{"title":"Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle","authors":"Michael J. O'Brien, Athar Ansari","doi":"10.1016/j.bbapap.2023.140968","DOIUrl":"10.1016/j.bbapap.2023.140968","url":null,"abstract":"<div><p>Although TFIIB is widely regarded as an initiation factor, recent reports have implicated it in multiple aspects of eukaryotic transcription. To investigate the broader role of TFIIB in transcription, we performed quantitative proteomic analysis of yeast TFIIB. We purified two different populations of TFIIB; one from soluble cell lysate, which is not engaged in transcription, and the other from the chromatin fraction which yields the transcriptionally active form of the protein. TFIIB purified from the chromatin exhibits several interactions that explain its non-canonical roles in transcription. RNAPII, TFIIF and TFIIH were the only components of the preinitiation complex with a significant presence in chromatin TFIIB. A notable feature was enrichment of all subunits of CF1 and Rat1 3′ end processing-termination complexes in chromatin-TFIIB preparation. Subunits of the CPF termination complex were also detected in both chromatin and soluble derived TFIIB preparations. These results may explain the presence of TFIIB at the 3′ end of genes during transcription as well as its role in promoter-termination interaction.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49673830","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":"Structure of the Borrelia burgdorferi ATP-dependent metalloprotease FtsH in its functionally relevant hexameric form","authors":"Kalvis Brangulis , Laura Drunka , Inara Akopjana , Kaspars Tars","doi":"10.1016/j.bbapap.2023.140969","DOIUrl":"10.1016/j.bbapap.2023.140969","url":null,"abstract":"<div><p>ATP-dependent proteases FtsH are conserved in bacteria, mitochondria, and chloroplasts, where they play an essential role in degradation of misfolded/unneeded membrane and cytosolic proteins. It has also been demonstrated that the FtsH homologous protein BB0789 is crucial for mouse and tick infectivity and in vitro growth of the Lyme disease-causing agent <em>Borrelia burgdorferi</em>. This is not surprising, considering <em>B. burgdorferi</em> complex life cycle, residing in both in mammals and ticks, which requires a wide range of membrane proteins and short-lived cytosolic regulatory proteins to invade and persist in the host organism.</p><p>In the current study, we have solved the crystal structure of the cytosolic BB0789<sub>166</sub><sub>–</sub><sub>614</sub>, lacking both N-terminal transmembrane α-helices and the small periplasmic domain. The structure revealed the arrangement of the AAA+ ATPase and the zinc-dependent metalloprotease domains in a hexamer ring, which is essential for ATPase and proteolytic activity. The AAA+ domain was found in an ADP-bound state, while the protease domain showed coordination of a zinc ion by two histidine residues and one aspartic acid residue. The loop region that forms the central pore in the oligomer was poorly defined in the crystal structure and therefore predicted by AlphaFold to complement the missing structural details, providing a complete picture of the functionally relevant hexameric form of BB0789. We confirmed that BB0789 is functionally active, possessing both protease and ATPase activities, thus providing novel structural-functional insights into the protein, which is known to be absolutely necessary for <em>B. burgdorferi</em> to survive and cause Lyme disease.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49673831","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":"Antibodies and α-synuclein: What to target against Parkinson's Disease?","authors":"Daniel E. Otzen","doi":"10.1016/j.bbapap.2023.140943","DOIUrl":"10.1016/j.bbapap.2023.140943","url":null,"abstract":"<div><p>Parkinson's Disease (PD) is strongly linked to the aggregation of the protein α-synuclein (α-syn), an intrinsically disordered protein. However, strategies to combat PD by targeting the aggregation of α-syn are challenged by the multiple types of aggregates formed both <em>in vivo</em> and <em>in vitro</em>, the potential influence of chemical modifications and the as yet unresolved question of which aggregate types (oligomeric or fibrillar) are most cytotoxic. Here I briefly review the social history of α-syn, the many efforts to raise antibodies against α-syn and the disappointing results of clinical trials based on such antibodies. Ultimately a thorough understanding of the molecular and mechanistic properties of mAbs towards aggregated species of α-syn is an essential prerequisite for any clinical trial, but this is missing in most cases. I highlight new microfluidic techniques which may address this need and call for a more concerted effort to standardize antibody studies as the basis to allow us to link molecular insights to clinical efficacy.