Pub Date : 2025-10-15DOI: 10.1016/j.jmb.2025.169486
Maria A. Schumacher, Rajiv R. Singh, Raul Salinas
Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. Interestingly, Mycobacterium tuberculosis (Mtb) lacks most common NAPs and only recently have NAPs been uncovered in this bacterium. One such protein, NapA, was revealed to be an essential Mtb NAP that can bridge DNA. NapA shows no sequence homology to any protein and hence its DNA-binding functions remain unclear. Here we describe structures of apo NapA and a DNA-bound complex of NapA. The NapA structures reveal a dimeric fold for the protein, which is supported by mass photometry analyses, with each subunit comprised of an extended α1 helix and C-terminal three-helix module. The α1 helices combine to form a helical-bundle dimer scaffold that forms dimer-of-dimers at elevated protein concentrations. Each NapA dimer projects two DNA interacting elements, that bind and link between DNA sites. Combined these studies provide mechanistic insight into the DNA binding and bridging capabilities of a unique NAP that appears broadly conserved among most Actinobacteria.
{"title":"Structural Studies on the M. tuberculosis Nucleoid-associated-Protein, NapA, Indicates DNA Bridging Mechanism","authors":"Maria A. Schumacher, Rajiv R. Singh, Raul Salinas","doi":"10.1016/j.jmb.2025.169486","DOIUrl":"10.1016/j.jmb.2025.169486","url":null,"abstract":"<div><div>Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. Interestingly, <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>) lacks most common NAPs and only recently have NAPs been uncovered in this bacterium. One such protein, NapA, was revealed to be an essential <em>Mtb</em> NAP that can bridge DNA. NapA shows no sequence homology to any protein and hence its DNA-binding functions remain unclear. Here we describe structures of apo NapA and a DNA-bound complex of NapA. The NapA structures reveal a dimeric fold for the protein, which is supported by mass photometry analyses, with each subunit comprised of an extended α1 helix and C-terminal three-helix module. The α1 helices combine to form a helical-bundle dimer scaffold that forms dimer-of-dimers at elevated protein concentrations. Each NapA dimer projects two DNA interacting elements, that bind and link between DNA sites. Combined these studies provide mechanistic insight into the DNA binding and bridging capabilities of a unique NAP that appears broadly conserved among most Actinobacteria.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169486"},"PeriodicalIF":4.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312013","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 cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no longer feasible. To address this, we developed NoAC (Non-model Organism Atlas Constructor), a web tool that automatically constructs knowledge bases and query interfaces for non-model organism genomes without programming skills. In NoAC, users simply upload the gene or transcript information of a given non-model organism genome and select an appropriate reference model organism. NoAC then identifies orthologous genes, infers functional annotations, and sets up a searchable knowledge base. Functional annotations for the non-model organism such as gene ontology (GO) terms, protein domains, pathways, and physical/genetic interactors are predicted and transferred from the reference organism to the target genome. In an example non-model organism Phalaenopsis equestris, NoAC associates functional annotations for more than half of its 21,938 genes. Through case studies of the non-model organism Phalaenopsis equestris, we demonstrated that the knowledge base constructed by NoAC can reveal key functional aspects of PeSEP2 and PaMLS, supporting the study of novel genes involved in flower development. Another case study on the gene Wnt-1 in Bicyclus anynana further illustrates the applicability of NoAC in investigating insect segmentation and morphogen activity, highlighting its broader utility across diverse taxonomic genomes. In summary, NoAC allows general researchers to study non-model organisms with minimal in silico barriers. NoAC and its user tutorial are freely available at https://github.com/cosbi-nckuee/NoAC/.
