BMC Biochemistry最新文献

{"title":"Characterization of a cold-active and salt tolerant esterase identified by functional screening of Arctic metagenomic libraries","authors":"Concetta De Santi, B. Altermark, M. Pierechod, Luca Ambrosino, D. de Pascale, N. Willassen","doi":"10.1186/s12858-016-0057-x","DOIUrl":"https://doi.org/10.1186/s12858-016-0057-x","url":null,"abstract":"","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-016-0057-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65930430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparison of the enzymatic properties of three recombinant isoforms of thrombolytic and antibacterial protein—Destabilase-Lysozyme from medicinal leech","authors":"A. Kurdyumov, V. Manuvera, I. Baskova, V. Lazarev","doi":"10.1186/s12858-015-0056-3","DOIUrl":"https://doi.org/10.1186/s12858-015-0056-3","url":null,"abstract":"","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0056-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65930422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The GH5 1,4-β-mannanase from Bifidobacterium animalis subsp. lactis Bl-04 possesses a low-affinity mannan-binding module and highlights the diversity of mannanolytic enzymes","authors":"J. Morrill, Evelina Kulcinskaja, A. Sulewska, S. Lahtinen, H. Stålbrand, B. Svensson, M. Abou Hachem","doi":"10.1186/s12858-015-0055-4","DOIUrl":"https://doi.org/10.1186/s12858-015-0055-4","url":null,"abstract":"","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0055-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65930416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The eukaryotic translation initiation factor 3f (eIF3f) interacts physically with the alpha 1B-adrenergic receptor and stimulates adrenoceptor activity.","authors":"Mario Javier Gutiérrez-Fernández,&nbsp;Ana Edith Higareda-Mendoza,&nbsp;César Adrián Gómez-Correa,&nbsp;Marco Aurelio Pardo-Galván","doi":"10.1186/s12858-015-0054-5","DOIUrl":"https://doi.org/10.1186/s12858-015-0054-5","url":null,"abstract":"<p><strong>Background: </strong>eIF3f is a multifunctional protein capable of interacting with proteins involved in different cellular processes, such as protein synthesis, DNA repair, and viral mRNA edition. In human cells, eIF3f is related to cell cycle and proliferation, and its deregulation compromises cell viability.</p><p><strong>Results: </strong>We here report that, in native conditions, eIF3f physically interacts with the alpha 1B-adrenergic receptor, a plasma membrane protein considered as a proto-oncogene, and involved in vasoconstriction and cell proliferation. The complex formed by eIF3f and alpha 1B-ADR was found in human and mouse cell lines. Upon catecholamine stimulation, eIF3f promotes adrenoceptor activity in vitro, independently of the eIF3f proline- and alanine-rich N-terminal region.</p><p><strong>Conclusions: </strong>The eIF3f/alpha adrenergic receptor interaction opens new insights regarding adrenoceptor-related transduction pathways and proliferation control in human cells. The eIf3f/alpha 1B-ADR complex is found in mammals and is not tissue specific.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2015-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0054-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34115200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The laforin/malin E3-ubiquitin ligase complex ubiquitinates pyruvate kinase M1/M2.","authors":"Rosa Viana, Pablo Lujan, Pascual Sanz","doi":"10.1186/s12858-015-0053-6","DOIUrl":"10.1186/s12858-015-0053-6","url":null,"abstract":"<p><strong>Background: </strong>Lafora disease (LD, OMIM 254780) is a fatal neurodegenerative disorder produced mainly by mutations in two genes: EPM2A, encoding the dual specificity phosphatase laforin, and EPM2B, encoding the E3-ubiquitin ligase malin. Although it is known that laforin and malin may form a functional complex, the underlying molecular mechanisms of this pathology are still far from being understood.</p><p><strong>Methods: </strong>In order to gain information about the substrates of the laforin/malin complex, we have carried out a yeast substrate-trapping screening, originally designed to identify substrates of protein tyrosine phosphatases.</p><p><strong>Results: </strong>Our results identify the two muscular isoforms of pyruvate kinase (PKM1 and PKM2) as novel interaction partners of laforin.