Protein Science最新文献_第7页

Chemically induced partial unfolding of the multifunctional apurinic/apyrimidinic endonuclease 1. 化学诱导的多功能无尿嘧啶/无嘧啶内切酶1的部分展开。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70148

Ratan Rai, Olabode I Dawodu, Jingwei Meng, Steven M Johnson, Jonah Z Vilseck, Mark R Kelley, Joshua J Ziarek, Millie M Georgiadis

{"title":"Chemically induced partial unfolding of the multifunctional apurinic/apyrimidinic endonuclease 1.","authors":"Ratan Rai, Olabode I Dawodu, Jingwei Meng, Steven M Johnson, Jonah Z Vilseck, Mark R Kelley, Joshua J Ziarek, Millie M Georgiadis","doi":"10.1002/pro.70148","DOIUrl":"10.1002/pro.70148","url":null,"abstract":"Apurinic/apyrimidinic endonuclease I (APE1) acts as both an endonuclease and a redox factor to ensure cell survival. The two activities require different conformations of APE1. As an endonuclease, APE1 is fully folded. As a redox factor, APE1 must be partially unfolded to expose the buried residue Cys65, which reduces transcription factors including AP-1, NF-κB, and HIF-1α and thereby enables them to bind DNA. To determine a molecular basis for partial unfolding associated with APE1's redox activity, we characterized specific interactions of a known redox inhibitor APX3330 with APE1 through waterLOGSY and 1H-15N HSQC NMR approaches using ethanol and acetonitrile as co-solvents. We find that APX3330 binds to the endonuclease active site in both co-solvents and to a distant small pocket in acetonitrile. Prolonged exposure of APE1 with APX3330 in acetonitrile resulted in a time-dependent loss of 1H-15N HSQC chemical shifts (~35%), consistent with partial unfolding. Regions that are partially unfolded include adjacent N- and C-terminal beta strands within one of the two sheets comprising the core, which converge within the small binding pocket defined by the CSPs. Removal of APX3330 via dialysis resulted in a slow reappearance of the 1H-15N HSQC chemical shifts suggesting that the effect of APX3330 is reversible. APX3330 significantly decreases the melting temperature of APE1 but has no effect on endonuclease activity using a standard assay in either co-solvent. Our results provide insights on reversible partial unfolding of APE1 relevant for its redox function as well as the mechanism of redox inhibition by APX3330.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70148"},"PeriodicalIF":5.2,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079811","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}

引用次数: 0

Protein-RNA condensation kinetics via filamentous nanoclusters. 通过丝状纳米团簇的蛋白质- rna缩聚动力学。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70136

Ramon Peralta-Martinez, Araceli Visentin, Mariano Salgueiro, Silvia Susana Borkosky, Mariana Araujo Ajalla Aleixo, Rodrigo Villares Portugal, Ignacio Enrique Sanchez, Gonzalo Prat-Gay

{"title":"Protein-RNA condensation kinetics via filamentous nanoclusters.","authors":"Ramon Peralta-Martinez, Araceli Visentin, Mariano Salgueiro, Silvia Susana Borkosky, Mariana Araujo Ajalla Aleixo, Rodrigo Villares Portugal, Ignacio Enrique Sanchez, Gonzalo Prat-Gay","doi":"10.1002/pro.70136","DOIUrl":"10.1002/pro.70136","url":null,"abstract":"Protein-RNA phase separation is at the center of membraneless biomolecular condensates governing cell physiology and pathology. Using an archetypical viral protein-RNA condensation model, we determined the sequence of events that starts with sub-second formation of a protomer with two RNAs per protein dimer. Association of additional RNA molecules to weaker secondary binding sites in this protomer kickstarts crystallization-like assembly of a molecular condensate. Primary nucleation is faster than the sum of secondary nucleation and growth, which is a multistep process. Protein-RNA nuclei grow over hundreds of seconds into filaments and subsequently into nanoclusters with approximately 600 nm diameter. Cryoelectron microscopy reveals an internal structure formed by incoming layers of protein-RNA filaments made of ribonucleoprotein oligomers, reminiscent of genome packing of a nucleocapsid. These nanoclusters progress to liquid condensate droplets that undergo further partial coalescence to yield typical hydrogel-like protein-RNA coacervates that may represent the scaffold of large viral factory condensates in infected cells. Our integrated experimental kinetic investigation exposes rate-limiting steps and structures along a key biological multistep pathway present across life kingdoms.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70136"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136422","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}

