{"title":"Identifying Bioactive Conformation of GnRH1 Based on Molecular Docking of NMR Conformers to GnRH1R and mAbs.","authors":"Madhavi Latha Yadav Bangaru, Anjali Anoop Karande, Nidhanapati Karanam Raghavendra","doi":"10.1002/prot.70111","DOIUrl":"10.1002/prot.70111","url":null,"abstract":"<p><p>GnRH1 binds to its receptor GnRH1R to stimulate release of FSH and LH. Earlier NMR analysis had reported several possible conformers of GnRH1; however, the biologically active conformation of GnRH1 is not identified so far. Here, molecular docking of different NMR conformers of GnRH1 to GnRH1R is performed. Based on: (a) residues of GnRH1R interacting with antagonist elagolix (as ligand-binding pocket), (b) intermolecular hydrogen bonds (for specificity of interaction), and (c) total intermolecular non-covalent interactions (for stability of interaction), one NMR conformation, having an asymmetric U-turn reverse coil structure with a beta strand comprised of residues Gly6 and Leu7, is identified as the bioactive conformation of GnRH1. Further, the identified bioactive NMR conformation of GnRH1 is used to explain in vivo GnRH1-neutralizing ability of monoclonal antibody (mAb) F1D3C5 and lack of neutralization by another mAb E2D2H12. In mice, F1D3C5 completely blocks estrus cycle, while E2D2H12, despite having a relatively higher affinity for GnRH1 in ELISA, does not alter the estrus cycle. Molecular docking of the identified bioactive NMR conformation of GnRH1 to homology models of scFv attributes in vivo neutralizing ability of F1D3C5 to structure-specific recognition of GnRH1. The bioactive conformation of GnRH1 identified here could guide co-crystallization studies, design of analogs and GnRH1 vaccination efforts.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1182-1198"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145913910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samuel A Barker, Porter K Ellis, Andrew Hammer, Sean J Johnson, Nicholas E Dickenson
{"title":"Structural and Biophysical Characterization of the Yersinia Type Three Secretion System ATPase YscN.","authors":"Samuel A Barker, Porter K Ellis, Andrew Hammer, Sean J Johnson, Nicholas E Dickenson","doi":"10.1002/prot.70112","DOIUrl":"10.1002/prot.70112","url":null,"abstract":"<p><p>Yersinia pestis was responsible for the Black Plague, one of the worst epidemiological disasters in recorded history. Today, Y. pestis , Y. enterocolitica , and Y. pseudotuberculosis remain clinically relevant human pathogens. Each of these pathogenic Yersinia species relies on a Type Three Secretion System (T3SS) for virulence, with the ATPase YscN playing a critical role in T3SS function. T3SS ATPases are responsible for powering apparatus formation and effector protein secretion through ATP hydrolysis. This study provides an extensive enzymatic characterization of recombinant YscN under several conditions, including variable pH and temperature, substrate and protein concentrations, and in the presence of putative inhibitors. Thermal stability data, assessed by circular dichroism, demonstrate that YscN exhibits increased stability in alkaline conditions, coinciding with greatest ATPase activity. Further, we report the first high-resolution crystal structure of YscN and leverage homology data to model an oligomeric active site. Mutational analysis of a predicted active site residue confirms oligomerization as necessary for YscN ATPase activity and corroborates our oligomeric model and enzyme concentration-dependent specific activity. Interestingly, however, AUC analysis reveals that the purified YscN predominantly exists as a monomer, despite oligomerization-dependent active site formation. Thus, we propose that transient oligomeric interactions support the observed ATP hydrolysis. Together, these data uncover structural and environmental impacts on YscN activity that may support the highly specialized Yersinia pathogenic lifecycle and leverage its role in virulence in search of pan-effective small molecule T3SS ATPase inhibitors.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1199-1211"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12863218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146004844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multi-Epitope Vaccine Design Against Leishmania donovani: An Immunoinformatic Based In Silico Approach.","authors":"Aviral Kaushik, Manisha Pritam, Sumit Govil, Radhey Shyam Kaushal","doi":"10.1002/prot.70102","DOIUrl":"10.1002/prot.70102","url":null,"abstract":"<p><p>Leishmaniasis, caused by Leishmania donovani, remains a major neglected tropical disease (NTD) with limited therapeutic options and the absence of a universally effective vaccine. Multi-epitope vaccines offer a promising strategy for combating this intracellular parasite by stimulating a robust and specific immune response. In this study, an immunoinformatics-driven, in silico reverse vaccinology approach was utilized to design a multi-epitope vaccine targeting key surface-exposed proteins of L. donovani , namely C-type lectin, Proteophosphoglycan (PPG4), Hydrophilic Acylated Surface Protein (HASP), Legume-like Lectin (LLL), and Kinetoplastid Membrane Protein (KMP-11). These proteins are implicated in essential processes such as parasite survival, immune