ruiz,&nbsp;Viktor I. Korolchuk","doi":"10.1021/acs.biochem.6c00482","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00482","url":null,"abstract":"<p>Autophagy is a fundamental catabolic pathway that maintainscellularhomeostasis through the degradation and recycling of intracellularcomponents in response to nutrient limitation and metabolic stress.Increasing evidence indicates that autophagy is tightly regulatedby cellular metabolism, with nutrients and metabolites acting notonly as energy substrates and biosynthetic intermediates, but alsoas signaling molecules that directly modulate the autophagic machinery.In this review, we discuss how different metabolites regulate autophagythrough interconnected nutrient- and energy-sensing pathways. We furtherexamine how these metabolic signals coordinate distinct stages ofautophagosome biogenesis and autophagic flux under conditions of nutrientdeprivation or energy stress. Collectively, metabolite-autophagy crosstalkemerges as a central mechanism that enables cells to balance metabolicdemand with intracellular resource availability, while its dysregulationcontributes to metabolic imbalance and age-associated pathology.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3349–3370"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305717","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}
引用次数: 0
The GndA Microprotein Promotes Cell Growth during Heat Shock in Escherichia coli GndA微蛋白促进大肠杆菌热休克中的细胞生长
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-16 DOI: 10.1021/acs.biochem.6c00391
Jessica J. Mohsen, Natalia R. Bertolotti, Kevin Jiang, Michael G. Mohsen, Christine M. DeRosa, Nikita Dewani, Laura Quinto, Georgina Dabdoub, Betel Erkalo, Ane Landajuela, Erdem Karatekin, Farren J. Isaacs, Sarah A. Slavoff
{"title":"The GndA Microprotein Promotes Cell Growth during Heat Shock in Escherichia coli","authors":"Jessica J. Mohsen,&nbsp;Natalia R. Bertolotti,&nbsp;Kevin Jiang,&nbsp;Michael G. Mohsen,&nbsp;Christine M. DeRosa,&nbsp;Nikita Dewani,&nbsp;Laura Quinto,&nbsp;Georgina Dabdoub,&nbsp;Betel Erkalo,&nbsp;Ane Landajuela,&nbsp;Erdem Karatekin,&nbsp;Farren J. Isaacs,&nbsp;Sarah A. Slavoff","doi":"10.1021/acs.biochem.6c00391","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00391","url":null,"abstract":"<p>Hundreds of bacterial small open reading frames (sORFs)encodingmicroproteins of fewer than 50 amino acids have recently been identified.Biological functions have been ascribed to an increasing number ofmicroproteins, some of which play roles in bacterial stress responses.In this work, we provide evidence that GndA, a frameshifted 36-aminoacid microprotein encoded in an internal open reading frame overlappingthe 6-phosphogluconate dehydrogenase (6PGD) coding sequence (CDS),functions in the response to heat shock. We demonstrate independentcontributions of GndA and 6PGD to cell growth at a high temperature.GndA is hydrophobic and associates with the pyruvate dehydrogenasecomplex and the inner membrane. Consistent with a role in cellularhomeostasis, GndA mutations alter the transcriptional response toheat shock. These results demonstrate that GndA promotes bacterialcell growth at high temperatures independently of the 6PGD proteinthat it overlaps. GndA thus expands the paradigm of bacterial microproteinsthat function in cellular stress responses.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3548–3558"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305763","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}
引用次数: 0
What Computational Simulations Tell Us about Cryptochromes in Magnetoreception 计算模拟告诉我们关于隐色素在磁感受中的作用
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-21 DOI: 10.1021/acs.biochem.6c00516
Mariastella Cascone, Lorenzo Cupellini, Benedetta Mennucci
{"title":"What Computational Simulations Tell Us about Cryptochromes in Magnetoreception","authors":"Mariastella Cascone,&nbsp;Lorenzo Cupellini,&nbsp;Benedetta Mennucci","doi":"10.1021/acs.biochem.6c00516","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00516","url":null,"abstract":"<p>The ability of migratorybirds to orient using the Earth’smagnetic field has been proposed to rely on a radical-pair mechanismoperating within Cryptochrome 4, a blue-light flavoprotein. In thisperspective, we review how computational approaches have shaped ourmolecular understanding of cryptochrome-based magnetoreception. Weorganize the discussion around the three steps that connect lightabsorption to a cellular signal: the photochemical step, in whichlight absorption by FAD drives a hole-hopping electron-transfer cascadealong a conserved tryptophan tetrad; the spin-dependent step, in