{"title":"NoAC: an automatic builder for knowledge bases and query interfaces on genomes of non-model organisms","authors":"Tzu-Hsien Yang , You-Yi Chen , Chien-Chi Liao , Hao-Chen Zheng , Chun-Lin Hsieh , Jia-Syuan Chen , Wen-Chieh Tsai , Yan-Yuan Tseng , Wei-Sheng Wu","doi":"10.1016/j.jmb.2025.169488","DOIUrl":"10.1016/j.jmb.2025.169488","url":null,"abstract":"<div><div>The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no longer feasible. To address this, we developed NoAC (Non-model Organism Atlas Constructor), a web tool that automatically constructs knowledge bases and query interfaces for non-model organism genomes without programming skills. In NoAC, users simply upload the gene or transcript information of a given non-model organism genome and select an appropriate reference model organism. NoAC then identifies orthologous genes, infers functional annotations, and sets up a searchable knowledge base. Functional annotations for the non-model organism such as gene ontology (GO) terms, protein domains, pathways, and physical/genetic interactors are predicted and transferred from the reference organism to the target genome. In an example non-model organism <em>Phalaenopsis equestris</em>, NoAC associates functional annotations for more than half of its 21,938 genes. Through case studies of the non-model organism <em>Phalaenopsis equestris</em>, we demonstrated that the knowledge base constructed by NoAC can reveal key functional aspects of <em>PeSEP2</em> and <em>PaMLS</em>, supporting the study of novel genes involved in flower development. Another case study on the gene <em>Wnt-1</em> in <em>Bicyclus anynana</em> further illustrates the applicability of NoAC in investigating insect segmentation and morphogen activity, highlighting its broader utility across diverse taxonomic genomes. In summary, NoAC allows general researchers to study non-model organisms with minimal <em>in silico</em> barriers. NoAC and its user tutorial are freely available at <span><span>https://github.com/cosbi-nckuee/NoAC/</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169488"},"PeriodicalIF":4.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312078","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 : 2025-10-15DOI: 10.1016/j.jmb.2025.169489
Lewis E. Kay, Remco Sprangers
{"title":"NMR Studies of Biomolecular Systems","authors":"Lewis E. Kay, Remco Sprangers","doi":"10.1016/j.jmb.2025.169489","DOIUrl":"10.1016/j.jmb.2025.169489","url":null,"abstract":"","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 23","pages":"Article 169489"},"PeriodicalIF":4.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312062","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 : 2025-10-11DOI: 10.1016/j.jmb.2025.169484
Megha N. Karanth , Debajyoti De , John P. Kirkpatrick , Mark Jeeves , Teresa Carlomagno
Non-ribosomal peptide synthetases (NRPSs) are complex molecular machineries that synthesize non-proteinaceous peptides in microorganisms. These peptides (NRPs) usually present a wide range of biological activities and are highly regarded as potential anti-cancer and anti-infective agents. Because of their chemical complexity, derivatives of NRPs with tailored pharmacological properties are difficult to synthesize chemically, which has triggered efforts to understand the functional mechanisms of NRPS systems and develop protein engineering strategies aimed at enabling enzymatic synthesis of non-natural NRPs. A fundamental reaction step of NRPS systems is the formation of peptide bonds between amino-acid-like building blocks. This reaction is catalyzed by so-called condensation domains. The structures of several condensation domains and their complexes have been solved by crystallography and electron microscopy, but these structures have failed to provide the key to the design of artificial condensation domains. Here, we use NMR spectroscopy to reveal a complex network of dynamics in the condensation domain of the NRPS responsible for the synthesis of Tomaymycin and reveal how these motions mediate communication between the two substrate binding sites, providing a means to synchronize interactions for efficient catalysis. Our results underline the impact of dynamics, next to structure, on the function of enzymatic units and reinforce the need to consider conformational flexibility in the design of proteins with altered functions.
{"title":"Slow Dynamics Orchestrate Communication Between Binding Sites in the Condensation Domain of a Non-ribosomal Peptide Synthetase","authors":"Megha N. Karanth , Debajyoti De , John P. Kirkpatrick , Mark Jeeves , Teresa Carlomagno","doi":"10.1016/j.jmb.2025.169484","DOIUrl":"10.1016/j.jmb.2025.169484","url":null,"abstract":"<div><div>Non-ribosomal peptide synthetases (NRPSs) are complex molecular machineries that synthesize non-proteinaceous peptides in microorganisms. These peptides (NRPs) usually present a wide range of biological activities and are highly regarded as potential anti-cancer and anti-infective agents. Because of their chemical complexity, derivatives of NRPs with tailored pharmacological properties are difficult to synthesize chemically, which has triggered efforts to understand the functional mechanisms of NRPS systems and develop protein engineering strategies aimed at enabling enzymatic synthesis of non-natural NRPs. A fundamental reaction step of NRPS systems is the formation of peptide bonds between amino-acid-like building blocks. This reaction is catalyzed by so-called condensation domains. The structures of several condensation domains and their complexes have been solved by crystallography and electron microscopy, but these structures have failed to provide the key to the design of artificial condensation domains. Here, we use NMR spectroscopy to reveal a complex network of dynamics in the condensation domain of the NRPS responsible for the synthesis of Tomaymycin and reveal how these motions mediate communication between the two substrate binding sites, providing a means to synchronize interactions for efficient catalysis. Our results underline the impact of dynamics, next to structure, on the function of enzymatic units and reinforce the need to consider conformational flexibility in the design of proteins with altered functions.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 23","pages":"Article 169484"},"PeriodicalIF":4.5,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285397","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}