引用次数: 0

Prion diseases: Lessons from historical outbreaks and potential emerging ones. 朊病毒疾病：历史疫情和潜在新发疫情的教训。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70175

Aidan P Holman, Dmitry Kurouski

{"title":"Prion diseases: Lessons from historical outbreaks and potential emerging ones.","authors":"Aidan P Holman, Dmitry Kurouski","doi":"10.1002/pro.70175","DOIUrl":"10.1002/pro.70175","url":null,"abstract":"Prion diseases (PrDs) are a unique and fatal class of neurodegenerative disorders caused by misfolded proteinaceous infectious particles, or prions. While the pathogenic form was first documented in humans nearly a century ago, the global monitoring of PrDs only gained momentum after the \"Mad Cow\" epizootic and its human counterpart of the 1980s and 1990s. Currently, 34 countries track human prion cases annually, with over 27,000 cases. However, true prevalence estimates suggest significantly higher numbers, millions, highlighting the urgency of addressing these enigmatic diseases. Prions are exceptionally resilient, resisting conventional sterilization methods and persisting in environmental reservoirs, such as soil and plants, raising concerns about environmental and cross-species transmission, particularly with the growing prevalence of chronic wasting disease (CWD) in cervids. This review explores the history, pathogenesis, presence, public health implications, and novel innovations in studying and treatment of PrDs. Future priorities should include the development of faster, cost-effective diagnostic tools and systemic therapies to neutralize prions in affected individuals and mitigate environmental risks. Understanding and addressing the challenges posed by prions is critical for global health security in the wake of CWD.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70175"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136413","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}

引用次数: 0

Enhanced secretion through type 1 secretion system by grafting a calcium-binding sequence to modify the folding of cargo proteins. 通过移植钙结合序列修饰货物蛋白的折叠，通过1型分泌系统增强分泌。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70165

Ryo Uehara, Yuka Kamiya, Shuta Maeda, Keisuke Okamoto, Shuntaro Toya, Ryohei Chiba, Hiroshi Amesaka, Kazufumi Takano, Hiroyoshi Matsumura, Shun-Ichi Tanaka

{"title":"Enhanced secretion through type 1 secretion system by grafting a calcium-binding sequence to modify the folding of cargo proteins.","authors":"Ryo Uehara, Yuka Kamiya, Shuta Maeda, Keisuke Okamoto, Shuntaro Toya, Ryohei Chiba, Hiroshi Amesaka, Kazufumi Takano, Hiroyoshi Matsumura, Shun-Ichi Tanaka","doi":"10.1002/pro.70165","DOIUrl":"10.1002/pro.70165","url":null,"abstract":"Extracellular secretion is a beneficial way to produce recombinant proteins at an industrial scale. Among bacterial secretion systems, the type 1 secretion system (T1SS) in Gram-negative bacteria is particularly attractive due to its simple architecture involving only three proteins and one-step translocation across both inner and outer membranes. However, proteins that fold rapidly within the cell often fail to pass through the narrow T1SS channel tunnel, limiting its industrial application. To address this limitation, we engineered a 10-amino-acid calcium-binding sequence (CBS) that disrupts proximal secondary structures through electrostatic repulsion at low Ca2+ concentrations, thereby inhibiting premature folding of target proteins in the cell. We demonstrated that CBS-grafted variants of three fast-folding proteins-mRFP1, RNase H1, and monobody-were efficiently secreted by Escherichia coli expressing the Serratia marcescens Lip T1SS as compared to their parental proteins. Remarkably, the CBS-grafted variants were fully active and structurally identical to the intracellularly produced parental proteins when isolated from culture supernatants. Furthermore, the removal of Ca2+ from CBS did not compromise the structure or function, indicating that the CBS-mediated calcium-dependent folding was irreversible. Our work will expand the utility of T1SS for secreting diverse proteins, paving the way for broader industrial applications.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70165"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12086511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094691","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}

引用次数: 0

AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes. AcrDB更新：预测人类肠道病毒组中抗crispr的3D结构。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70177

Minal Khatri, N R Siva Shanmugam, Xinpeng Zhang, Revanth Sai Kumar Reddy Patel, Yanbin Yin