</p><p><strong>Conclusions: </strong>We present evidence indicating that the laforin/malin complex is able to interact with and ubiquitinate both PKM1 and PKM2. This post-translational modification, although it does not affect the catalytic activity of PKM1, it impairs the nuclear localization of PKM2.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2015-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0053-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34110953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the role of a trypsin inhibitor from soap nut (Sapindus trifoliatus L. Var. Emarginatus) seeds against larval gut proteases, its purification and characterization.","authors":"V D Sirisha Gandreddi, Vijaya Rachel Kappala, Kunal Zaveri, Kiranmayi Patnala","doi":"10.1186/s12858-015-0052-7","DOIUrl":"10.1186/s12858-015-0052-7","url":null,"abstract":"<p><strong>Background: </strong>The defensive capacities of plant protease Inhibitors (PI) rely on inhibition of proteases in insect guts or those secreted by microorganisms; and also prevent uncontrolled proteolysis and offer protection against proteolytic enzymes of pathogens.</p><p><strong>Methods: </strong>An array of chromatographic techniques were employed for purification, homogeneity was assessed by electrophoresis. Specificity, Ki value, nature of inhibition, complex formation was carried out by standard protocols. Action of SNTI on insect gut proteases was computationally evaluated by modeling the proteins by threading and docking studies by piper using Schrodinger tools.</p><p><strong>Results: </strong>We have isolated and purified Soap Nut Trypsin Inhibitor (SNTI) by acetone fractionation, ammonium sulphate precipitation, ion exchange and gel permeation chromatography. The purified inhibitor was homogeneous by both gel filtration and polyacrylamide gel electrophoresis (PAGE). SNTI exhibited a molecular weight of 29 kDa on SDS-PAGE, gel filtration and was negative to Periodic Acid Schiff's stain. SNTI inhibited trypsin and pronase of serine class. SNTI demonstrated non-competitive inhibition with a Ki value of 0.75 ± 0.05×10-10 M. The monoheaded inhibitor formed a stable complex in 1:1 molar ratio. Action of SNTI was computationally evaluated on larval gut proteases from Helicoverpa armigera and Spodoptera frugiperda. SNTI and larval gut proteases were modeled and docked using Schrodinger software. Docking studies revealed strong hydrogen bond interactions between Lys10 and Pro71, Lys299 and Met80 and Van Der Waals interactions between Leu11 and Cys76amino acid residues of SNTI and protease from H. Armigera. Strong hydrogen bonds were observed between SNTI and protease of S. frugiperda at positions Thr79 and Arg80, Asp90 and Gly73, Asp2 and Gly160 respectively.</p><p><strong>Conclusion: </strong>We conclude that SNTI potentially inhibits larval gut proteases of insects and the kinetics exhibited by the protease inhibitor further substantiates its efficacy against serine proteases.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2015-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34107745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Respiration and substrate transport rates as well as reactive oxygen species production distinguish mitochondria from brain and liver.","authors":"Aaron M Gusdon, Gabriel A Fernandez-Bueno, Stephanie Wohlgemuth, Jenelle Fernandez, Jing Chen, Clayton E Mathews","doi":"10.1186/s12858-015-0051-8","DOIUrl":"10.1186/s12858-015-0051-8","url":null,"abstract":"<p><strong>Background: </strong>Aberrant mitochondrial function, including excessive reactive oxygen species (ROS) production, has been implicated in the pathogenesis of human diseases. The use of mitochondrial inhibitors to ascertain the sites in the electron transport chain (ETC) resulting in altered ROS production can be an important tool. However, the response of mouse mitochondria to ETC inhibitors has not been thoroughly assessed. Here we set out to characterize the differences in phenotypic response to ETC inhibitors between the more energetically demanding brain mitochondria and less energetically demanding liver mitochondria in commonly utilized C57BL/6J mice.