Escherichia coli is a Gram-negative opportunistic pathogen causing nosocomial infections through the production of various virulence factors. Type 1 secretion systems (T1SS) contribute to virulence by mediating the one-step secretion of unfolded substrates into the extracellular space, bypassing the periplasm. A well-studied example is the hemolysin A (HlyA) system, which secretes HlyA toxin in an unfolded state across the inner and outer membranes. T1SS typically comprise a homodimeric ABC transporter (HlyB), a membrane fusion protein (HlyD), and the outer membrane protein TolC. Some ABC transporters in T1SS also contain N-terminal C39 peptidase or peptidase-like (CLD) domains implicated in substrate interaction or activation. Recent cryo-EM studies have resolved the inner-membrane complex as trimer of HlyB homodimers with associated HlyD protomers. However, a full structural model including TolC remains unavailable. We present the first complete structural model of the HlyA T1SS, constructed using template- and MSA-based information and validated by SAXS. Molecular dynamics simulations provide insights into the function of the CLD domains, which are partially absent from existing cryo-EM structures. These domains may modulate transport by stabilizing specific conformations of the complex. Simulations with a C-terminal fragment of HlyA indicate that toxin binding occurs in the occluded conformation of HlyB, potentially initiating substrate transport through a single HlyB protomer before transitioning to an inward-facing state. HlyA binding also induces allosteric effects on HlyD, affecting key residues involved in TolC recruitment. These results indicate how substrate recognition and transport are coupled and may support the development of antimicrobial strategies targeting the T1SS.
{"title":"Molecular Insights into CLD Domain Dynamics and Toxin Recruitment of the HlyA E. coli T1SS","authors":"Rocco Gentile , Stephan Schott-Verdugo , Sakshi Khosa , Cigdem Günes , Michele Bonus , Jens Reiners , Sander H.J. Smits , Lutz Schmitt , Holger Gohlke","doi":"10.1016/j.jmb.2025.169485","DOIUrl":"10.1016/j.jmb.2025.169485","url":null,"abstract":"<div><div><em>Escherichia coli</em> is a Gram-negative opportunistic pathogen causing nosocomial infections through the production of various virulence factors. Type 1 secretion systems (T1SS) contribute to virulence by mediating the one-step secretion of unfolded substrates into the extracellular space, bypassing the periplasm. A well-studied example is the hemolysin A (HlyA) system, which secretes HlyA toxin in an unfolded state across the inner and outer membranes. T1SS typically comprise a homodimeric ABC transporter (HlyB), a membrane fusion protein (HlyD), and the outer membrane protein TolC. Some ABC transporters in T1SS also contain N-terminal C39 peptidase or peptidase-like (CLD) domains implicated in substrate interaction or activation. Recent cryo-EM studies have resolved the inner-membrane complex as trimer of HlyB homodimers with associated HlyD protomers. However, a full structural model including TolC remains unavailable. We present the first complete structural model of the HlyA T1SS, constructed using template- and MSA-based information and validated by SAXS. Molecular dynamics simulations provide insights into the function of the CLD domains, which are partially absent from existing cryo-EM structures. These domains may modulate transport by stabilizing specific conformations of the complex. Simulations with a C-terminal fragment of HlyA indicate that toxin binding occurs in the occluded conformation of HlyB, potentially initiating substrate transport through a single HlyB protomer before transitioning to an inward-facing state. HlyA binding also induces allosteric effects on HlyD, affecting key residues involved in TolC recruitment. These results indicate how substrate recognition and transport are coupled and may support the development of antimicrobial strategies targeting the T1SS.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169485"},"PeriodicalIF":4.5,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285329","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 : 2025-10-10DOI: 10.1016/j.jmb.2025.169483
Weiyu Tao , Xiao He , Lei Chen
Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral attachment to host cells, serves as the primary target for neutralizing antibodies (NAbs), and is subject to escape mutations. Previous studies have shown that the AGL exhibits two different structures (Type A and Type B) dictated by distinct disulfide bond linkage. However, due to the flexibility of some regions in previous structure, the complete model of AGLType B and its symmetry remain elusive. Here, we present the cryo-EM structure of AGLType B in complex with the Fab fragment of the NAb H020. The complete structure of AGLType B reveals its two-fold symmetry and it can bind two FabH020 fragments simultaneously. Further analysis elucidates the underlying mechanism of pan-serotype neutralizing capability of H020 and how escape mutations hinder its binding.