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1570963923000572/pdfft?md5=f552b3b8ed7908aa2862434b374887f3&pid=1-s2.0-S1570963923000572-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41123165","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":"Calcium binding of AtCBL1: Structural and functional insights","authors":"Alexandra Bork , Sander H.J. Smits , Lutz Schmitt","doi":"10.1016/j.bbapap.2023.140967","DOIUrl":"10.1016/j.bbapap.2023.140967","url":null,"abstract":"<div><p><span>CBL1 is an EF hand Ca</span><sup>2+</sup> binding protein from <em>A. thaliana</em> that is involved in the detection of cellular Ca<sup>2+</sup><span><span> signals and the downstream signal transmission by interaction with the protein kinase CIPK23. So far, the structure and </span>calcium ion<span><span> binding affinities of CBL1 remain elusive. In this study it was observed that CBL1 tends to form higher oligomeric states due to an intrinsic </span>hydrophobicity<span> and the presence of the detergent BriJ35 was required for the purification of monomeric and functional protein. Functional insights into the </span></span></span><em>in vitro</em> Ca<sup>2+</sup><span> binding capabilities of CBL1 were obtained by isothermal titration calorimetry (ITC) of the wildtype protein as well as single site EF hand mutants. Based on our results, a binding model of CBL1 for Ca</span><sup>2+</sup> <em>in vivo</em> is proposed. Additionally, upon both, ITC measurements and the analysis of an AlphaFold2 model of CBL1, we could gain first insights into the formation of the dimer interface. We could identify an area around EF hand 4 to be relevant for the structural and functional integrity of monomeric CBL1 and likely EF hand 1 to be involved in the dimer interface.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41098502","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}
Evgeniia V. Leisi , Andrey V. Moiseenko , Sofia S. Kudryavtseva , Denis V. Pozdyshev , Vladimir I. Muronetz , Lidia P. Kurochkina
{"title":"Bacteriophage-encoded chaperonins stimulate prion protein fibrillation in an ATP-dependent manner","authors":"Evgeniia V. Leisi , Andrey V. Moiseenko , Sofia S. Kudryavtseva , Denis V. Pozdyshev , Vladimir I. Muronetz , Lidia P. Kurochkina","doi":"10.1016/j.bbapap.2023.140965","DOIUrl":"10.1016/j.bbapap.2023.140965","url":null,"abstract":"<div><p><span><span>The pathogenesis of the various prion diseases is based on the conformational conversion of the prion protein from its physiological cellular form to the insoluble scrapie<span> isoform. Several chaperones, including the Hsp60 family of group I </span></span>chaperonins, are known to contribute to this transformation, but data on their effects are scarce and conflicting. In this work, two GroEL-like phage chaperonins, the single-ring OBP and the double-ring EL, were found to stimulate monomeric prion protein fibrillation in an ATP-dependent manner. The resulting fibrils were characterised by </span>thioflavin<span><span> T fluorescence, electron microscopy<span>, proteinase K<span> digestion assay and other methods. In the presence of ATP, chaperonins were found to promote the conversion of prion protein </span></span></span>monomers<span> into short amyloid fibrils with their further aggregation into less toxic large clusters. Fibrils generated with the assistance of phage chaperonins differ in morphology and properties from those formed spontaneously from monomeric prion in the presence of denaturants at acidic pH.</span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41096571","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}
MeiLing Zhang , JiaXiang Zhang , Yan Liang, ShiCheng Tian, ShuYang Xie, Tong Zhou, Qin Wang