whichthe resulting radical pair interconverts between singlet and tripletstates under the influence of the magnetic field; and the structuralstep, in which this transient information is converted into a long-livedsignaling state. The early electron-transfer events are now describedwith growing confidence and appear conserved across avian orthologs,although the relative stability of the final radical-pair states remainsdebated. The spin-dependent step remains more problematic: once thefluctuations of the hyperfine couplings and a realistic number ofnuclear spins are included, the predicted magnetic sensitivity atgeomagnetic field intensities becomes very small, and explaining themagnitude of the effect is still a central open problem. The postactivationconformational dynamics, involving intrinsically disordered regions,remains the principal challenge. We suggest that atomistic multiscalemodeling, integrated with artificial intelligence-based approaches,has become indispensable for connecting the conserved photochemistryto this downstream process.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3311–3321"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305885","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}
引用次数: 0
Stacking Up: The Expanding Catalog of Filament-Forming Enzymes 堆积:纤维形成酶的扩展目录
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-15 DOI: 10.1021/acs.biochem.6c00586
Nancy C. Horton
{"title":"Stacking Up: The Expanding Catalog of Filament-Forming Enzymes","authors":"Nancy C. Horton","doi":"10.1021/acs.biochem.6c00586","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00586","url":null,"abstract":"<p>Enzyme filamentationhas emerged as a widespread and functionallyimportant mode of macromolecular organization. Once viewed as an unusualproperty of a few metabolic enzymes, reversible filament formationis now known for more than 50 enzymes across bacteria, archaea, plants,fungi, and animals. This review summarizes recent progress in thefield, expanding substantially on our 2019 analysis and incorporatingmore than 300 new publications. We survey the known filament-formingenzymes, their catalytic activities, biological contexts, filamentarchitectures, and available structural information from X-ray crystallography,cryo-electron microscopy, and <em>in cellulo</em> imagingapproaches. Filamenting enzymes span five major enzyme classes andfunction in metabolism, stress responses, signaling, replication,and host defense. In many cases, polymerization occurs at criticalmetabolic branch points and appears to regulate enzyme activity, allostery,substrate channeling, localization, or sequestration. Distinct filamentgeometries, including linear stacks, solenoidal coils, tubes, andrings, are associated with specific functional outcomes and cellularroles. We also highlight emerging <em>in cellulo</em> structuralstudies of enzyme filaments, summarizing the insights they provideinto filament organization and cellular assembly when available. Together,these findings highlight enzyme filamentation as a common mode ofmacromolecular organization with consequences for structure, assembly,and function in diverse biological contexts.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3322–3348"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305748","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}
引用次数: 0
Targeting Tyrosine-Anchored Nonapeptides for Lipid-Binding Events 针对酪氨酸锚定的非肽脂质结合事件
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-15 DOI: 10.1021/acs.biochem.6c00372
Ann C. Kimble-Hill, Bruce D. Ray, Horia I. Petrache
{"title":"Targeting Tyrosine-Anchored Nonapeptides for Lipid-Binding Events","authors":"Ann C. Kimble-Hill,&nbsp;Bruce D. Ray,&nbsp;Horia I. Petrache","doi":"10.1021/acs.biochem.6c00372","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00372","url":null,"abstract":"<p>Short polypeptides are increasingly used in cancer researchasmodular systems for selectively targeting cellular environments, includingmembrane interfaces that regulate signaling and trafficking. Theseapplications rely on the ability of short sequences to encode specificinteractions with defined biological targets. One such target classis angiomotins (Amots), adaptor proteins that regulate cell proliferationand differentiation through selective binding to phosphatidylinositol-containingmembranes, followed by membrane deformation and lipid reorganization.Because this activity depends on sequence-specific membrane recognition,angiomotin provides a useful model for determining how local peptidestructure drives selective membrane interaction. However, the structuralbasis for this interaction and the role