modulation, and host-pathogen interactions, making them prime candidates for vaccine development. A comprehensive analysis was conducted to identify and screen B-cell and T-cell (MHC-I and MHC-II) epitopes for immunogenicity, antigenicity, and population coverage. Multi-epitope vaccines, incorporating individual proteins or chimeric constructs, were developed with IFN-gamma as an adjuvant. The vaccine constructs were prioritized based on factors such as IC<sub>50</sub> values and immunogenic potential. Subsequently, the selected epitopes were analyzed for physicochemical properties, and secondary and tertiary structural predictions were made and validated. Molecular docking simulations were employed to examine the interaction of the vaccine constructs with immune receptors, ensuring optimal immune system activation. Based on the molecular docking score, the vaccine candidates were screened and top four constructs (vaccines based on C-type lectin, LLL, PPG and chimeric vaccine; -1048.9, -1025.8, -1291.8, and -852.1 Kcal/mol respectively) were processed through immunogenic simulation. This in silico analysis indicates that lectins are highly effective vaccine candidates. Further, top two constructs, based on the immunogenic simulations, underwent molecular dynamics simulations. In the end, the final constructs were computationally cloned in pET28a vector. This study underscores the potential of multi-epitope vaccines as a cost-effective and efficient strategy for addressing L. donovani infections, providing a foundation for subsequent experimental validation and clinical trial development.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1131-1169"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145859679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A X Quintana-Armas, E Flores-Hernández, C Cardona-Félix, E Rudiño-Piñera
{"title":"Snapshots of Motion: A Novel Structural Intermediate Reveals Conserved Dynamics in Archaeal DNA Ligases.","authors":"A X Quintana-Armas, E Flores-Hernández, C Cardona-Félix, E Rudiño-Piñera","doi":"10.1002/prot.70116","DOIUrl":"10.1002/prot.70116","url":null,"abstract":"<p><p>We present the first x-ray crystallographic structural evidence of an archaeal DNA ligase showing the AMP covalent adduct together with further cofactor hydrolysis, capturing a transient intermediary in the first step of the ligation reaction, triggered by the pyrophosphate hydrolysis. Our crystallographic models of Thermococcus gammatolerans DNA ligase (LigTgam), coupled with bioinformatic analysis of at least 28 crystallographic structures from ATP- and NAD<sup>+</sup>-dependent DNA ligases, highlight the central role of domain mobility. Notably, elevated B-values are consistently observed in key catalytic and binding regions, suggesting a link between structural flexibility and enzymatic efficiency. Remarkably, this pattern of high B-values is conserved in replicative ligases, including bacterial Lig A, indicating a broader evolutionary relevance. These fluctuations emphasize the importance of conformational adaptability in accommodating substrate DNA and facilitating catalytic steps, including adenylation and phosphodiester bond formation. In this work, we delve deeper into this dynamic behavior, providing evidence of its critical role in ligase function.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1245-1258"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13136779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Integration of Evolutionary Analysis With RFdiffusion for De Novo Design of Aggregation-Resistant Frataxin.","authors":"Kevser Kübra Kırboğa, Ecir Uğur Küçüksille","doi":"10.1002/prot.70114","DOIUrl":"10.1002/prot.70114","url":null,"abstract":"<p><p>Friedreich's ataxia (FRDA) is a neurodegenerative disorder caused by frataxin (FXN) deficiency, where protein replacement therapy is hampered by the inherent instability and aggregation propensity of wild-type (WT) FXN. The structural flexibility of Loop-1 (residues 115-123), a critical region within the acidic ridge, represents a key determinant of protein stability. This study introduces a computational pipeline integrating evolutionary conservation analysis (ConSurf) with diffusion-based de novo design (RFdiffusion) to redesign both the backbone and sequence of Loop-1. Through systematic filtration of 1000 ProteinMPNN-generated variants using aggregation propensity screening (AGGRESCAN) and 450 ns of molecular dynamics (MD) simulations, four lead candidates were identified. Design_188 (EERVGGREI) demonstrated optimal performance with 2.3-fold improvement in aggregation resistance (Na4vSS: -53.8 vs. -23.5 for WT), superior structural stability (RMSD: 0.486 nm), reduced conformational diversity (62.3% dominant cluster occupancy), and 93% retention of ISCU binding capacity (ΔΔG: +6.4 kcal/mol). Experimental validation through <sup>15</sup>N NMR relaxation analysis confirmed computational predictions, with Design_188 exhibiting uniform backbone rigidification (S<sup>2</sup> = 0.81-0.95) and strong MD-NMR correlation (Pearson r = 0.675, p = 0.003). SEC-MALS analysis demonstrated near-complete monomeric behavior (> 98% monomer content) compared to WT's heterogeneous oligomerization (68% monomer, 32% oligomers), directly confirming the predicted anti-aggregation properties. K-means clustering analysis revealed an inverse relationship between conformational heterogeneity and stability, while correlation analysis identified a fundamental trade-off between aggregation resistance and structural stability (r = -0.82, p < 0.01). This work establishes a generalizable framework for therapeutic protein engineering where backbone redesign enables conformational ensemble modulation beyond the limitations of sequence optimization alone.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1225-1244"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stephen Kyle C Arcan, Gyraldin Marietony D Gan, Debrah Jannsen N Almazan, Zairus N Duquilla, Azenith Vincent D Barbosa, Rainier Ulrich D Velasco