{"title":"The regulation of RGLG2-VWA by Ca2+ ions","authors":"MeiLing Zhang , JiaXiang Zhang , Yan Liang, ShiCheng Tian, ShuYang Xie, Tong Zhou, Qin Wang","doi":"10.1016/j.bbapap.2023.140966","DOIUrl":"https://doi.org/10.1016/j.bbapap.2023.140966","url":null,"abstract":"<div><p><span>RGLG2, an E3 ubiquitin ligase in </span><span><em>Arabidopsis thaliana</em></span>, affects hormone signaling and participates in drought regulation. Here, we determined two crystal structures of RGLG2 VWA domain, representing two conformations, open and closed, respectively. The two structures reveal that Ca<sup>2+</sup><span> ions are allosteric regulators of RGLG2-VWA, which adopts open state when NCBS1(Novel Calcium ions Binding Site 1) binds Ca</span><sup>2+</sup> ions and switches to closed state after Ca<sup>2+</sup><span><span> ions are removed. This mechanism of allosteric regulation is identical to RGLG1-VWA, but distinct from </span>integrin α and β VWA domains. Therefore, our data provide a backdrop for understanding the role of the Ca</span><sup>2+</sup><span> ions in conformational change of VWA domain. In addition, we found that RGLG2</span><sup>closed</sup>, corresponding to low affinity, can bind pseudo-ligand, which has never been observed in other VWA domains.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49888360","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":"Importance of aspartate 4 in the Mg2+ dependent regulation of Leishmania major PAS domain-containing phosphoglycerate kinase","authors":"Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak","doi":"10.1016/j.bbapap.2023.140964","DOIUrl":"https://doi.org/10.1016/j.bbapap.2023.140964","url":null,"abstract":"<div><p><span><span>Magnesium is an important divalent cation for the regulation of </span>catalytic activity. Recently, we have described that the Mg</span><sup>2+</sup><span> binding through the PAS domain inhibits the phosphoglycerate kinase (PGK) activity in PAS domain-containing PGK from </span><span><em>Leishmania major</em></span><span> (LmPAS-PGK) at neutral pH 7.5, but PGK activity is derepressed at acidic pH 5.5. The acidic residue within the PAS domain of LmPAS-PGK is expected to bind the cofactor Mg</span><sup>2+</sup><span> ion at neutral pH, but which specific acidic residue(s) is/are responsible for the Mg</span><sup>2+</sup> binding is still unknown. To identify the residues, we exploited mutational studies of all acidic (twelve Asp/Glu) residues in the PAS domain for plausible Mg<sup>2+</sup> binding. Mg<sup>2+</sup><span><span> ion-dependent repression at pH 7.5 is withdrawn by substitution of Asp-4 with Ala, whereas other acidic residue mutants (D16A, D22A, D24A, D29A, D43A, D44A, D60A, D63A, D77A, D87A, and E107A) showed similar features compared to the wild-type protein. Fluorescence spectroscopic studies and </span>isothermal titration calorimetry analysis showed that the Asp-4 is crucial for Mg</span><sup>2+</sup><span> binding in the absence of both PGK's substrates. These results suggest that Asp-4 residue in the regulatory (PAS) domain of wild type enzymes is required for Mg</span><sup>2+</sup> dependent repressed state of the catalytic PGK domain at neutral pH.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49786063","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}
Shima Ghaedizadeh , Majid Zeinali , Bahareh Dabirmanesh , Behnam Rasekh , Khosrow Khajeh , Ali Mohammad Banaei-Moghaddam
{"title":"Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies","authors":"Shima Ghaedizadeh , Majid Zeinali , Bahareh Dabirmanesh , Behnam Rasekh , Khosrow Khajeh , Ali Mohammad Banaei-Moghaddam","doi":"10.1016/j.bbapap.2023.140962","DOIUrl":"10.1016/j.bbapap.2023.140962","url":null,"abstract":"<div><p><span>Implementing hyperthermostable carbonic anhydrases into CO</span><sub>2</sub> capture and storage technologies in order to increase the rate of CO<sub>2</sub><span> absorption from the industrial flue gases<span> is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from </span></span><em>Sulfurihydrogenibium yellowstonense.</em><span><span> Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency<span> but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the </span></span>molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.