Protein Science最新文献

{"title":"Quantitative detection of amyloid fibrils using fluorescence resonance energy transfer between engineered yellow and cyan proteins.","authors":"Caitlyn Moustouka, George I Makhatadze","doi":"10.1002/pro.70094","DOIUrl":"10.1002/pro.70094","url":null,"abstract":"<p><p>Over 20 human diseases are caused by or associated with amyloid formation. Developing diagnostic tools to understand the process of amyloid fibril formation is essential for creating therapeutic agents to combat these widespread and growing health problems. Here, we capitalize on our recent striking discovery that green fluorescent protein (GFP), one of the most-used proteins in molecular and cell biology, has a high intrinsic binding affinity to various structural intermediates along the fibrillation pathway, independent of amyloid sequence. Using engineered GFP with the fluorescence properties of Aquamarine and mCitrine, we developed a fluorescence resonance energy transfer (FRET)-based sensor to quantitatively monitor amyloid fibrils. The proof-of-principle characterization was performed on a test system consisting of PAPf39 fibrils.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70094"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data-driven evaluation of suitable immunogens for improved antibody selection.","authors":"Katharina Waury, Hlin Kvartsberg, Henrik Zetterberg, Kaj Blennow, Charlotte E Teunissen, Sanne Abeln","doi":"10.1002/pro.70100","DOIUrl":"10.1002/pro.70100","url":null,"abstract":"<p><p>Antibodies are indispensable in laboratory and clinical applications due to their high specificity and affinity for protein antigens. However, selecting the right protein fragments as immunogens for antibody production remains challenging. Leveraging the Human Protein Atlas, this study systematically evaluates immunogen properties aiming to identify key factors that influence their suitability. Antibodies were classified as successful or unsuccessful based on standardized validation experiments, and the structural and functional properties of their immunogens were analyzed. Results indicated that longer immunogens often resulted in more successful but less specific antibodies. Shorter immunogens (50 residues or fewer) with disordered or unfolded regions at the N- or C-terminus and long coil stretches were more likely to generate successful antibodies. Conversely, immunogens with high beta sheet content, transmembrane regions, or disulfide bridges were associated with poorer antibody performance. Post-translational modification sites within immunogens appeared to mark beneficial regions for antibody generation. To support antibody selection, a novel R package, immunogenViewer, was developed, enabling researchers to easily apply these insights when immunogen sequences are disclosed. By providing a deeper understanding of immunogen suitability, this study promotes the development of more effective antibodies, ultimately addressing issues of reproducibility and reliability in antibody-based research. The findings are highly relevant to the research community, as end users often lack control over the immunogen selection process in antibody production. The R package is freely available as part of Bioconductor: https://bioconductor.org/packages/release/bioc/html/immunogenViewer.html.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70100"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11926642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting the structure of UBR box from human UBR6.","authors":"Bokyung Kim, Sohae Lee, Bong Heon Kim, Leehyeon Kim, Hyun Kyu Song","doi":"10.1002/pro.70092","DOIUrl":"10.1002/pro.70092","url":null,"abstract":"<p><p>Eukaryotic N-degron pathways are proteolytic systems with the ability to recognize specific N-terminal residues of substrate proteins, which are essential parts of their degradation signals. Domains, referred to as UBR boxes, of several E3 ubiquitin ligases can recognize basic N-terminal residues as N-degrons. UBR6 is among the seven mammalian UBR family proteins containing the UBR box domain. However, the recognition of basic type-1 N-degrons by UBR6 is still not well understood. The crystal structure of the UBR box from human UBR6 revealed zinc-mediated dimerization, a structural feature distinct from other monomeric UBR boxes. Furthermore, its folding pattern differed from that of the UBR fold, although the sequences aligned well with those of other UBR boxes. In this study, we re-determined the structure of the UBR box from human UBR6 to investigate whether the unusual domain-swapped dimer was structurally relevant. The newly determined UBR box of UBR6 at 1.5 Å resolution was a monomer with a classical UBR fold. Our structure was compared with previously reported structures of UBR boxes, and its structural features were further analyzed using N-degron binding assays.