Biochimica et biophysica acta. Proteins and proteomics最新文献

{"title":"PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2","authors":"Marta Montserrat-Gomez ,&nbsp;Gergo Gogl ,&nbsp;Kendall Carrasco ,&nbsp;Stephane Betzi ,&nbsp;Fabien Durbesson ,&nbsp;Alexandra Cousido-Siah ,&nbsp;Camille Kostmann ,&nbsp;Dominic J. Essig ,&nbsp;Kristian Strømgaard ,&nbsp;Søren Østergaard ,&nbsp;Xavier Morelli ,&nbsp;Gilles Trave ,&nbsp;Renaud Vincentelli ,&nbsp;Eric Bailly ,&nbsp;Jean-Paul Borg","doi":"10.1016/j.bbapap.2023.140989","DOIUrl":"10.1016/j.bbapap.2023.140989","url":null,"abstract":"<div><p>VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity<span><span> signaling pathway<span> that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains<span>. Truncation and point mutation<span> analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, </span></span></span></span>SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.</span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 3","pages":"Article 140989"},"PeriodicalIF":3.2,"publicationDate":"2023-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032141","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":"BthTX-I, a phospholipase A2-like toxin, is inhibited by the plant cinnamic acid derivative: chlorogenic acid","authors":"Fábio Florença Cardoso ,&nbsp;Guilherme Henrique Marchi Salvador ,&nbsp;Walter Luís Garrido Cavalcante ,&nbsp;Maeli Dal-Pai ,&nbsp;Marcos Roberto de Mattos Fontes","doi":"10.1016/j.bbapap.2023.140988","DOIUrl":"10.1016/j.bbapap.2023.140988","url":null,"abstract":"<div><p>Snakebite is a significant health concern in tropical and subtropical regions, particularly in Africa, Asia, and Latin America, resulting in more than 2.7 million envenomations and an estimated one hundred thousand fatalities annually. The <span><em>Bothrops</em></span><span> genus is responsible for the majority of snakebite envenomings in Latin America and Caribbean countries. Accidents involving snakes from this genus are characterized by local symptoms that often lead to permanent sequelae and death. However, specific antivenoms exhibit limited effectiveness in inhibiting local tissue damage. Phospholipase A</span>₂-like (PLA₂-like) toxins emerge as significant contributors to local myotoxicity in accidents involving <em>Bothrops</em> species. As a result, they represent a crucial target for prospective treatments. Some natural and synthetic compounds have shown the ability to reduce or abolish the myotoxic effects of PLA₂<span>-like proteins. In this study, we employed a combination approach involving myographic, morphological, biophysical and bioinformatic techniques to investigate the interaction between chlorogenic acid (CGA) and BthTX-I, a PLA</span>₂<span>-like toxin. CGA provided a protection of 71.8% on muscle damage in a pre-incubation treatment. Microscale thermophoresis and circular dichroism<span><span> experiments revealed that CGA interacted with the BthTX-I while preserving its secondary structure. CGA exhibited an affinity to the toxin that ranks among the highest observed for a </span>natural compound<span>. Bioinformatics simulations indicated that CGA inhibitor binds to the toxin's hydrophobic channel in a manner similar to other phenolic compounds previously investigated. These findings suggest that CGA interferes with the allosteric transition of the non-activated toxin, and the stability of the dimeric assembly of its activated state.</span></span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 2","pages":"Article 140988"},"PeriodicalIF":3.2,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139020605","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":"FunPredCATH: An ensemble method for predicting protein function using CATH","authors":"Joseph Bonello ,&nbsp;Christine Orengo","doi":"10.1016/j.bbapap.2023.140985","DOIUrl":"10.1016/j.bbapap.2023.140985","url":null,"abstract":"<div><h3>Motivation</h3><p>The growth of unannotated proteins in UniProt increases at a very high rate every year due to more efficient sequencing methods. However, the experimental annotation of proteins is a lengthy and expensive process. Using computational techniques to narrow the search can speed up the process by providing highly specific Gene Ontology (GO) terms.