of individual tyrosine residueswithin the Amot80/130 coiled-coil homology domain remain unclear.To address this, nine-amino-acid peptides (nonapeptides) centeredon the five native tyrosines were studied to determine how local sequencecontext influences membrane interaction. Nuclear magnetic resonancespectroscopy in solution indicates that these peptides adopt definedstructural features, including restricted tyrosine ring motion andinter-residue contacts. Absorbance and fluorescence measurements inhydrophobic solvent systems and lipid-containing vesicle preparationsshow sequence-dependent differences consistent with variations inhydrophobic partitioning and lipid headgroup interactions. Computationalmodeling using solution NMR structural models further identifies sequence-and conformation-dependent differences in lipid-headgroup contacts,membrane orientation, and predicted membrane insertion. Together,these results support a model that local sequence context surroundingindividual tyrosines governs selective interaction with hydrophobicenvironments and phosphatidylinositol-containing membranes, providinga framework for peptide-based membrane targeting in cancer-relevantsystems.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3434–3450"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305757","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}
引用次数: 0
Distributed Structural Elements of DWORF Coordinate Activation of the Sarcoplasmic Reticulum Calcium Pump SERCA 肌浆网钙泵(SERCA) DWORF协调激活的分布结构元件
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-26 DOI: 10.1021/acs.biochem.6c00662
Justin Gregory, M’lynn E. Fisher, M. Joanne Lemieux, Howard S. Young
{"title":"Distributed Structural Elements of DWORF Coordinate Activation of the Sarcoplasmic Reticulum Calcium Pump SERCA","authors":"Justin Gregory,&nbsp;M’lynn E. Fisher,&nbsp;M. Joanne Lemieux,&nbsp;Howard S. Young","doi":"10.1021/acs.biochem.6c00662","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00662","url":null,"abstract":"<p>Many physiological processes are controlled by changesin cytosoliccalcium, including muscle contraction, neuronal transmission, andcell proliferation. In muscle, the sarco-endoplasmic reticulum calciumATPase (SERCA) restores resting cytosolic calcium by transportingcalcium into the sarcoplasmic reticulum, thereby promoting relaxation.In cardiac muscle, SERCA is regulated by phospholamban (PLN) and dwarfopen reading frame (DWORF), which inhibit and activate SERCA, respectively.To investigate the mechanism of DWORF-mediated activation, we focusedon Trp<sup>22</sup>, an unusual tryptophan residue positioned nearthe center of the DWORF transmembrane domain. This position resemblesthe recently identified transmembrane binding site for small-moleculeSERCA activators, suggesting that Trp<sup>22</sup> may play a directrole in activation. Consistent with this hypothesis, calcium-dependentATPase measurements in reconstituted membranes showed that a Trp<sup>22</sup>-Ala substitution completely abolished SERCA activation.We next tested whether residues outside the central transmembraneregion contribute to activation by modulating SERCA-DWORF interactions.Phosphomimetic substitutions at the N-terminal residues Ser<sup>7</sup>, Thr<sup>8</sup>, and Ser<sup>10</sup> eliminated SERCA activation,suggesting that the N-terminus modulates DWORF positioning. More strikingly,substitutions within the C-terminal motif Tyr<sup>31</sup>, Val<sup>32</sup>, Phe<sup>34</sup>, and Ser<sup>35</sup> profoundly alteredfunction. Tyr<sup>31</sup>-Ala, Val<sup>32</sup>-Ala, and Phe<sup>34</sup>-Ala converted DWORF from an activator to an inhibitor, whereasSer<sup>35</sup>-Ala and Ser<sup>35</sup>-Pro caused loss of activation.Together, these results support a coordinated mechanism in which Trp<sup>22</sup> acts as a critical determinant of SERCA activation, theN-terminus provides the potential for reversible regulation, and theC-terminus constrains the DWORF transmembrane helix in an activation-competentstate.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3451–3461"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305963","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}
引用次数: 0
Characterization of a Unique Carbohydrate-Binding Module from Akkermansia muciniphila that Binds Ganglioside-Associated Glycans 一种独特的碳水化合物结合模块的表征,该模块结合神经节苷类相关聚糖
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-15 DOI: 10.1021/acs.biochem.6c00509
Janique Miller, Joshua Steward, Davide Rossotto, Omid Haji-Ghassemi, Melanie A. Higgins