{"title":"In Silico Functional and Structural Characterization of Streptococcus pneumoniae Atypical Rib Domain-Containing Hypothetical Protein Unravels Conserved Immunogenic Epitopes.","authors":"Stephen Kyle C Arcan, Gyraldin Marietony D Gan, Debrah Jannsen N Almazan, Zairus N Duquilla, Azenith Vincent D Barbosa, Rainier Ulrich D Velasco","doi":"10.1002/prot.70115","DOIUrl":"10.1002/prot.70115","url":null,"abstract":"<p><p>Streptococcus pneumoniae is a high-mortality pathogen exhibiting broad-spectrum antibiotic resistance, necessitating the development of alternative therapies, such as antigenic protein-based vaccines, which have recently gained interest due to their novelty. Here, we characterized antigenic hypothetical proteins (HPs) of S. pneumoniae and determined their potential as vaccine construct targets. Subcellular localization reported 10 extracellular proteins, six of which were antigenic and nonallergenic, thus making them ideal vaccine construct targets. Functional annotation through conserved protein domain and motif prediction identified a unique, atypical Rib (aRib) domain from WP_001166178.1, widely distributed on bacterial cell surface proteins. A comparison with a canonical Rib domain showed domain atrophy, highlighting the lack of structural core elements. Further analysis revealed non-covalent interactions of Thr47, Ala48, Val41, and Phe38 interacting with an alpha-d-mannopyranose ligand, triggering S. pneumoniae colonization and capsule synthesis mechanism, with highly dynamic and flexible residues present on the ligand binding site. A strong immune response was observed from a computational immune response simulation, likely attributed to the presence of predicted 4 cytotoxic T lymphocyte (CTL), 10 helper T lymphocyte (HTL), and 5 B-cell lymphocyte (BCL) epitopes. Therefore, the study presents a novel protein for designing a vaccine construct against S. pneumoniae , thus offering a new target for future vaccinology studies. Future studies should confirm protective efficacy of this candidate in vitro and in vivo through immunological assays.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1259-1274"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146020705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Allosteric Regulation of RNA Affinity by Motif V-VI Coupling in West Nile Virus NS3 Helicase.","authors":"Priti Roy, Martin McCullagh","doi":"10.1002/prot.70113","DOIUrl":"10.1002/prot.70113","url":null,"abstract":"<p><p>The rise of flaviviral diseases, including West Nile virus (WNV), presents a growing threat to global public health and underscores the urgent need for new therapeutic strategies. The non-structural protein 3 helicase (NS3h) of the Orthoflavivirus genus, including WNV, is essential for viral replication and a promising antiviral target. Previously [Roy et al., Nucleic Acids Research, 52 (13), 2024, 7447-7464], we showed that the motif VI loop (VIL) in WNV NS3h functions as a nucleotide valve, regulating ADP affinity during hydrolysis. In this study, we uncover an ATP-dependent coupling between nucleotide affinity at motif VIL and RNA affinity at motifs IVa and V, suggesting a coordinated mechanism of ssRNA translocation. Using microsecond-scale all-atom molecular dynamics simulations of hydrolysis-cycle intermediates, we find that key VIL residues (R461, R464) correlate strongly with RNA phosphate affinity of motif V. Structural analyses reveal an ATP-sensitive interaction between E413 (motif V) and R461 (motif VIL) that modulates the conformation of the motif V 3<sub>10</sub>-helix, thereby influencing RNA binding. This dynamic interaction is lost in catalytically deficient VIL mutants, which have been experimentally shown to impair hydrolysis and attenuate viral replication. These findings provide mechanistic insights into NS3h function and identify new opportunities for structure-based antiviral design.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1212-1224"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12882695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lijun Liu, Elizabeth K Harmon, Justin K Craig, Huili Yao, Kevin P Battaile, David K Johnson, Sandhya Subramanian, Wesley C Van Voorhis, Mario Rivera, Scott Lovell