</p><p><strong>Results: </strong>We show that in contrast to brain mitochondria, inhibiting distally within complex I or within complex III does not increase liver mitochondrial ROS production supported by complex I substrates, and liver mitochondrial ROS production supported by complex II substrates occurred primarily independent of membrane potential. Complex I, II, and III enzymatic activities and membrane potential were equivalent between liver and brain and responded to ETC. inhibitors similarly. Brain mitochondria exhibited an approximately two-fold increase in complex I and II supported respiration compared with liver mitochondria while exhibiting similar responses to inhibitors. Elevated NADH transport and heightened complex II-III coupled activity accounted for increased complex I and II supported respiration, respectively in brain mitochondria.</p><p><strong>Conclusions: </strong>We conclude that important mechanistic differences exist between mouse liver and brain mitochondria and that mouse mitochondria exhibit phenotypic differences compared with mitochondria from other species.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2015-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34165184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase.","authors":"Ariana Labastida-Polito,&nbsp;Georgina Garza-Ramos,&nbsp;Menandro Camarillo-Cadena,&nbsp;Rafael A Zubillaga,&nbsp;Andrés Hernández-Arana","doi":"10.1186/s12858-015-0049-2","DOIUrl":"https://doi.org/10.1186/s12858-015-0049-2","url":null,"abstract":"<p><strong>Background: </strong>Saccharomyces cerevisiae triosephosphate isomerase (yTIM) is a dimeric protein that shows noncoincident unfolding and refolding transitions (hysteresis) in temperature scans, a phenomenon indicative of the slow forward and backward reactions of the native-unfolded process. Thermal unfolding scans suggest that no stable intermediates appear in the unfolding of yTIM. However, reported evidence points to the presence of residual structure in the denatured monomer at high temperature.</p><p><strong>Results: </strong>Thermally denatured yTIM showed a clear trend towards the formation of aggregation-prone, β-strand-like residual structure when pH decreased from 8.0 to 6.0, even though thermal unfolding profiles retained a simple monophasic appearance regardless of pH. However, kinetic studies performed over a relatively wide temperature range revealed a complex unfolding mechanism comprising up to three observable phases, with largely different time constants, each accompanied by changes in secondary structure. Besides, a simple sequential mechanism is unlikely to explain the observed variation of amplitudes and rate constants with temperature. This kinetic complexity is, however, not linked to the appearance of residual structure. Furthermore, the rate constant for the main unfolding phase shows small, rather unvarying values in the pH region where denatured yTIM gradually acquires a β-strand-like conformation. It appears, therefore, that the residual structure has no influence on the kinetic stability of the native protein. However, the presence of residual structure is clearly associated with increased irreversibility.</p><p><strong>Conclusions: </strong>The slow temperature-induced unfolding of yeast TIM shows three kinetic phases. Rather than a simple sequential pathway, a complex mechanism involving off-pathway intermediates or even parallel pathways may be operating. β-strand-type residual structure, which appears below pH 8.0, is likely to be associated with increased irreversible aggregation of the unfolded protein. However, this denatured form apparently accelerates the refolding process.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2015-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0049-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33973630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purification and characterization of a cytochrome c with novel caspase-3 activation activity from the pathogenic fungus Rhizopus arrhizus.","authors":"Manoj Saxena, Rohit Kumar Sharma, Josell Ramirez-Paz, Arthur D Tinoco, Kai Griebenow","doi":"10.1186/s12858-015-0050-9","DOIUrl":"10.1186/s12858-015-0050-9","url":null,"abstract":"<p><strong>Background: </strong>Members of Rhizopus species are the most common cause of mucormycosis, a rare but often fatal fungal infection. Host induced pathogen apoptosis and pathogen induced host cell apoptosis are often involved in fungal infections. In many organisms, the release of mitochondrial cytochrome c can trigger apoptosis by activating caspase proteases, but the role of fungal cytochrome c in apoptosis remains unknown.