{"title":"Characterization of a Unique Carbohydrate-Binding Module from Akkermansia muciniphila that Binds Ganglioside-Associated Glycans","authors":"Janique Miller,&nbsp;Joshua Steward,&nbsp;Davide Rossotto,&nbsp;Omid Haji-Ghassemi,&nbsp;Melanie A. Higgins","doi":"10.1021/acs.biochem.6c00509","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00509","url":null,"abstract":"<p><em>Akkermansia muciniphila</em> is a mucin-degradinggutsymbiont that promotes host metabolic health through its ability toutilize host-derived glycans. Central to this microbe is its diverseset of glycoside hydrolases (GHs), specifically GHs involved in degradinghost glycans like mucin. Here, we characterize an <em>A. muciniphila</em> GH from family 123 (AmGH123), that has β-<em>N</em>-acetyl-<span>d</span>-galactosaminidase activity, removing terminalβ-linked GalNAc from ganglioside-associated glycans similarto other GH123s. In addition, we identify and characterize a uniquecarbohydrate-binding module from family 32 associated with AmGH123(AmGH123<sup>CBM32</sup>), representing the first CBM characterizedfrom <em>A. muciniphila</em>. AmGH123<sup>CBM32</sup> selectivelybinds GalNAc-terminated ganglioside-associated glycans, revealingpreviously unrecognized ligand specificity for CBM32 members. Structuralanalysis and site-directed mutagenesis reveal a distinct ligand-bindingpocket in AmGH123<sup>CBM32</sup>, highlighting diverse strategiesfor glycan recognition within this family.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3383–3388"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305725","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}
引用次数: 0
Beyond the Active Site: Allosteric Tail of HIV-1 Protease Is a Potential Target for Inhibiting Dimerization 超越活性位点:HIV-1蛋白酶的变构尾部是抑制二聚化的潜在靶标
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-19 DOI: 10.1021/acs.biochem.6c00441
Avinash Dakshinamoorthy, Sanjib Senapati
{"title":"Beyond the Active Site: Allosteric Tail of HIV-1 Protease Is a Potential Target for Inhibiting Dimerization","authors":"Avinash Dakshinamoorthy,&nbsp;Sanjib Senapati","doi":"10.1021/acs.biochem.6c00441","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00441","url":null,"abstract":"<p>HIVprotease (HIVPR) is one of the key targets in AIDStherapy.All ten FDA-approved drugs targeting this enzyme compete with thesubstrates in binding to its active site. However, the emergence ofdrug-resistant mutants in active and nonactive sites of HIVPR hascompromised the efficacy of these drugs. Nonetheless, darunavir (DRV)and tipranavir (TPV) have exhibited greater success than the othereight drugs, presumably due to their dual mode of action: (i) inhibitingprotease activity and (ii) blocking protease dimerization. Althoughcrystal structures have explained the inhibitory mechanism of proteaseactivity, the mechanism of inhibiting the dimerization process ispoorly understood. In this study, we employ advanced molecular dynamicssimulation methods to identify the precise binding motifs of DRV andTPV with monomeric HIVPR. Our results suggest that both inhibitorsbind stably to an allosteric pocket located in the tail region ofthe enzyme. Results also elucidate reversible association–dissociationof the drugs between the conventional active site and the newly identifiedtail cavity through surface diffusion. Structural analysis revealedthat drug binding to the tail pocket induces a conformational extensionof the C-terminal α-helix, a change that sequesters the terminalresidues required for stable dimer formation. Our finding aligns verywell with the reported ESI-MS spectra showing the tail interface asa crucial domain in forming a stable HIV protease dimer. Our resultpaves the way for designing a new class of HIVPR drugs that couldtarget the C-terminal to effectively lock it in the monomeric form,potentially bypassing the cross-resistance due to active-site mutations.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3462–3476"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305837","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}
引用次数: 0
Quinone Reductase 2 Dimerization is Dynamically Driven by Ligand Binding 醌还原酶2二聚化是由配体结合动态驱动的
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-09-24 DOI: 10.1021/acs.biochem.6c00461
Maya Miller, Dan Loewenthal, Philipp Kukura, Nathaniel Gould