</p></div><div><h3>Methodology</h3><p>We propose an ensemble approach that combines three generic base predictors that predict Gene Ontology (BP, CC and MF) terms from sequences across different species. We train our models on UniProtGOA annotation data and use the CATH domain resources to identify the protein families. We then calculate a score based on the prevalence of individual GO terms in the functional families that is then used as an indicator of confidence when assigning the GO term to an uncharacterised protein.</p></div><div><h3>Methods</h3><p>In the ensemble, we use a statistics-based method that scores the occurrence of GO terms in a CATH FunFam against a background set of proteins annotated by the same GO term. We also developed a set-based method that uses Set Intersection and Set Union to score the occurrence of GO terms within the same CATH FunFam. Finally, we also use FunFams-Plus, a predictor method developed by the Orengo Group at UCL to predict GO terms for uncharacterised proteins in the CAFA3 challenge.</p></div><div><h3>Evaluation</h3><p>We evaluated the methods against the CAFA3 benchmark and DomFun. We used the Precision, Recall and F_max metrics and the benchmark datasets that are used in CAFA3 to evaluate our models and compare them to the CAFA3 results. Our results show that FunPredCATH compares well with top CAFA methods in the different ontologies and benchmarks.</p></div><div><h3>Contributions</h3><p>FunPredCATH compares well with other prediction methods on CAFA3, and the ensemble approach outperforms the base methods. We show that non-IEA models obtain higher F_max scores than the IEA counterparts, while the models including IEA annotations have higher coverage at the expense of a lower F_max score.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 2","pages":"Article 140985"},"PeriodicalIF":3.2,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1570963923000997/pdfft?md5=0f4fa65f8e4df32c9a5a9a3d8e17897f&pid=1-s2.0-S1570963923000997-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138743449","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":"Classification of binding property of amyloid β to lipid membranes: Membranomic research using quartz crystal microbalance combined with the immobilization of lipid planar membranes","authors":"Toshinori Shimanouchi ,&nbsp;Miki Iwamura ,&nbsp;Yasuhiro Sano ,&nbsp;Keita Hayashi ,&nbsp;Minoru Noda ,&nbsp;Yukitaka Kimura","doi":"10.1016/j.bbapap.2023.140987","DOIUrl":"10.1016/j.bbapap.2023.140987","url":null,"abstract":"<div><p><span><span><span>A biomembrane-related fibrillogenesis of </span>Amyloid β from Alzheimer’ disease (Aβ) is closely related to its accumulation behavior. A binding property of Aβ peptides from Alzheimer’ disease to </span>lipid membranes was then classified by a quartz crystal microbalance (QCM) method combined with an immobilization technique using thiol self-assembled membrane. The accumulated amounts of Aβ, Δ</span><em>f</em>_max, was determined from the measurement of the maximal frequency reduction using QCM. The plots of Δ<em>f</em>_max to Aβ concentration gave the slope and saturated value of Δ<em>f</em>_max, (Δ<em>f</em>_max)^sat<span> that are the parameters for binding property of Aβ to lipid membranes. Therefore, the Aβ-binding property on lipid membranes was classified by the slope and (Δ</span><em>f</em>_max)^sat. The plural lipid system was described as X + Y where X = L₁, L₁/L₂, and L₁/L₂/L₃. The slope and (Δ<em>f</em>_max)^sat values plotted as a function of mixing ratio of Y to X was classified on a basis of the lever principle (LP). The LP violation observed in both parameters resulted from the formation of the crevice or pothole, as Aβ-specific binding site, generated at the boundary between <em>l</em>_d and <em>l</em>_o phases. The LP violation observed only in the slope resulted from glycolipid-rich domain acting as Aβ-specific binding site. Furthermore, lipid planar membranes indicating strong LP violation favored strong fibrillogenesis. Especially, lipid planar membranes indicating the LP violation only in the slope induced lateral aggregated and spherulitic fibrillar aggregates. Thus, the classification of Aβ binding property on lipid membranes appeared to be related to the fibrillogenesis with a certain morphology.