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70092"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fibrinogen-binding M-related proteins facilitate the recruitment of plasminogen by Streptococcus pyogenes.","authors":"Emma-Jayne Proctor, Hannah R Frost, Bhanu Mantri, Sandeep Satapathy, Gwenaëlle Botquin, Jody Gorman, David M P De Oliveira, Jason McArthur, Mark R Davies, Gökhan Tolun, Anne Botteaux, Pierre Smeesters, Martina Sanderson-Smith","doi":"10.1002/pro.70078","DOIUrl":"10.1002/pro.70078","url":null,"abstract":"<p><p>Group A Streptococcus (GAS) M-related proteins (Mrp) are dimeric α-helical coiled-coil cell-wall-attached proteins. During infection, Mrp recruit human fibrinogen (Fg) to the bacterial surface, enhancing phagocytosis resistance and promoting growth in human blood. However, Mrp exhibit a high degree of sequence diversity, clustering into four evolutionarily distinct groups. It is currently unknown whether this diversity affects the host-pathogen interactions mediated by Mrp. In this study, nine Mrp sequences from the four major evolutionary groups were selected to examine the effect of sequence diversity on protein-protein interactions with Fg. Negative staining transmission electron microscopy confirmed that Mrp are fibrillar proteins measuring between 45.4 and 47.3 nm in length, and mass photometry confirmed the ability of Mrp to form dimers. Surface plasmon resonance was used to evaluate the affinity of each Mrp for Fg. All Mrp studied bound to Fg via Fragment D (FgD) with nanomolar affinity. Previous studies have linked the acquisition of plasminogen (Plg) by GAS Fg-binding M proteins to tissue destruction and excessive stimulation of the human inflammatory response during infection. Our findings show that Mrp provide an alternative mechanism for Plg recruitment, as Plg binding by Mrp was significantly enhanced following pre-incubation with Fg. These data suggest that Mrp play an important role in GAS host-pathogen interactions. However, further studies are necessary to investigate the relevance of these findings in vivo.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70078"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lysine carbamoylation during urea denaturation remodels the energy landscape of human transthyretin dissociation linked to unfolding.","authors":"Marcus Jäger, David E Mortenson, Maziar S Ardejani, Gabriel M Kline, Maria T Dendle, Nicholas L Yan, Evan T Powers, Martin Gruebele, Jeffery W Kelly","doi":"10.1002/pro.70009","DOIUrl":"10.1002/pro.70009","url":null,"abstract":"<p><p>Chemical denaturants such as urea have become indispensable in modern protein science for measuring the energetics of protein folding and assembly. Denaturants bind to and preferentially stabilize denatured states, folding transition states, and folding intermediates over the native state, allowing experimental access to free energies of folding and insights into folding mechanisms. However, too little attention is paid to the established chemical instability of aqueous urea, that is, its decomposition into the reactive electrophile ammonium cyanate or isocyanic acid depending on the solution pH. Protein carbamoylation by cyanate/isocyanic acid can change the dissociation and/or unfolding free energy landscape of the protein under study with time. This problem is exemplified using the human blood protein transthyretin (TTR), a kinetically stable transporter of thyroid hormone and holo-retinol binding protein. The dissociation, misfolding, and aggregation of TTR are associated with a prominent human amyloid disease. We demonstrate that modification of TTR by cyanate reshapes the energy landscape of TTR tetramer dissociation and unfolding on multiple time scales. Like certain halide anions and the more chemically inert thiocyanate anion, cyanate binds weakly and non-covalently to the thyroid hormone binding interface in the TTR tetramer. The close proximity of the bound cyanate ion to the pK_a-perturbed lysine 15 ε-amino side chain nucleophile in the thyroid hormone binding sites of TTR favors carbamoylation of this nitrogen. Lysine 15 ε-amino carbamoylation substantially slows down TTR tetramer dissociation mediated by urea denaturation, thus introducing kinetic heterogeneity early in the unfolding reaction. Slower carbamoylation of the subpopulation of other, less pK_a-perturbed lysine ε-amino groups hastens tetramer unfolding, leading to non-exponential, sigmoidal unfolding trajectories. We thus demonstrate that lysine carbamoylation in urea solutions can strongly alter protein unfolding energetics and the mechanism of unfolding.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70009"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput amino acid-level characterization of the interactions of plasminogen activator inhibitor-1 with variably divergent proteases.","authors":"Laura M Haynes, Matthew L Holding, Hannah L DiGiovanni, David Siemieniak, David Ginsburg","doi":"10.1002/pro.70088","DOIUrl":"10.1002/pro.70088","url":null,"abstract":"<p><p>While members of large paralogous protein families share structural features, their functional niches often diverge significantly. Serine protease inhibitors (SERPINs), whose members typically function as covalent inhibitors of serine proteases, are one such family. Plasminogen activator inhibitor-1 (PAI-1) is a prototypic SERPIN, which canonically inhibits tissue- and urokinase-type plasminogen activators (tPA and uPA) to regulate fibrinolysis. PAI-1 has been shown to also inhibit other serine proteases, including coagulation factor XIIa (FXIIa) and transmembrane serine protease 2 (TMPRSS2). The structural determinants of PAI-1 inhibitory function toward these non-canonical protease targets, and the biological significance of these functions, are unknown. We applied deep mutational scanning (DMS) to assess the effects of ~80% of all possible single-amino acid substitutions in PAI-1 on its ability to inhibit three putative serine protease targets (uPA, FXIIa, and TMPRSS2). Selection with each target protease generated a unique PAI-1 mutational landscape, with the determinants of protease specificity distributed throughout PAI-1's primary sequence. Next, we conducted a comparative analysis of extant orthologous sequences, demonstrating that key residues modulating PAI-1 inhibition of uPA and FXIIa, but not TMPRSS2, are maintained by purifying selection (also referred to as \"negative selection\"). PAI-1's activity toward FXIIa may reflect how protease evolutionary relationships predict SERPIN functional divergence, which we support via a cophylogenetic analysis of secreted SERPINs and their cognate serine proteases. This work provides insight into the functional diversification of SERPINs and lays the framework for extending these studies to other proteases and their regulators.