</p><p><strong>Results: </strong>DNA sequence encoding Rhizopus arrhizus cytochrome c was cloned and expressed in E. coli. Both native and recombinant cytochrome c were purified using ion exchange followed by gel filtration chromatography. The identities of purified proteins were confirmed by MALDI-MS and UV-Visible spectroscopy. For the first time, we demonstrated that Rhizopus arrhizus cytochrome c could activate human capspase-3 in HeLa cell extracts. We also found that Rhizopus arrhizus cytochrome c has redox potential, peroxidase activity, and spectral properties similar to human and horse cytochrome c proteins.</p><p><strong>Conclusions: </strong>Rhizopus arrhizus cytochrome c can activate human caspase-3 in HeLa cell extracts and it possesses similar physical and spectral properties as human and horse cytochrome c. This protein was found to have a previously unknown potential to activate human caspase-3, an important step in the apoptosis cascade.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2015-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12858-015-0050-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33974324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets.","authors":"Terrence S Neumann, Elise A Span, Kelsey S Kalous, Robert Bongard, Adam Gastonguay, Michael A Lepley, Raman G Kutty, Jaladhi Nayak, Chris Bohl, Rachel G Lange, Majher I Sarker, Marat R Talipov, Rajendra Rathore, Ramani Ramchandran, Daniel S Sem","doi":"10.1186/s12858-015-0048-3","DOIUrl":"10.1186/s12858-015-0048-3","url":null,"abstract":"<p><strong>Background: </strong>Dual-specificity phosphatase-5 (DUSP5) plays a central role in vascular development and disease. We present a p-nitrophenol phosphate (pNPP) based enzymatic assay to screen for inhibitors of the phosphatase domain of DUSP5.</p><p><strong>Methods: </strong>pNPP is a mimic of the phosphorylated tyrosine on the ERK2 substrate (pERK2) and binds the DUSP5 phosphatase domain with a Km of 7.6 ± 0.4 mM. Docking followed by inhibitor verification using the pNPP assay identified a series of polysulfonated aromatic inhibitors that occupy the DUSP5 active site in the region that is likely occupied by the dual-phosphorylated ERK2 substrate tripeptide (pThr-Glu-pTyr). Secondary assays were performed with full length DUSP5 with ERK2 as substrate.</p><p><strong>Results: </strong>The most potent inhibitor has a naphthalene trisulfonate (NTS) core. A search for similar compounds in a drug database identified suramin, a dimerized form of NTS. While suramin appears to be a potent and competitive inhibitor (25 ± 5 μM), binding to the DUSP5 phosphatase domain more tightly than the monomeric ligands of which it is comprised, it also aggregates. Further ligand-based screening, based on a pharmacophore derived from the 7 Å separation of sulfonates on inhibitors and on sulfates present in the DUSP5 crystal structure, identified a disulfonated and phenolic naphthalene inhibitor (CSD (3) _2320) with IC₅₀ of 33 μM that is similar to NTS and does not aggregate.</p><p><strong>Conclusions: </strong>The new DUSP5 inhibitors we identify in this study typically have sulfonates 7 Å apart, likely positioning them where the two phosphates of the substrate peptide (pThr-Glu-pTyr) bind, with one inhibitor also positioning a phenolic hydroxyl where the water nucleophile may reside. Polysulfonated aromatic compounds do not commonly appear in drugs and have a tendency to aggregate. One FDA-approved polysulfonated drug, suramin, inhibits DUSP5 and also aggregates. Docking and modeling studies presented herein identify polysulfonated aromatic inhibitors that do not aggregate, and provide insights to guide future design of mimics of the dual-phosphate loops of the ERK substrates for DUSPs.</p>","PeriodicalId":9113,"journal":{"name":"BMC Biochemistry","volume":"16 ","pages":"19"},"PeriodicalIF":0.0,"publicationDate":"2015-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4545774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34102624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}