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 3","pages":"Article 140987"},"PeriodicalIF":3.2,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138820194","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":"Kinetic characterization of the N-terminal domain of Malonyl-CoA reductase","authors":"Mirela Tkalcic Cavuzic,&nbsp;Grover L. Waldrop","doi":"10.1016/j.bbapap.2023.140986","DOIUrl":"10.1016/j.bbapap.2023.140986","url":null,"abstract":"<div><p><span>Climate change is driving a search for environmentally safe methods to produce chemicals used in ordinary life. One such molecule is 3-hydroxypropionic acid, which is a platform industrial chemical used as a precursor for a variety of other chemical end products. The biosynthesis<span> of 3-hydroxypropionic acid can be achieved in recombinant microorganisms via malonyl-CoA reductase<span> in two separate reactions. The reduction of malonyl-CoA by NADPH to form malonic semialdehyde is catalyzed in the C-terminal domain of malonyl-CoA reductase, while the subsequent reduction of malonic semialdehyde to 3-hydroxypropionic acid is accomplished in the N-terminal domain of the enzyme. A new assay for the reverse reaction of the N-terminal domain of malonyl-CoA reductase from </span></span></span><span><em>Chloroflexus aurantiacus</em></span><span> activity has been developed. This assay was used to determine the kinetic mechanism and for isotope effect studies. Kinetic characterization using initial velocity patterns revealed random binding of the substrates NADP</span>⁺ and 3-hydroxypropionic acid. Isotope effects showed substrates react to give products faster than they dissociate and that the products of the reverse reaction, NADPH and malonic semialdehyde, have a low affinity for the enzyme. Multiple isotope effects suggest proton and hydride transfer occur in a concerted fashion. This detailed kinetic characterization of the reaction catalyzed by the N-terminal domain of malonyl-CoA reductase could aid in engineering of the enzyme to make the biosynthesis of 3-hydroxypropionic acid commercially competitive with its production from fossil fuels.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 2","pages":"Article 140986"},"PeriodicalIF":3.2,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138743316","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":"Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha","authors":"Ivan R. Moraes ,&nbsp;Hamine C. de Oliveira ,&nbsp;Marcos R.M. Fontes","doi":"10.1016/j.bbapap.2023.140974","DOIUrl":"10.1016/j.bbapap.2023.140974","url":null,"abstract":"<div><p><span><span>NEIL glycosylases, including </span>NEIL1<span><span>, NEIL2, and NEIL3, play a crucial role in the base excision DNA<span> repair pathway (BER). The classical importin<span> pathway mediated by importin α/β and cargo proteins containing nuclear localization sequences (NLS) is the most common transport mechanism of DNA repair proteins to the nucleus. Previous studies have identified putative NLSs located at the C-terminus of NEIL3 and NEIL1. Crystallographic, bioinformatics, calorimetric (ITC), and </span></span></span>fluorescence assays<span> were used to investigate the interaction between NEIL1 and NEIL3 putative NLSs and importin-α (Impα). Our findings showed that NEIL3 contains a typical cNLS, with medium affinity for the major binding site of Impα. In contrast, crystallographic analysis of NEIL1 NLS revealed its binding to Impα, but with high B-factors and a lack of electron density at the linker region. ITC and fluorescence assays indicated no detectable affinity between NEIL1 NLS and Impα. These data suggest that NEIL1 NLS is a non-classical NLS with low affinity to Impα. Additionally, we compared the binding mode of NEIL3 and NEIL1 with </span></span></span><span><em>Mus musculus</em></span><span><span> Impα to human isoforms HsImpα1 and HsImpα3, which revealed interesting binding differences for HsImpα3 variant. NEIL3 is a classical medium affinity </span>monopartite<span> NLS, while NEIL1 is likely to be an unclassical low-affinity bipartite NLS. The base excision repair pathway is one of the primary systems involved in repairing DNA. Thus, understanding the mechanisms of nuclear transport of NEIL proteins is crucial for comprehending the role of these proteins in DNA repair and disease development.