The Open Biochemistry Journal最新文献

{"title":"Primary Structure Revision and Active Site Mapping of E. Coli Isoleucyl-tRNA Synthetase by Means of Maldi Mass Spectrometry.","authors":"Soria Baouz,&nbsp;Jean-Marie Schmitter,&nbsp;Lila Chenoune,&nbsp;Christian Beauvallet,&nbsp;Sylvain Blanquet,&nbsp;Anne Woisard,&nbsp;Codjo Hountondji","doi":"10.2174/1874091X00903010026","DOIUrl":"https://doi.org/10.2174/1874091X00903010026","url":null,"abstract":"<p><p>The correct amino acid sequence of E. coli isoleucyl-tRNA synthetase (IleRS) was established by means of peptide mapping by MALDI mass spectrometry, using a set of four endoproteases (trypsin, LysC, AspN and GluC). Thereafter, the active site of IleRS was mapped by affinity labeling with reactive analogs of the substrates. For the ATP binding site, the affinity labeling reagent was pyridoxal 5'-diphospho-5'-adenosine (ADP-PL), whereas periodate-oxidized tRNA(Ile), the 2',3'-dialdehyde derivative of tRNA(Ile) was used to label the binding site for the 3'-end of tRNA on the synthetase. Incubation of either reagent with IleRS resulted in a rapid loss of both the tRNA(Ile) aminoacylation and isoleucinedependent isotopic ATP-PPi exchange activities. The stoichiometries of IleRS labeling by ADP-PL or tRNA(Ile)ox corresponded to 1 mol of reagent incorporated per mol of enzyme. Altogether, the oxidized 3'-end of tRNA(Ile) and the pyridoxal moiety of the ATP analog ADP-PL react with the lysyl residues 601 and 604 of the consensus sequence (601)KMSKS(605). Identification of the binding site for L-isoleucine or for non cognate amino acids on E. coli IleRS was achieved by qualitative comparative labeling of the synthetase with bromomethyl ketone derivatives of L-isoleucine (IBMK) or of the non-cognate amino acids valine (VBMK), phenylalanine (FBMK) and norleucine (NleBMK). Labeling of the enzyme with IBMK resulted in a complete loss of isoleucine-dependent isotopic [(32)P]PPi-ATP exchange activity. VBMK, NleBMK and FBMK were also capable of abolishing the activity of IleRS, FBMK being the less efficient in inactivating the synthetase. Analysis by MALDI mass spectrometry designated cysteines-462 and -718 as the target residues of the substrate analog IBMK on E. coli IleRS, whereas VBMK, NleBMK and FBMK labeled in common His-394, His-478 and Cys-718. In addition, VBMK and NleBMK, which are chemically similar to IBMK, were found covalently bound to Cys-462, and VBMK was specifically attached to His-332 (or His-337) of the synthetase. The amino acid residues labeled by the substrate analogs are mainly distributed between three regions in the primary structure of E. coli IleRS: these are segments [325-394], [451-479] and [591-604]. In the 3-D structures of IleRS from T. thermophilus and S. aureus, the [325-394] stretch is part of the editing domain, while fragments [451-479] and [591-604] representing the isoleucine binding domain and the dinucleotide (or Rossmann) fold domain, respectively, are located in the catalytic core. His-332 of E. coli IleRS, that is strictly conserved among all the available IleRS sequences is located in the editing active site of the synthetase. It is proposed that His-332 of E. coli IleRS participates directly in hydrolysis, or helps to deprotonate the hydroxyl group of threonine at the hydrolytic site.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"3 ","pages":"26-38"},"PeriodicalIF":0.0,"publicationDate":"2009-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e9/aa/TOBIOCJ-3-26.PMC2695604.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28345523","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":"Protein domain boundary predictions: a structural biology perspective.","authors":"Svetlana Kirillova,&nbsp;Suresh Kumar,&nbsp;Oliviero Carugo","doi":"10.2174/1874091X00903010001","DOIUrl":"https://doi.org/10.2174/1874091X00903010001","url":null,"abstract":"<p><p>One of the important fields to apply computational tools for domain boundaries prediction is structural biology. They can be used to design protein constructs that must be expressed in a stable and functional form and must produce diffraction-quality crystals. However, prediction of protein domain boundaries on the basis of amino acid sequences is still very problematical. In present study the performance of several computational approaches are compared. It is observed that the statistical significance of most of the predictions is rather poor. Nevertheless, when the right number of domains is correctly predicted, domain boundaries are predicted within very few residues from their real location. It can be concluded that prediction methods cannot be used yet as routine tools in structural biology, though some of them are rather promising.