{"title":"AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes.","authors":"Minal Khatri, N R Siva Shanmugam, Xinpeng Zhang, Revanth Sai Kumar Reddy Patel, Yanbin Yin","doi":"10.1002/pro.70177","DOIUrl":"10.1002/pro.70177","url":null,"abstract":"Anti-CRISPR (Acr) proteins play a key role in phage-host interactions and hold great promise for advancing genome-editing technologies. However, finding new Acrs has been challenging due to their low sequence similarity. Recent advances in protein structure prediction have opened new pathways for Acr discovery by using 3D structure similarity. This study presents an updated AcrDB, with the following new features not available in other databases: (1) predicted Acrs from human gut virome databases, (2) Acr structures predicted by AlphaFold2, (3) a structural similarity search function to allow users to submit new sequences and structures to search against 3D structures of experimentally known Acrs. The updated AcrDB contains predicted 3D structures of 795 candidate Acrs with structural similarity (TM-score ≥0.7) to known Acrs supported by at least two of the three non-sequence similarity-based tools (TM-Vec, Foldseek, AcrPred). Among these candidate Acrs, 121 are supported by all three tools. AcrDB also includes 3D structures of 122 experimentally characterized Acr proteins. The 121 most confident candidate Acrs were combined with the 122 known Acrs and clustered into 163 sequence similarity-based Acr families. The 163 families were further subject to a structure similarity-based hierarchical clustering, revealing structural similarity between 44 candidate Acr (cAcr) families and 119 known Acr families. The bacterial hosts of these 163 Acr families are mainly from Bacillota, Pseudomonadota, and Bacteroidota, which are all dominant gut bacterial phyla. Many of these 163 Acr families are also co-localized in Acr operons. All the data and visualization are provided on our website: https://pro.unl.edu/AcrDB.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70177"},"PeriodicalIF":5.2,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120642","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}

引用次数: 0

Extrinsic and intrinsic factors affect copper-induced protein precipitation across eukaryotic and prokaryotic proteomes. 外在和内在因素影响真核和原核蛋白质组中铜诱导的蛋白质沉淀。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70158

Grace R Sturrock, Amy T R Robison, Azim Dharani, Eric E Monson, Katherine J Franz, Michael C Fitzgerald

{"title":"Extrinsic and intrinsic factors affect copper-induced protein precipitation across eukaryotic and prokaryotic proteomes.","authors":"Grace R Sturrock, Amy T R Robison, Azim Dharani, Eric E Monson, Katherine J Franz, Michael C Fitzgerald","doi":"10.1002/pro.70158","DOIUrl":"10.1002/pro.70158","url":null,"abstract":"The susceptibility of a protein to aggregation upon exposure to copper ions (Cu) has been recognized as a contributor to Cu-induced cellular dysfunction and toxicity. Different cell types succumb to Cu to varying degrees, indicating innate differences between species in the mechanisms used to tolerate exposure to Cu in excess of their biological needs. Investigated here are properties associated with metal-induced protein precipitation (MiPP) compared across cell lysates generated from three cell lines from three different species: Escherichia coli, Candida albicans, and the human prostate cancer cell line 22Rv1. The human cell line was the most sensitive to Cu-induced protein precipitation, while C. albicans was the most tolerant. This trend aligns with the relative susceptibilities of these cells to Cu-induced cytotoxicity. The unique susceptibilities of these proteomes to precipitation by Cu were examined to identify factors that influence a protein's relative sensitivity to this effect. Identified were intrinsic factors such as frequency and solvent accessibility of known metal-binding amino acids, as well as external factors related to the molecular composition of their native cell lysates. Overall, our findings help to elucidate the biomolecular basis underpinning the unique capacity of adventitious Cu to have differential effects on eukaryotic and prokaryotic organisms and the level of Cu needed to induce protein precipitation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70158"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079905","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}

引用次数: 0

New glycoside hydrolase families of β-1,2-glucanases. β-1,2-葡聚糖酶苷水解酶新家族。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70147

Masahiro Nakajima, Nobukiyo Tanaka, Sei Motouchi, Kaito Kobayashi, Hisaka Shimizu, Koichi Abe, Naoya Hosoyamada, Naoya Abara, Naoko Morimoto, Narumi Hiramoto, Ryosuke Nakata, Akira Takashima, Marie Hosoki, Soichiro Suzuki, Kako Shikano, Takahiro Fujimaru, Shiho Imagawa, Yukiya Kawadai, Ziyu Wang, Yoshinao Kitano, Takanori Nihira, Hiroyuki Nakai, Hayao Taguchi