</span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 2","pages":"Article 140974"},"PeriodicalIF":3.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138564206","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":"Crystal structure and interconversion of monomers and domain-swapped dimers of the walnut tree phytocystatin","authors":"Gisele Alvarenga Simpson,&nbsp;Isabela Fernandes Rezende,&nbsp;Alencar da Silva Peixoto,&nbsp;Igor Barbosa de Oliveira Soares,&nbsp;João Alexandre Ribeiro Gonçalves Barbosa,&nbsp;Sônia Maria de Freitas,&nbsp;Napoleão Fonseca Valadares","doi":"10.1016/j.bbapap.2023.140975","DOIUrl":"10.1016/j.bbapap.2023.140975","url":null,"abstract":"<div><p><span>Biotechnological applications of phytocystatins have garnered significant interest due to their potential applications in crop protection and improve crop resistance to abiotic stress factors. Cof1 and Wal1 are phytocystatins derived from </span><span><em>Coffea arabica</em></span> and <em>Juglans regia</em><span>, respectively. These plants hold significant economic value due to coffee's global demand and the walnut tree's production of valuable timber and widely consumed walnuts with culinary and nutritional benefits. The study involved the heterologous expression in </span><em>E. coli</em><span><span><span> Lemo 21(DE3), purification by immobilized </span>metal ion affinity and size exclusion chromatography, and biophysical characterization of both phytocystatins, focusing on isolating and interconverting their </span>monomers<span><span><span> and dimers. The crystal structure of the domain-swapped dimer of Wal1 was determined revealing two domain-swapped dimers in the asymmetric unit, an arrangement reminiscent of the human </span>cystatin C structure. Alphafold models of monomers and Alphafold-Multimer models of domain-swapped dimers of Cof1 and Wal1 were analyzed in the context of the crystal structure. The methodology and data presented here contribute to a deeper understanding of the </span>oligomerization mechanisms of phytocystatins and their potential biotechnological applications in agriculture.</span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 2","pages":"Article 140975"},"PeriodicalIF":3.2,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497715","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":"Paradoxical effects on ice nucleation are intrinsic to a small winter flounder antifreeze protein","authors":"Xing Jian Chang ,&nbsp;Dane C. Sands ,&nbsp;Kathryn Vanya Ewart","doi":"10.1016/j.bbapap.2023.140973","DOIUrl":"10.1016/j.bbapap.2023.140973","url":null,"abstract":"<div><p><span>Antifreeze proteins<span> (AFPs) bind to ice in solutions, resulting in non-colligative freezing point depression; however, their effects on ice nucleation are not well understood. The predominant plasma AFP of winter flounder (</span></span><em>Pseudopleuronectes americanus</em><span><span>) is AFP6, which is an amphiphilic alpha helix. In this study, AFP6 and modified constructs were produced as </span>fusion proteins in </span><em>Escherichia coli</em><span><span>, subjected to proteolysis<span> when required and purified prior to use. AFP6 and its recombinant fusion precursor generated similar thermal hysteresis and bipyramidal ice crystals, whereas an inactive mutant AFP6 produced hexagonal crystals and no hysteresis. </span></span>Circular dichroism<span> spectra of the wild-type and mutant AFP6 were consistent with an alpha helix. The effects of these proteins on ice nucleation were investigated alongside non-AFP proteins using a standard droplet freezing assay. In the presence of nucleating AgI, modest reductions in the nucleation temperature occurred with the addition of mutant AFP6, and several non-AFPs, suggesting non-specific inhibition of AgI-induced ice nucleation. In these experiments, both AFP6 and its recombinant precursor resulted in lower nucleation temperatures, consistent with an additional inhibitory effect. Conversely, in the absence of AgI, AFP6 induced ice nucleation, with no other proteins showing this effect. Nucleation by AFP6 was dose-dependent, reaching a maximum at 1.5 mM protein. Nucleation by AFP6 also required an ice-binding site, as the inactive mutant had no effect. Furthermore, the absence of nucleation by the recombinant precursor protein suggested that the fusion moiety was interfering with the formation of a surface capable of nucleating ice.