{"title":"The Symmetric Structure of the Antigenic Loop in Type B HBV Surface Antigen","authors":"Weiyu Tao , Xiao He , Lei Chen","doi":"10.1016/j.jmb.2025.169483","DOIUrl":"10.1016/j.jmb.2025.169483","url":null,"abstract":"<div><div>Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral attachment to host cells, serves as the primary target for neutralizing antibodies (NAbs), and is subject to escape mutations. Previous studies have shown that the AGL exhibits two different structures (Type A and Type B) dictated by distinct disulfide bond linkage. However, due to the flexibility of some regions in previous structure, the complete model of AGL<sub>Type B</sub> and its symmetry remain elusive. Here, we present the cryo-EM structure of AGL<sub>Type B</sub> in complex with the Fab fragment of the NAb H020. The complete structure of AGL<sub>Type B</sub> reveals its two-fold symmetry and it can bind two Fab<sub>H020</sub> fragments simultaneously. Further analysis elucidates the underlying mechanism of pan-serotype neutralizing capability of H020 and how escape mutations hinder its binding.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169483"},"PeriodicalIF":4.5,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273314","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 : 2025-10-10DOI: 10.1016/j.jmb.2025.169482
Ruilin Qian , Radoslaw J. Gora , Sowmya Chandrasekar, Shu-ou Shan
Signal recognition particle (SRP) is a universally conserved protein targeting machine that directs newly synthesized proteins to the endoplasmic reticulum (ER). SRP recognizes signal sequences on nascent ER proteins as they emerge from the ribosome and, in response, activates interaction with the SRP receptor (SR) at the ER membrane. Early work suggested that SRP loses targeting competence as the nascent chain elongates; however, the underlying molecular mechanism remains unclear. Here we address this question using a combination of steady-state and single-molecule fluorescence spectroscopy measurements. A Förster resonance energy transfer (FRET) assay revealed increased dynamic excursions of the signal sequence from SRP on ribosomes bearing longer nascent chains, leading to a suboptimal conformation of SRP and its impaired interaction kinetics with SR. In addition, the nascent polypeptide associated complex (NAC) amplifies the effects of longer nascent chains to further exclude SRP from ER targeting. Our findings reveal the profound effects of an elongating nascent polypeptide on the conformation and activity of SRP and a key role of NAC in the temporal regulation of SRP, which together impose a limited window for cotranslational ER protein targeting during protein synthesis.
{"title":"Temporal Regulation of Signal Recognition Particle During Translation","authors":"Ruilin Qian , Radoslaw J. Gora , Sowmya Chandrasekar, Shu-ou Shan","doi":"10.1016/j.jmb.2025.169482","DOIUrl":"10.1016/j.jmb.2025.169482","url":null,"abstract":"<div><div>Signal recognition particle (SRP) is a universally conserved protein targeting machine that directs newly synthesized proteins to the endoplasmic reticulum (ER). SRP recognizes signal sequences on nascent ER proteins as they emerge from the ribosome and, in response, activates interaction with the SRP receptor (SR) at the ER membrane. Early work suggested that SRP loses targeting competence as the nascent chain elongates; however, the underlying molecular mechanism remains unclear. Here we address this question using a combination of steady-state and single-molecule fluorescence spectroscopy measurements. A Förster resonance energy transfer (FRET) assay revealed increased dynamic excursions of the signal sequence from SRP on ribosomes bearing longer nascent chains, leading to a suboptimal conformation of SRP and its impaired interaction kinetics with SR. In addition, the nascent polypeptide associated complex (NAC) amplifies the effects of longer nascent chains to further exclude SRP from ER targeting. Our findings reveal the profound effects of an elongating nascent polypeptide on the conformation and activity of SRP and a key role of NAC in the temporal regulation of SRP, which together impose a limited window for cotranslational ER protein targeting during protein synthesis.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169482"},"PeriodicalIF":4.5,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273423","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 : 2025-10-09DOI: 10.1016/j.jmb.2025.169481
Tsz-Fung Wong , Pui-Kin So , Wai-Po Kong , Zhong-Ping Yao
Extended-spectrum β-lactamases (ESBLs) are bacteria-produced enzymes that can hydrolyze and confer extra resistance to new generation β-lactam antibiotics. TEM-type ESBLs are clinically prevalent and have caused serious health problems worldwide. TEM-type ESBLs are the evolutionary products of wild-type TEM-1 β-lactamase mainly through individual or combined mutations of G238S, E104K and M182T, but how these mutations cause conformational dynamics changes of the enzymes and how these changes correlate to their extended-spectrum antibiotic resistance remain unclear. Using hydrogen/deuterium exchange mass spectrometry integrated with molecular dynamics simulation, we revealed the significant effects of these individual or combined mutations on the conformational dynamics of the all-α-domain, α/β-domain and interdomain loop of the enzymes. Particularly, we observed different conformational dynamics changes of the interdomain loop in response to different mutations and substrate binding, which indicated the important role of the interdomain loop in modulating conformational dynamics of ESBLs for the catalytic efficiency. These new findings shed new insights into the antibiotic-resistance mechanism of TEM-type ESBLs and designing of novel inhibitors, and provide clues for the evolutionary strategy of β-lactamases and the studies of proteins with similar linking loops.