{"title":"New glycoside hydrolase families of β-1,2-glucanases.","authors":"Masahiro Nakajima, Nobukiyo Tanaka, Sei Motouchi, Kaito Kobayashi, Hisaka Shimizu, Koichi Abe, Naoya Hosoyamada, Naoya Abara, Naoko Morimoto, Narumi Hiramoto, Ryosuke Nakata, Akira Takashima, Marie Hosoki, Soichiro Suzuki, Kako Shikano, Takahiro Fujimaru, Shiho Imagawa, Yukiya Kawadai, Ziyu Wang, Yoshinao Kitano, Takanori Nihira, Hiroyuki Nakai, Hayao Taguchi","doi":"10.1002/pro.70147","DOIUrl":"10.1002/pro.70147","url":null,"abstract":"β-1,2-Glucans are natural glucose polymers produced by bacteria and play important physiological roles, including as symbiotic or pathogenic factors and in osmoregulation. Glycoside hydrolase (GH) families related to β-1,2-glucan metabolism (GH144, GH162, and GH189) have recently been created by identification of two β-1,2-glucanases and a β-1,2-glucanotransferase, respectively. In this study, we further found four phylogenetically new groups with unknown functions (Groups 1-4) by sequence database analysis using enzymes from GH144 and GH162 as queries. Biochemical analysis of representative proteins in these groups revealed that the proteins in Groups 1-3 showed hydrolytic activity specific to β-1,2-glucan, while no substrate was found for the Group 4 protein. The kinetic parameters of the enzymes of Groups 1-3 were similar to GH144 and GH162 β-1,2-glucanases, indicating that these enzymes were β-1,2-glucanases. Optical rotation analysis revealed that the β-1,2-glucanases followed an anomer-inverting mechanism. Structural analysis of the proteins in Groups 1-4 revealed that they possess (α/α)6-barrel folds similar to those of GH144, GH162, and GH189 enzymes. Comparison of spatial positions of predicted acidic catalytic residues suggested that Groups 1-3 and GH144 had the same reaction mechanism. Overall, phylogenetic, biochemical, and structural analyses revealed that Groups 1-3 are new GH families, GH192, GH193, and GH194, respectively, and that the three families belong to clan GH-S (clan GH, classification based on structural similarity) as GH144 and GH162.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70147"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136384","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}

引用次数: 0

Lysine acetylation modulates s-OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling. 赖氨酸乙酰化调节s-OPA1 GTPase活性和线粒体膜重塑中的寡聚化。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70179

Javaid Jabbar, Bakht Afroze, Naomi X Y Ling, Jonathan S Oakhill, Isabelle Rouiller

{"title":"Lysine acetylation modulates s-OPA1 GTPase activity and oligomerization in mitochondrial membrane remodeling.","authors":"Javaid Jabbar, Bakht Afroze, Naomi X Y Ling, Jonathan S Oakhill, Isabelle Rouiller","doi":"10.1002/pro.70179","DOIUrl":"10.1002/pro.70179","url":null,"abstract":"Mitochondrial dynamics are regulated by coordinated fission and fusion events that rely on key proteins and lipids organized spatially within the mitochondria. The dynamin-related GTPase Optic Atrophy 1 (OPA1) is essential for inner mitochondrial membrane fusion and cristae structure maintenance. While post-translational modifications, particularly lysine acetylation, are emerging as critical regulators of mitochondrial protein function, their impact on OPA1 remains poorly characterized. In this study, we explored the effects of lysine acetylation on the short form of OPA1 (s-OPA1) using acetylation and deacetylation mimetic mutations. Through a combination of in silico analyses and functional assays, we identified lysine residues in s-OPA1 that are conserved across species and significantly influence protein stability, GTPase activity, and oligomeric assembly upon acetylation or deacetylation. Our findings reveal that acetylation at K328 and deacetylation at K342 within the G domain enhance the GTPase activity of s-OPA1 upon lipid membrane binding, whereas deacetylation at K772 abolishes membrane binding-induced GTPase activity. Negative-stain transmission electron microscopy indicated that while lysine acetylation does not alter the ability of s-OPA1 to bind and tubulate liposomes, it significantly impacts higher-order filament formation. These findings provide novel insights into how acetylation modulates s-OPA1 function, highlighting a potential mechanism for post-translational regulation of mitochondrial dynamics. Our study contributes to the understanding of how molecular changes influence broader cellular processes, with implications for mitochondrial function and related disorders.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70179"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174688","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}