</span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 1","pages":"Article 140973"},"PeriodicalIF":3.2,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92152584","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":"A dissected non-ribosomal peptide synthetase maintains activity","authors":"Amanda J. Platt ,&nbsp;Shae Padrick ,&nbsp;Amy T. Ma ,&nbsp;Joris Beld","doi":"10.1016/j.bbapap.2023.140972","DOIUrl":"10.1016/j.bbapap.2023.140972","url":null,"abstract":"<div><p><span><span>Non-ribosomal peptide synthetases (NRPSs) generate chemically complex compounds and their modular architecture suggests that changing their domain organization can predictably alter their products. Ebony, a small three-domain NRPS, catalyzes the formation of β-alanine containing amides from biogenic amines. To examine the necessity of interdomain interactions, we modeled and docked domains of Ebony to reveal </span>potential interfaces between them. Testing the same domain combinations </span><em>in vitro</em> showed that 8 % of activity was preserved after Ebony was dissected into a di-domain and a detached C-terminal domain, suggesting that sufficient interaction was maintained after dissection. Our work creates a model to identify domain interfaces necessary for catalysis, an important step toward utilizing Ebony as a combinatorial engineering platform for novel amides.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 1","pages":"Article 140972"},"PeriodicalIF":3.2,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89716806","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":"Structural conservation in the glutathione binding in Sphingomonas sp. glutaredoxin Grx3 and variations for cold adaptation","authors":"Trang Van Tran,&nbsp;Hoa Nguyen,&nbsp;Luyen Vu,&nbsp;ChangWoo Lee","doi":"10.1016/j.bbapap.2023.140971","DOIUrl":"10.1016/j.bbapap.2023.140971","url":null,"abstract":"<div><p>Glutaredoxin 3 (Grx3), a redox protein with a thioredoxin-fold structure, maintains structural integrity and glutathione (GSH) binding capabilities across varying habitat temperatures. The cis-Pro loop, essential for GSH binding, relies on the Arg-Asp salt bridge (α2-α3) and Gln-His hydrogen bond (β3-β4) for its conformation. In some psychrophilic Grx3 variants, Arg in α2 is replaced with Tyr, and His in β4 is replaced with Phe. This study examines the roles of these bonds in Grx3's structure, function, and cold adaptation, using SpGrx3 from the Arctic bacterium <em>Sphingomonas</em> sp. Despite its cold habitat, SpGrx3 maintains the Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond. The R51Y substitution disrupts the α2-α3 salt bridge, while the H63F and H63Y substitutions hinder the salt bridge through cation-π interactions with Arg51, involving Phe63/Tyr63, thereby enhancing flexibility. Conversely, mutations that disrupt the hydrogen bond (Q56A, H63A, and H63F) reduce thermal stability. In the psychrophilic Grx3 configuration A48T/R51Y/H63F, a Thr48-Gln56 hydrogen bond stabilizes the cis-Pro loop, enhancing flexibility by disrupting both bonds. Furthermore, all mutants exhibit reduced α-helical content and catalytic efficiency. In summary, the highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the cis-Pro loop and catalytic activity in SpGrx3. His63 is favored as it avoids cation-π interactions with Arg51, unlike Phe63/Tyr63. Psychrophilic Grx3 variants have adapted to cold environments by reducing GSH binding and increasing structural flexibility. These findings deepen our understanding of the structural conservation in Grx3 for GSH binding and the critical alterations required for cold adaptation.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 1","pages":"Article 140971"},"PeriodicalIF":3.2,"publicationDate":"2023-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71477530","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}