{"title":"The Interdomain Loop Modulates Conformational Dynamics for the Antibiotic-resistant Activity of TEM-type Extended-spectrum β-lactamases","authors":"Tsz-Fung Wong , Pui-Kin So , Wai-Po Kong , Zhong-Ping Yao","doi":"10.1016/j.jmb.2025.169481","DOIUrl":"10.1016/j.jmb.2025.169481","url":null,"abstract":"<div><div>Extended-spectrum β-lactamases (ESBLs) are bacteria-produced enzymes that can hydrolyze and confer extra resistance to new generation β-lactam antibiotics. TEM-type ESBLs are clinically prevalent and have caused serious health problems worldwide. TEM-type ESBLs are the evolutionary products of wild-type TEM-1 β-lactamase mainly through individual or combined mutations of G238S, E104K and M182T, but how these mutations cause conformational dynamics changes of the enzymes and how these changes correlate to their extended-spectrum antibiotic resistance remain unclear. Using hydrogen/deuterium exchange mass spectrometry integrated with molecular dynamics simulation, we revealed the significant effects of these individual or combined mutations on the conformational dynamics of the all-α-domain, α/β-domain and interdomain loop of the enzymes. Particularly, we observed different conformational dynamics changes of the interdomain loop in response to different mutations and substrate binding, which indicated the important role of the interdomain loop in modulating conformational dynamics of ESBLs for the catalytic efficiency. These new findings shed new insights into the antibiotic-resistance mechanism of TEM-type ESBLs and designing of novel inhibitors, and provide clues for the evolutionary strategy of β-lactamases and the studies of proteins with similar linking loops.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169481"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257066","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 : 2025-10-09DOI: 10.1016/j.jmb.2025.169475
Shengnan Zhang , Kaien Liu , Dan Li , Cong Liu
Parkinson’s disease (PD) is a prevalent neurodegenerative disorder characterized by progressive neuronal loss and pathological aggregation of α-synuclein (α-syn) into amyloid fibrils, which propagate between cells and drive disease progression. Over the past decade, our laboratory has implemented an integrated strategy—combining high-resolution structural biology, molecular biophysics, biochemical and cellular analyses, chemical biology approaches, and in vivo disease models—to elucidate the molecular basis of α-syn pathology. We first determined atomic-resolution structures of full-length α-syn fibrils, revealing diverse polymorphs shaped by familial mutations and post-translational modifications, and linking conformational heterogeneity to phenotypic and pathological diversity. We further elucidated the structural basis underlying the interaction between amyloid fibril and chemical ligands, enabling the rational development of imaging probes and therapeutic modulators. In parallel, we found that the conserved acidic C-terminal region of α-syn fibrils acts as a central interface for driving pathogenic engagement with multiple receptors for neural propagation and inflammation induction, while also binding the autophagy adaptor LC3B to disrupt p62-mediated selective autophagy. Targeting this interface with small molecule inhibitors alleviates α-syn–induced toxicity in cellular models. Together, these findings provide an integrated molecular roadmap for understanding α-syn pathology and advancing precision diagnostics and targeted interventions in PD and related synucleinopathies.