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"3 ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/50/eb/TOBIOCJ-3-1.PMC2669640.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28138383","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":"Does phenoloxidase contributed to the resistance? Selection with butane-fipronil enhanced its activities from diamondback moths.","authors":"Shouzhu Liu,&nbsp;Hongtao Niu,&nbsp;Ting Xiao,&nbsp;Chaobin Xue,&nbsp;Zhongde Liu,&nbsp;Wanchun Luo","doi":"10.2174/1874091X00903010009","DOIUrl":"https://doi.org/10.2174/1874091X00903010009","url":null,"abstract":"<p><p>Using microtitration method, the relationship between Phenoloxidase activity and the resistance of the diamondback moth Plutella xylostella (Linnaeus) to the novel insecticide butane-fipronil was determined in vitro. After selection of the tenth-generation by butane-fipronil, the resistance of the fourth instar larvae was increased 83.80-fold as compared to the susceptible strain. Phenoloxidase activity of the resistant strain (PO(r)) was 1.29-fold higher than the susceptible one (PO(s)). However, the Km and optimum pH values were similar in resistant and susceptible strains, which were 1.11 mM and 6.5, respectively. Both PO(r) and PO(s) have maximum stability at pH values less than 7.0, although PO(s) was less stable at lower pH values than PO(r). In addition, the thermal stabilities of the two phenoloxidase were very similar. It is suggested that PO may play an important role in the increasing resistance of pests to pesticides.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"3 ","pages":"9-13"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3a/68/TOBIOCJ-3-9.PMC2674291.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28212783","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":"Calcium-induced conformational transition of trout ependymins monitored by tryptophan fluorescence.","authors":"Bernhard Ganss,&nbsp;Werner Hoffmann","doi":"10.2174/1874091X00903010014","DOIUrl":"https://doi.org/10.2174/1874091X00903010014","url":null,"abstract":"<p><p>Ependymins are secretory, calcium-binding sialoproteins which are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these regeneration-responsive glycoproteins is associated with collagen fibrils of the extracellular matrix. Here, the tryptophan fluorescence of ependymins was monitored at various Ca(2+) concentrations. Two distinct states were identified with a relatively sharp transition at about 1 mM Ca(2+). In agreement with previous circular dichroism measurements, this strongly supports the hypothesis that a calcium-induced conformational change is important for the interaction of ependymins with components of the extracellular matrix. Such interactions with constituents of various basal laminae would also explain the important roles of piscine ependymins as well as invertebrate and mammalian ependymin-related proteins for cell adhesion processes and cell migration.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"3 ","pages":"14-7"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/45/c0/TOBIOCJ-3-14.PMC2669641.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28138869","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":"Differential activity of caspase-3 regulates susceptibility of lung and breast tumor cell lines to Paclitaxel.","authors":"Charles Amoatey Odonkor,&nbsp;Samuel Achilefu","doi":"10.2174/1874091X00802010121","DOIUrl":"https://doi.org/10.2174/1874091X00802010121","url":null,"abstract":"<p><p>Recent development of tumor resistance to paclitaxel presents a major problem to cancer treatment. An unsettled controversy in the cancer chemotherapy field, however, is whether caspases play a prominent role in paclitaxel-induced death in tumors. Previous studies suggest that cleavage of caspase-3 is not instrumental for the execution of death in tumors treated with paclitaxel, while other reports indicate that caspase-dependent pathways may be critical for paclitaxel cytotoxicity. In this study, we investigated the role of caspase-3 in breast and lung tumor cell line sensitivity to paclitaxel. Clonogenic survival and live/dead viability-assays, together with enzymatic activity and cell proliferation assays, reveal that the levels of paclitaxel-induced caspase-3 enzymatic activity in tumor cells correlate directly with tumor sensitivity to the drug.We observed a 2-fold increase in caspase-3 activity in 4T1-Luc breast tumor cells, but a 3-fold and 4-fold decrease in A549 and A427 lung tumor cell lines, respectively. Together, our results suggest that caspase-activation and activity levels are not only key determinants of paclitaxel-induced death in tumors but also serve as good indicators for tumor susceptibility to paclitaxel therapy. Our studies also indicate that within clinically relevant doses of paclitaxel, the ability to rid tumor populations of dormant tumor cells controls the rate of tumor recurrence.