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70088"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A naturally occurring standalone TrpB enzyme provides insights into allosteric communication within tryptophan synthase.","authors":"Thomas Kinateder, Lukas Drexler, Cristina Duran, Sílvia Osuna, Reinhard Sterner","doi":"10.1002/pro.70103","DOIUrl":"10.1002/pro.70103","url":null,"abstract":"<p><p>Allosteric regulation of catalytic activity is a widespread property of multi-enzyme complexes. The tryptophan synthase is a prototypical allosteric enzyme where the constituting α (TrpA) and β (TrpB) subunits mutually activate each other in a manner that is incompletely understood. Experimental and computational studies have shown that LBCA-TrpB from the last bacterial common ancestor contains six residues (Res₆) distal from the active site that allow for high stand-alone catalytic activity in the absence of a TrpA subunit. In the present study, a database search revealed that Res₆ is also present in the extant plTrpB from Pelodictyon luteolum. The plTrpB enzyme showed a high stand-alone activity and only a moderate activation by plTrpA. The replacement of LBCA-Res₆ in plTrpB with the consensus residues from a multiple sequence alignment yielded plTrpB-con, which showed a dramatically decreased stand-alone activity but was strongly stimulated by plTrpA. These findings suggest that the effect of these six key allosteric residues is largely independent of the protein context within a specific TrpB enzyme. Analysis of the conformational landscapes of plTrpB and plTrpB-con revealed that plTrpB in isolation displays efficient closure of both the active site and the communication (COMM) domain. In contrast, these catalytically competent states are destabilized in plTrpB-con but can be recovered by the addition of plTrpA. A correlation-based shortest path map (SPM) analysis reveals that the catalytically and allosterically relevant domains-specifically, the COMM domain in TrpB and loops 2 and 6 in TrpA-are tightly interconnected exclusively in plTrpA:plTrpB-con.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70103"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides.","authors":"Chenkai Li, Darcy Sutherland, Ali Salehi, Amelia Richter, Diana Lin, Sambina Islam Aninta, Hossein Ebrahimikondori, Anat Yanai, Lauren Coombe, René L Warren, Monica Kotkoff, Linda M N Hoang, Caren C Helbing, Inanc Birol","doi":"10.1002/pro.70083","DOIUrl":"10.1002/pro.70083","url":null,"abstract":"<p><p>The ever-growing global health threat of antibiotic resistance is compelling researchers to explore alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging as a promising solution to fill this need. Naturally occurring AMPs are produced by all forms of life as part of the innate immune system. High-throughput bioinformatics tools have enabled fast and large-scale discovery of AMPs from genomic, transcriptomic, and proteomic resources of selected organisms. Public protein sequence databases, comprising over 200 million records and growing, serve as comprehensive compendia of sequences from a broad range of source organisms. Yet, large-scale in silico probing of those databases for novel AMP discovery using modern deep learning techniques has rarely been reported. In the present study, we propose an AMP mining workflow to predict novel AMPs from the UniProtKB/Swiss-Prot database using the AMP prediction tool, AMPlify, as its discovery engine. Using this workflow, we identified 8008 novel putative AMPs from all eukaryotic sequences in the database. Focusing on the practical use of AMPs as suitable antimicrobial agents with applications in the poultry industry, we prioritized 40 of those AMPs based on their similarities to known chicken AMPs in predicted structures. In our tests, 13 out of the 38 successfully synthesized peptides showed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus. AMPlify and the companion scripts supporting the AMP mining workflow presented herein are publicly available at https://github.com/bcgsc/AMPlify.