{"title":"Quinone Reductase 2 Dimerization is Dynamically Driven by Ligand Binding","authors":"Maya Miller,&nbsp;Dan Loewenthal,&nbsp;Philipp Kukura,&nbsp;Nathaniel Gould","doi":"10.1021/acs.biochem.6c00461","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00461","url":null,"abstract":"<p>Human quinone reductase 2 is a cytosolic flavoproteininvolvedin cell physiology and metabolism, and implicated in several diseases.However, the mechanisms that govern its oligomeric assembly and diversefunctional outcomes remain incompletely understood. Here, we employnative mass spectrometry to directly resolve the dynamic oligomericlandscape of recombinant human quinone reductase 2 expressed in <em>Escherichia coli</em>, preserving noncovalent interactionsand enabling analysis of assembly behavior under native conditions.Quinone reductase 2 is predominantly observed as a dimer stabilizedby multiple noncovalently bound ligands, giving rise to discrete species.Top-down native mass spectrometry reveals a single intact proteoform,excluding covalent modification or covalently bound flavins as driversof oligomerization. Binding of flavin adenine dinucleotide robustlystabilizes the dimer, while unexpectedly, flavin mononucleotide alsopromotes dimer formation. As flavin mononucleotide and flavin adeninedinucleotide differ structurally by the presence of an adenine dinucleotidemoiety, we hypothesized that purine nucleotide binding itself maymodulate quinone reductase 2 assembly. Consistent with this, we identifya new concentration-dependent effect of guanosine triphosphate onquinone reductase 2 dimerization. Functional reductase assays showthat flavin-stabilized dimers exhibit the highest catalytic activity,whereas guanosine triphosphate-induced dimers retain reduced activity.Binding of the inhibitor YB537 abolishes activity despite promotingdimer formation. Together, these findings reveal ligand-dependentstructural plasticity in quinone reductase 2 oligomerization thatis decoupled from reductase activity. This supports a model in whichdimerization is shaped by the local ligand environment, enabling distinctfunctional states and suggesting a broader regulatory role beyondreductase catalysis.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3559–3568"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149306011","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}
引用次数: 0
Structure and Dynamics of Burkholderia pseudomallei OXA-57, a Distinctive Low-Efficiency Class D β-Lactamase with Carbapenem-Hydrolyzing Activity 具有碳青霉烯水解活性的D类β-内酰胺酶OXA-57的结构与动力学研究
IF 2.7 3区 生物学
Biochemistry Biochemistry Pub Date : 2026-11-03 Epub Date: 2026-10-22 DOI: 10.1021/acs.biochem.6c00668
Éilís C. Bragginton, Charlotte K. Colenso, Michael Beer, Karina Calvopiña, Philip Hinchliffe, John M. Shaw, Catherine. L. Tooke, Rathanin Seng, Narisara Chantratita, Adrian J. Mulholland, Christopher J. Schofield, James Spencer
{"title":"Structure and Dynamics of Burkholderia pseudomallei OXA-57, a Distinctive Low-Efficiency Class D β-Lactamase with Carbapenem-Hydrolyzing Activity","authors":"Éilís C. Bragginton,&nbsp;Charlotte K. Colenso,&nbsp;Michael Beer,&nbsp;Karina Calvopiña,&nbsp;Philip Hinchliffe,&nbsp;John M. Shaw,&nbsp;Catherine. L. Tooke,&nbsp;Rathanin Seng,&nbsp;Narisara Chantratita,&nbsp;Adrian J. Mulholland,&nbsp;Christopher J. Schofield,&nbsp;James Spencer","doi":"10.1021/acs.biochem.6c00668","DOIUrl":"https://doi.org/10.1021/acs.biochem.6c00668","url":null,"abstract":"<p>The Gram-negativebacterium <em>Burkholderia pseudomallei</em> causes the severe disease melioidosis. β-Lactams, includingcarbapenems, are the primary treatment for <em>B. pseudomallei</em> infections, but are susceptible to chromosomal serine β-lactamases(SBLs), including the class D enzyme OXA-57. Here we show that recombinantOXA-57 is active toward penicillins and first-generation cephalosporins,slowly hydrolyzes carbapenems, including imipenem and meropenem, butis inactive toward oxyimino-cephalosporins (e.g., ceftazidime). Unlikemany OXA enzymes, OXA-57 is sensitive to the mechanism-based SBL inhibitorclavulanic acid, but less so to the diazabicyclooctane avibactam andnot to the cyclic boronate vaborbactam. Crystal structures of covalentOXA-57:avibactam and OXA-57:meropenem complexes reveal limited hydrogen-bondinginteractions with bound ligands. In molecular dynamics simulations,the bound meropenem acyl-enzyme is mobile, with the 6α-hydroxyethylgroup able to sample different orientations, while the water moleculenecessary for deacylation is bound only transiently. These observationsare consistent with the low level of meropenem turnover, supportingproposals that limited carbapenemase activity is a general propertyof OXA β-lactamases, and highlight the potential importanceof OXA-57 in <em>B. pseudomallei</em> β-lactamresistance.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"65 21","pages":"3514–3532"},"PeriodicalIF":2.7,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149306072","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}
引用次数: 0
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