</span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10269191","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":"Enzymatic and biophysical characterization of a novel modular cellulosomal GH5 endoglucanase multifunctional from the anaerobic gut fungus Piromyces finnis","authors":"Viviane Brito Andrade , Geizecler Tomazetto , Dnane Vieira Almeida , Robson Tramontina , Fabio Marcio Squina , Wanius Garcia","doi":"10.1016/j.bbapap.2023.140963","DOIUrl":"10.1016/j.bbapap.2023.140963","url":null,"abstract":"<div><p><span>Cellulases<span><span> from anaerobic fungi are enzymes less-studied biochemically and structurally than cellulases from bacteria and aerobic fungi. Currently, only thirteen GH5 cellulases from anaerobic fungi were biochemically characterized and two crystal structures were reported. In this context, here, we report the functional and biophysical characterization of a novel multi-modular cellulosomal GH5 </span>endoglucanase from the anaerobic gut fungus </span></span><span><em>Piromyces</em><em> finnis</em></span> (named here <em>Pf</em><span>GH5). Multiple sequences alignments indicate that </span><em>Pf</em><span><span>GH5 is composed of a GH5 catalytic domain and a </span>CBM1<span> carbohydrate-binding module connected through a CBM10 dockerin module. Our results showed that </span></span><em>Pf</em>GH5 is an endoglucanase from anaerobic fungus with a large spectrum of activity. <em>Pf</em><span><span>GH5 exhibited preference for hydrolysis<span> of oat β-glucan, followed by galactomannan, </span></span>carboxymethyl cellulose, mannan, lichenan and barley β-glucan, therefore displaying multi-functionality. For oat β-glucan, </span><em>Pf</em><span>GH5 reaches its optimum enzymatic activity at 40 °C and pH 5.5, with K</span><sub>m</sub><span><span> of 7.1 μM. Ion exchange chromatography analyzes revealed the production of </span>oligosaccharides with a wide degree of polymerization indicated that </span><em>Pf</em>GH5 has endoglucanase activity. The ability to bind and cleave different types of carbohydrates evidence the potential of <em>Pf</em>GH5 for use in biotechnology and provide a useful basis for future investigation and application of new anaerobic fungi enzymes.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10617016","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":"Modulation of the conformation, fibrillation, and fibril morphologies of human brain α-, β-, and γ-synuclein proteins by the disaccharide chemical chaperone trehalose","authors":"Manish K. Jain , Rajiv Bhat","doi":"10.1016/j.bbapap.2023.140932","DOIUrl":"10.1016/j.bbapap.2023.140932","url":null,"abstract":"<div><p><span>Human α-, β-, and γ-synuclein (syn) are natively unfolded proteins present in the brain. Deposition of aggregated α-syn in Lewy bodies is associated with Parkinson's disease (PD) and γ-syn is known to be involved in both neurodegeneration and breast cancer. At physiological pH, while α-syn has the highest propensity for fibrillation followed by γ-syn, β-syn does not form any fibrils. Fibril formation in these proteins could be modulated by protein structure stabilizing </span>osmolytes<span><span> such as trehalose which has an exceptional stabilizing effect for </span>globular proteins<span><span>. We present a comprehensive study of the effect of trehalose on the conformation, aggregation, and fibril morphology of α-, β-, and γ-syn proteins. Rather than stabilizing the intrinsically disordered state of the synucleins, trehalose accelerates the rate of fibril formation by forming aggregation-competent partially folded intermediate structures. Fibril morphologies are also strongly dependent on the concentration of trehalose with ≤ 0.4M favoring the formation of mature fibrils in α-, and γ-syn with no effect on the fibrillation of β-syn. At ≥ 0.8M, trehalose promotes the formation of smaller aggregates that are more cytotoxic. Live </span>cell imaging<span> of preformed aggregates of a labeled A90C α-syn shows their rapid internalization into neural cells which could be useful in reducing the load of aggregated species of α-syn. The findings throw light on the differential effect of trehalose on the conformation and aggregation of disordered synuclein proteins with respect to globular proteins and could help in understanding the effect of osmolytes on intrinsically disordered proteins under cellular stress conditions.</span></span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9860112","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}