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70083"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.","authors":"Mauro L Mugnai, Debayan Chakraborty, Hung T Nguyen, Farkhad Maksudov, Abhinaw Kumar, Wade Zeno, Jeanne C Stachowiak, John E Straub, D Thirumalai","doi":"10.1002/pro.70067","DOIUrl":"10.1002/pro.70067","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The preponderance of intrinsically disordered proteins (IDPs) in the eukaryotic proteome, and their ability to interact with each other, and with folded proteins, RNA, and DNA for functional purposes, have made it important to quantitatively characterize their biophysical properties. Toward this end, we developed the transferable self-organized polymer (SOP-IDP) model to calculate the properties of several IDPs. The values of the radius of gyration ( &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;g&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_g $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; ) obtained from SOP-IDP simulations are in excellent agreement (correlation coefficient of 0.96) with those estimated from SAXS experiments. For AP180 and Epsin, the predicted values of the hydrodynamic radii ( &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;h&lt;/mi&gt;&lt;/msub&gt; &lt;mi&gt;s&lt;/mi&gt;&lt;/mrow&gt; &lt;annotation&gt;$$ {R}_hmathrm{s} $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; ) are in nearly quantitative agreement with those from fluorescence correlation spectroscopy (FCS) experiments. Strikingly, the calculated SAXS profiles for 36 IDPs are also nearly superimposable on the experimental profiles. The dependence of &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;g&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_g $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; and the mean end-to-end distance ( &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;ee&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_{ee} $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; ) on chain length, &lt;math&gt; &lt;semantics&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt; &lt;annotation&gt;$$ N $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; , follows Flory's scaling law, &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;α&lt;/mi&gt;&lt;/msub&gt; &lt;mo&gt;≈&lt;/mo&gt; &lt;msub&gt;&lt;mi&gt;a&lt;/mi&gt; &lt;mi&gt;α&lt;/mi&gt;&lt;/msub&gt; &lt;msup&gt;&lt;mi&gt;N&lt;/mi&gt; &lt;mn&gt;0.588&lt;/mn&gt;&lt;/msup&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_{alpha}approx {a}_{alpha }{N}^{0.588} $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; ( &lt;math&gt; &lt;semantics&gt;&lt;mrow&gt;&lt;mi&gt;α&lt;/mi&gt; &lt;mo&gt;=&lt;/mo&gt; &lt;mi&gt;g&lt;/mi&gt; &lt;mo&gt;,&lt;/mo&gt;&lt;/mrow&gt; &lt;annotation&gt;$$ alpha =g, $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; and &lt;math&gt; &lt;semantics&gt;&lt;mrow&gt;&lt;mi&gt;e&lt;/mi&gt;&lt;/mrow&gt; &lt;annotation&gt;$$ e $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; ), suggesting that globally IDPs behave as synthetic polymers in a good solvent. This finding depends on the solvent quality, which can be altered by changing variables such as pH and salt concentration. The values of &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;a&lt;/mi&gt; &lt;mi&gt;g&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {a}_g $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; and &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;a&lt;/mi&gt; &lt;mi&gt;e&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {a}_e $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; are 0.20 and 0.48 nm, respectively. Surprisingly, finite size corrections to scaling, expected on theoretical grounds, are negligible for &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;g&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_g $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; and &lt;math&gt; &lt;semantics&gt; &lt;mrow&gt;&lt;msub&gt;&lt;mi&gt;R&lt;/mi&gt; &lt;mi&gt;ee&lt;/mi&gt;&lt;/msub&gt; &lt;/mrow&gt; &lt;annotation&gt;$$ {R}_{ee} $$&lt;/annotation&gt;&lt;/semantics&gt; &lt;/math&gt; . In contrast, only by account","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70067"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143650314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus.","authors":"Frank Gondelaud, Christophe Bignon, Denis Ptchelkine, Frédéric Carrière, Sonia Longhi","doi":"10.1002/pro.70085","DOIUrl":"10.1002/pro.70085","url":null,"abstract":"<p><p>The Hendra (HeV) and Nipah (NiV) viruses are high-priority, biosafety level-4 pathogens that cause fatal neurological and respiratory disease. Their P gene encodes not only the P protein, an essential polymerase cofactor, but also the virulence factors V and W. We previously showed that the W protein of HeV (W^HeV) forms amyloid-like fibrils and that one of its subdomains, PNT3, fibrillates in isolation. However, the fibrillation kinetics is much faster in the case of the full-length W^HeV compared to PNT3, suggesting that another W^HeV region contributes to the fibrillation process. In this work, we identified the region spanning residues 2-110 (PNT1) as the crucial region implicated in W^HeV fibrillation. Through site-directed mutagenesis, combined with thioflavin T binding experiments and negative-staining transmission electron microscopy, we showed that a predicted cryptic amyloidogenic region (CAR) within PNT1 is the main driver of fibrillation and deciphered the underlying molecular mechanism. Using FTIR, we showed that PNT1 fibrils are enriched in cross β-sheets. Sequence alignment revealed conservation of the CAR across the Henipavirus genus and enabled the identification of a hitherto never reported pro-amyloidogenic motif. The ability to form fibrils was experimentally shown to be a common property shared by Henipavirus PNT1 proteins. Overall, this study sheds light on the molecular mechanisms underlying W^HeV fibrillation and calls for future studies aimed at exploring the relevance of the newly identified pro-amyloidogenic motif as a valuable target for antiviral approaches.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 4","pages":"e70085"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}