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"121-8"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0a/4b/TOBIOCJ-2-121.PMC2627519.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28003890","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":"Characterization of the Cdc6 Homologues from the Euryarchaeon Thermoplasma acidophilum.","authors":"Gyri Teien Haugland,&nbsp;Marte Innselset,&nbsp;Dominique Madern,&nbsp;Nils-Kåre Birkeland","doi":"10.2174/1874091X00802010129","DOIUrl":"https://doi.org/10.2174/1874091X00802010129","url":null,"abstract":"<p><p>Archaeal cell division cycle protein 6 (Cdc6) homologues are thought to be involved in the initiation process of DNA replication. In the present study, a biochemical characterization of the two Cdc6 proteins from the archaeon Thermoplasma acidophilum has been performed. Both TaCdc6-1 and TaCdc6-2 behave as monomers in solution and both are abundantly expressed in vivo. Further, TaCdc6-1 shows strong ability to undergo autophosphorylation compared to TaCdc6-2 and the autophosphorylation activity is not affected by DNA or MCM.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"129-34"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0a/b5/TOBIOCJ-2-129.PMC2627522.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28003893","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":"Biosynthesis of natural and hyperelongated chondroitin sulfate glycosaminoglycans: new insights into an elusive process.","authors":"Peter J Little,&nbsp;Mandy L Ballinger,&nbsp;Micah L Burch,&nbsp;Narin Osman","doi":"10.2174/1874091X00802010135","DOIUrl":"https://doi.org/10.2174/1874091X00802010135","url":null,"abstract":"<p><p>Proteoglycans are important components of the extracellular matrix of all tissues. Proteoglycans are comprised of a core protein and one or more covalently attached glycosaminoglycan (GAG) chains. The major chondroitin sulfate (CS) and dermatan sulfate (DS) proteoglycans are aggrecan, versican, biglycan and decorin. Cells synthesize GAGs of natural or basal lengths and the GAG chains are subject to considerable growth factor, hormonal and metabolic regulation to yield longer GAG chains with altered structure and function. The mechanism by which the CS/DS GAG chains are polymerized is unknown. Recent work has identified several monosaccharide transferases which when co-expressed yield GAG polymers and the length of the polymers depends upon the pair of enzymes coexpressed. The further extension of these chains is regulated by signaling pathways. Inhibition of these latter pathways may be a therapeutic target to prevent the elongation which is associated with increased binding of atherogenic lipids and the disease process of atherosclerosis.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"135-42"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c5/9d/TOBIOCJ-2-135.PMC2627520.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28003891","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 Metastasis Associated Antigen 1 (MTA1) by Serological Screening of Prostate Cancer cDNA Libraries.","authors":"Li Geng,&nbsp;Assudani Deepak P,&nbsp;Line Aija,&nbsp;Cao Fuming,&nbsp;Miles Amanda,&nbsp;Rees Robert C,&nbsp;McArdle Stephanie E B","doi":"10.2174/1874091X00802010100","DOIUrl":"https://doi.org/10.2174/1874091X00802010100","url":null,"abstract":"<p><p>Over the past 10 years the serological analysis of recombinant cDNA expression libraries (SEREX) has proved to be an effective method for the identification of tumour antigens. In the present study, two prostate cancer libraries were constructed and screened using autologous sera. Fifty five genes were isolated, including 46 known genes and 9 previously uncharacterised genes. Among the known genes, a metastasis-associated gene, MTA1, previously identified by differential cDNA hybridisation, was preferentially expressed in a panel of malignant tissues compared with normal tissues, as