{"title":"Structural Analysis and Inhibitor Modeling of Bacterioferritin From Brucella abortus.","authors":"Lijun Liu, Elizabeth K Harmon, Justin K Craig, Huili Yao, Kevin P Battaile, David K Johnson, Sandhya Subramanian, Wesley C Van Voorhis, Mario Rivera, Scott Lovell","doi":"10.1002/prot.70109","DOIUrl":"10.1002/prot.70109","url":null,"abstract":"<p><p>Iron homeostasis in various pathogenic bacteria is regulated by bacterioferritins (Bfr) which function to store Fe<sup>3+</sup> and release Fe<sup>2+</sup> as needed for metabolic processes. The Bfr structure consists of 18 kDa subunits in which dimer pairs bind a heme molecule and are assembled into a highly symmetrical 24-meric spherical structure with an internal core diameter of approximately 80 Å. Release of iron is facilitated by the binding of a 7 kDa [2Fe-2S] ferredoxin (Bfd) to specific sites on the surface of Bfr which transfers electrons to the core thereby reducing the stored Fe<sup>3+</sup> to Fe<sup>2+</sup> for mobilization. The crystal structures of Bfr from Brucella abortus (Ba) in the apo and iron bound forms are presented and compared with those from Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa). Additionally, models of the Bfr:Bfd complexes for Ba and Ab are provided and compared with the Pa complex. Finally, compounds known to target the Bfr:Bfd interaction in Pa were docked to the Ba and Ab structures which provided insight regarding the potential binding mode and inhibitory mechanism.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1170-1181"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13136788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145893518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julia Malec, Karina Rusen, G Brian Golding, Lucian Ilie
{"title":"Ankh-Score Produces Better Sequence Alignments Than AlphaFold3.","authors":"Julia Malec, Karina Rusen, G Brian Golding, Lucian Ilie","doi":"10.1002/prot.70143","DOIUrl":"https://doi.org/10.1002/prot.70143","url":null,"abstract":"<p><p>Protein sequence alignment is one of the most fundamental procedures in bioinformatics. Due to its many downstream applications, improvements to this procedure are of great importance. We consider two revolutionary concepts that emerged recently as candidates for improving the state-of-the-art alignment methods: AlphaFold and protein language models such as Ankh, ProtT5, or ESM-C. Alignment improvements can come from the structural alignment of AlphaFold-predicted structures or the scoring based on the similarity of protein embeddings produced by the protein language models. Thorough comparison on many domains from BAliBASE and CDD demonstrates that the Ankh-score method produces much better sequence alignments than the structural alignments using US-align of AlphaFold3-predicted structures. Both are better than the traditional method using BLOSUM matrices. This suggests that Ankh embeddings may possess certain information that is not available in the AlphaFold3-predicted structures. The alignment software is freely available as a web server at e-score.csd.uwo.ca and as source code at github.com/lucian-ilie/E-score.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rui Guo, Jimin Pei, Jing Zhang, Qian Cong, Nick V Grishin, R Dustin Schaeffer
{"title":"Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.","authors":"Rui Guo, Jimin Pei, Jing Zhang, Qian Cong, Nick V Grishin, R Dustin Schaeffer","doi":"10.1002/prot.70144","DOIUrl":"https://doi.org/10.1002/prot.70144","url":null,"abstract":"<p><p>Proteins are built from modular domains that serve as fundamental units of structure and evolution. While individual domains have been extensively cataloged, their collective distribution across the lineages of life has remained poorly resolved. Here, we use the Evolutionary Classification of Protein Domains (ECOD) to chart the occurrence of domain homology groups (H-groups) across 44 model proteomes representing Eukaryota, Bacteria, and Archaea, in which 1.16 million domains are assigned to 3320 H-groups. H-groups are categorized as universal (occupying all three superkingdoms), shared between superkingdoms, or lineage-specific. The fold architecture distributions were examined: α/β sandwiches and other mixed architectures were abundant in universal H-groups, whereas α-rich architectures are expanded in eukaryotic H-groups and β-rich folds in bacterial H-groups. 126 (3.8%) H-groups occur in all organisms, forming a universal structural core that supports central processes of energy conversion, metabolism, and information flow. These widely distributed folds coincide with canonical superfolds-robust, adaptable architectures repeatedly repurposed for key biochemical roles. Two superkingdom groups trace evolutionary connections between lineages: bacterial metabolic and chaperone systems inherited by eukaryotes, archaeal informational machinery conserved in eukaryotic nuclei, and ancient redox scaffolds linking bacteria and archaea. Lineage-exclusive domains, in turn, highlight distinct adaptive strategies-regulatory and cytoskeletal innovation in eukaryotes, envelope and motility specialization in bacteria, and redox or replication refinements in archaea. Together, these data provide a quantitative, structure-based view of protein domain evolution across the tree of life, showing that the essential architecture of life relies on a conserved set of ancient folds, while lineage-specific diversity has largely arisen through the recombination and functional diversification of pre-existing domains.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}