{"title":"Rising Stars: Molecular Mechanisms and Chemical Interventions of α-Synuclein Amyloid Aggregation in Parkinson’s Disease","authors":"Shengnan Zhang , Kaien Liu , Dan Li , Cong Liu","doi":"10.1016/j.jmb.2025.169475","DOIUrl":"10.1016/j.jmb.2025.169475","url":null,"abstract":"<div><div>Parkinson’s disease (PD) is a prevalent neurodegenerative disorder characterized by progressive neuronal loss and pathological aggregation of α-synuclein (α-syn) into amyloid fibrils, which propagate between cells and drive disease progression. Over the past decade, our laboratory has implemented an integrated strategy—combining high-resolution structural biology, molecular biophysics, biochemical and cellular analyses, chemical biology approaches, and <em>in vivo</em> disease models—to elucidate the molecular basis of α-syn pathology. We first determined atomic-resolution structures of full-length α-syn fibrils, revealing diverse polymorphs shaped by familial mutations and post-translational modifications, and linking conformational heterogeneity to phenotypic and pathological diversity. We further elucidated the structural basis underlying the interaction between amyloid fibril and chemical ligands, enabling the rational development of imaging probes and therapeutic modulators. In parallel, we found that the conserved acidic C-terminal region of α-syn fibrils acts as a central interface for driving pathogenic engagement with multiple receptors for neural propagation and inflammation induction, while also binding the autophagy adaptor LC3B to disrupt p62-mediated selective autophagy. Targeting this interface with small molecule inhibitors alleviates α-syn–induced toxicity in cellular models. Together, these findings provide an integrated molecular roadmap for understanding α-syn pathology and advancing precision diagnostics and targeted interventions in PD and related synucleinopathies.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169475"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257018","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 : 2025-10-09DOI: 10.1016/j.jmb.2025.169478
Yu Xue
Yu Xue is a professor in the College of Life Science and Technology at Huazhong University of Science and Technology, and hold a joint position in the Hubei Hongshan Laboratory at Huazhong Agricultural University. He received two B.E. degrees in polymer science and technology and computer science from the University of Science and Technology of China (USTC) in 2002, and a Ph.D. degree in cell biology from USTC in 2006. His major research interest is the computational analysis of post-translational modifications (PTMs) in proteins, a field he terms PTM bioinformatics. Since 2004, his group has developed a number of algorithms, including the Group-based Prediction System (GPS), for prediction of PTM sites and their functional relevance. They have also constructed several PTM-related databases and designed methods to analyze PTMomic data and infer key regulatory enzymes. Through extensive collaboration and their own experimental work, they have predicted and uncovered new PTM sites and regulators in dynamic biological processes. He served as a co-founder and secretary general of the Artificial Intelligence Biology (AIBIO) Sub-branch of the Biophysical Society of China. In 2023, he proposed the concept of “vit-molecular language”, drawing an analogy between PTM regulation and human natural languages. He anticipates that cutting-edge AI technology, combined with conventional bioinformatics and experimental approaches, will profoundly empower future PTM studies.
{"title":"Rising Stars: Bioinformatics of Post-translational Modifications","authors":"Yu Xue","doi":"10.1016/j.jmb.2025.169478","DOIUrl":"10.1016/j.jmb.2025.169478","url":null,"abstract":"<div><div>Yu Xue is a professor in the College of Life Science and Technology at Huazhong University of Science and Technology, and hold a joint position in the Hubei Hongshan Laboratory at Huazhong Agricultural University. He received two B.E. degrees in polymer science and technology and computer science from the University of Science and Technology of China (USTC) in 2002, and a Ph.D. degree in cell biology from USTC in 2006. His major research interest is the computational analysis of post-translational modifications (PTMs) in proteins, a field he terms PTM bioinformatics. Since 2004, his group has developed a number of algorithms, including the Group-based Prediction System (GPS), for prediction of PTM sites and their functional relevance. They have also constructed several PTM-related databases and designed methods to analyze PTMomic data and infer key regulatory enzymes. Through extensive collaboration and their own experimental work, they have predicted and uncovered new PTM sites and regulators in dynamic biological processes. He served as a co-founder and secretary general of the Artificial Intelligence Biology (AIBIO) Sub-branch of the Biophysical Society of China. In 2023, he proposed the concept of “vit-molecular language”, drawing an analogy between PTM regulation and human natural languages. He anticipates that cutting-edge AI technology, combined with conventional bioinformatics and experimental approaches, will profoundly empower future PTM studies.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169478"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257058","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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