analysed by reverse transcriptase-polymerase chain reaction (RT-PCR). MTA1 transcripts were observed to be over-expressed in normal human testes as well as various cancer tissues when compared to the panel of normal tissues. MTA1 antigen reacted with 2 of 13 allogeneic prostate cancer patient sera tested, but no sera reactivity was observed to any of the normal adult sera tested. Furthermore, a similar distribution and expression level of MTA-1 was observed in murine tissues and cancer cell lines. Based on these findings and previous reports on the literature on this gene, MTA-1 can be considered not only as a \"biomarker\" of aggressive disease but also as a potential therapeutic target.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"100-7"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27816713","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":"Regulation of glycogen synthase kinase 3beta functions by modification of the small ubiquitin-like modifier.","authors":"Lee Eun Jeoung,&nbsp;Hyun Sung Hee,&nbsp;Chun Jaesun,&nbsp;Shin Sung Hwa,&nbsp;Yeon Kwang Hum,&nbsp;Kwak Min Kyoung,&nbsp;Park Tae Yoon,&nbsp;Kang Sang Sun","doi":"10.2174/1874091X00802010067","DOIUrl":"https://doi.org/10.2174/1874091X00802010067","url":null,"abstract":"<p><p>Modification of the Small Ubiquitin-like Modifier (SUMO) (SUMOylation) appears to regulate diverse cellular processes, including nuclear transport, signal transduction, apoptosis, autophagy, cell cycle control, ubiquitin-dependent degradation and gene transcription. Glycogen synthase kinase 3beta (GSK 3beta) is a serine/threonine kinase that is thought to contribute to a variety of biological events, including embryonic development, metabolism, tumorigenesis, and cell death. GSK 3beta is a constitutively active kinase that regulates many intracellular signaling pathways by phosphorylating substrates such as beta-catenin. We noticed that the putative SUMOylation sites are localized on K(292 )residueof (291)FKFPQ(295) in GSK 3beta based on analysis of the SUMOylation consensus sequence. In this report, we showed that the SUMOylation of GSK 3beta occurs on its K(292) residue, and this modification promotes its nuclear localization in COS-1. Additionally, our data showed that the GSK 3beta SUMO mutant (K292R) decreased its kinase activity and protein stability, affecting cell death. Therefore, our observations at first time suggested that SUMOylation on the K(292) residue of GSK 3beta might be a GSK 3beta regulation mechanism for its kinase activation, subcellular localization, protein stability, and cell apoptosis.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"67-76"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27816281","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":"Heparin alters viral serpin, serp-1, anti-thrombolytic activity to anti-thrombotic activity.","authors":"Xing Li,&nbsp;Heather Schneider,&nbsp;Andrew Peters,&nbsp;Colin Macaulay,&nbsp;Elaine King,&nbsp;Yunming Sun,&nbsp;Liying Liu,&nbsp;Erbin Dai,&nbsp;Jennifer A Davids,&nbsp;Grant McFadden,&nbsp;Alexandra Lucas","doi":"10.2174/1874091X00802010006","DOIUrl":"https://doi.org/10.2174/1874091X00802010006","url":null,"abstract":"<p><p>Serine protease inhibitors (serpins) regulate coagulation and inflammation. Heparin, a glycosaminoglycan, is an important cofactor for modulation of the inhibitory function of mammalian serpins. The secreted myxoma viral serpin, Serp-1 exerts profound anti-inflammatory activity in a wide range of animal models. Serp-1 anti-inflammatory and anti-atherogenic activity is dependent upon inhibition of the uPA / uPA receptor thrombolytic complex. We demonstrate here that heparin binds to Serp-1 and enhances Serp-1 inhibition of thrombin, a human pro-thrombotic serine protease, in vitro, altering inhibitory activity to a more predominant anti-thrombotic activity. Heparin also facilitates the simultaneous thrombin-mediated cleavage of Serp-1 and prevents formation of a serpin-typical SDS-resistant complex, implying mutual neutralization of Serp-1 and thrombin. In a cell-based assay, heparin facilitates Serp-1 reversal of cellular activation by stabilizing cellular membrane fluidity in thrombin-activated monocytes. In conclusion, heparin and other GAGs serve as cofactors enhancing Serp-1 regulation of local thrombotic and inflammatory pathways.</p>","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"2 ","pages":"6-15"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27816322","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}