引用次数: 0

Cryo-EM structures of engineered Shiga toxin-based immunogens capable of eliciting neutralizing antibodies with therapeutic potential against hemolytic uremic syndrome. 志贺毒素免疫原的低温电镜结构能够激发具有治疗溶血性尿毒症综合征潜力的中和抗体。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70178

Alejandro Ezequiel Cristófalo, Arvind Sharma, María Laura Cerutti, Kedar Sharma, Roberto Melero, Romina Pardo, Fernando Alberto Goldbaum, Mario Borgnia, Vanesa Zylberman, Lisandro Horacio Otero

{"title":"Cryo-EM structures of engineered Shiga toxin-based immunogens capable of eliciting neutralizing antibodies with therapeutic potential against hemolytic uremic syndrome.","authors":"Alejandro Ezequiel Cristófalo, Arvind Sharma, María Laura Cerutti, Kedar Sharma, Roberto Melero, Romina Pardo, Fernando Alberto Goldbaum, Mario Borgnia, Vanesa Zylberman, Lisandro Horacio Otero","doi":"10.1002/pro.70178","DOIUrl":"10.1002/pro.70178","url":null,"abstract":"Shiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome (STEC-HUS) is a serious disease that causes renal failure predominantly in children. Despite its significant impact, there are currently no licensed vaccines or effective therapies available. The B subunits of Shiga toxins 1 and 2 (Stx1B and Stx2B) are suitable targets for developing neutralizing antibodies, but their pentameric assembly is unstable when isolated from the whole toxin. Taking advantage of the oligomeric symmetry shared between Stx1B and Stx2B with the lumazine synthase from Brucella spp. (BLS), we have previously engineered the chimeric toxoids BLS-Stx1B and BLS-Stx2B as immunogens to generate therapeutic equine polyclonal antibodies. The resulting product (INM004) has successfully passed Phases 1 and 2 clinical trials, and a Phase 3 has been launched in Argentina and seven European countries. In this work, we present the cryo-electron microscopy structures of BLS-Stx1B and BLS-Stx2B, which confirm that these engineered immunogens effectively stabilize the StxB pentamers. Moreover, our results reveal that both chimeric constructs present high flexibility at their extremes, corresponding to motions of the StxBs with respect to the BLS core. Additionally, we present structural evidence of the interaction between the chimeras and polyclonal Fab (pFab) fragments derived from INM004, demonstrating that the elicited neutralizing antibodies block most of the interaction surface of the toxins with their cellular receptors. These findings further validate this promising antibody-based therapy for mitigating STEC-HUS and demonstrate that the BLS-Stx1B and BLS-Stx2B chimeras are potential candidates for developing a human vaccine.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70178"},"PeriodicalIF":5.2,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136344","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}

引用次数: 0

Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations. 通过分子模拟探索Abeta42单体在纤维表面的扩散动力学。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70131

Yuan-Wei Ma, Guan-Fang Wang, Hong-Yi Chen, Min-Yeh Tsai

{"title":"Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.","authors":"Yuan-Wei Ma, Guan-Fang Wang, Hong-Yi Chen, Min-Yeh Tsai","doi":"10.1002/pro.70131","DOIUrl":"10.1002/pro.70131","url":null,"abstract":"This study provides critical insights into the role of surface-mediated processes in Alzheimer's disease, with implications for the aggregation of Abeta42 peptides. Employing coarse-grained molecular dynamics simulations, we focus on elucidating the molecular intricacies of these processes beyond primary nucleation. Central to our investigation is the analysis of a freely diffusing Abeta42 monomer on preformed fibril structures. We conduct detailed calculations of the monomer's diffusion coefficient on fibril surfaces (as a one-dimensional case), along with various monomer orientations. Our findings reveal a strong and consistent correlation between the monomer's diffusion coefficient and its orientation on the surface. Further analysis differentiates the effects of parallel and perpendicular alignments with respect to the fibril axis. Additionally, we explore how different fibril surfaces influence monomer dynamics by comparing the C-terminal and N-terminal surfaces. We find that the monomer exhibits faster diffusion coefficients on the C-terminal surface. Differences in surface roughness (SR), quantified using root-mean-square distances, significantly affect monomer dynamics, thereby influencing its diffusion on the surface. Importantly, this study underscores that fibril twisting acts as a regulatory niche, selectively influencing these orientations and their diffusion properties necessary for facilitating fibril growth within biologically relevant time scales. This discovery opens new avenues for targeted therapeutic strategies aimed at manipulating fibril dynamics to mitigate the progression of Alzheimer's disease.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70131"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079902","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}

引用次数: 0