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The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations
Michael Widmann, Robert Radloff, Jürgen Pleiss BMC Biochemistry 2010, 11:9 (1 February 2010)
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Editor’s summary
A database of thiamine diphosphate (ThDP) dependent enzymes includes multisequence alignments and phylogenetic trees for families of the enzymes, structural information, and SNPs of human enzymes that might be related to disease.
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Orthophosphate binding at the dimer interface of Corynebacterium callunae starch phosphorylase: mutational analysis of its role for activity and stability of the enzyme
Mario Mueller, Bernd Nidetzky BMC Biochemistry 2010, 11:8 (29 January 2010)
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NMR characterisation of the minimal interacting regions of centrosomal proteins 4.1R and NuMA1: effect of phosphorylation
Miguel A Treviño, Mar Rodríguez-Rodríguez, Isabel Correas, Miguel Marcilla, Juan P Albar, Manuel Rico, M Ángeles Jiménez, Marta Bruix BMC Biochemistry 2010, 11:7 (28 January 2010)
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Two chitinase-like proteins abundantly accumulated in latex of mulberry show insecticidal activity
Sakihito Kitajima, Kaeko Kamei, Shigeru Taketani, Masamitsu Yamaguchi, Fumiko Kawai, Aino Komatsu, Yoshihiro Inukai BMC Biochemistry 2010, 11:6 (28 January 2010)
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Rapid determination of tricarboxylic acid cycle enzyme activities in biological samples
Sergio Goncalves, Vincent Paupe, Emmanuel P Dassa, Jean-Jacques Brière, Judith Favier, Anne-Paule Gimenez-Roqueplo, Paule Bénit, Pierre Rustin BMC Biochemistry 2010, 11:5 (28 January 2010)
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Identification of inhibitors of Plasmodium falciparum phosphoethanolamine methyltransferase using an enzyme-coupled transmethylation assay
April M Bobenchik, Jae-Yeon Choi, Arunima Mishra, Iulian N Rujan, Bing Hao, Dennis R Voelker, Jeffrey C Hoch, Choukri Mamoun BMC Biochemistry 2010, 11:4 (19 January 2010)
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Editor’s summary
Amodiaquine inhibits the activity of Plasmodium falciparum phosphoethanolamine methyltransferase and, as this enzyme is essential for survival of the malaria parasite and is not found in mammals, the inhibitor is an ideal candidate for drug development.
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Thioredoxins function as deglutathionylase enzymes in the yeast Saccharomyces cerevisiae
Darren Greetham, Jill Vickerstaff, Daniel Shenton, Gabriel G Perrone, Ian W Dawes, Chris M Grant BMC Biochemistry 2010, 11:3 (14 January 2010)
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Mechanism of attenuation of leptin signaling under chronic ligand stimulation
Holger Knobelspies, Julia Zeidler, Paul Hekerman, Simone Bamberg-Lemper, Walter Becker BMC Biochemistry 2010, 11:2 (8 January 2010)
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Cloning and characterization of Escherichia coli DUF299: a bifunctional ADP-dependent kinase - Pi-dependent pyrophosphorylase from bacteria
Jim N Burnell BMC Biochemistry 2010, 11:1 (3 January 2010)
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Editor’s summary
A bacterial homologue of the maize orthophosphate dikinase regulatory protein, cloned from Escherichia coli, catalyses both the inactivation and activation of phosphoenolpyruvate synthetase, by ADP-dependent phosphorylation, and Pi-dependent pyrophosphorylation respectively.
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Identification of four novel phosphorylation sites in estrogen receptor α: impact on receptor-dependent gene expression and phosphorylation by protein kinase CK2
Christopher C Williams, Aninda Basu, Abeer El-Gharbawy, Latonya M Carrier, Carolyn L Smith, Brian G Rowan BMC Biochemistry 2009, 10:36 (31 December 2009)
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The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains
Lynn GL Richardson, Masoud Jelokhani-Niaraki, Matthew D Smith BMC Biochemistry 2009, 10:35 (30 December 2009)
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The variable N-terminal acidic domains of the Toc159 chloroplast preprotein receptor family in Arabidopsis are intrinsically disordered, which may facilitate interactions with transit peptides, and explain how these receptors serve to import a wide variety of proteins into chloroplasts.
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Identification and characterization of endonuclein binding proteins: evidence of modulatory effects on signal transduction and chaperone activity
Maja Ludvigsen, Morten Østergaard, Henrik Vorum, Christian Jacobsen, Bent Honoré BMC Biochemistry 2009, 10:34 (22 December 2009)
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Comparison of the receptor FGFRL1 from sea urchins and humans illustrates evolution of a zinc binding motif in the intracellular domain
Lei Zhuang, Andrei V Karotki, Philip Bruecker, Beat Trueb BMC Biochemistry 2009, 10:33 (18 December 2009)
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Analysis of the stoichiometric metal activation of methionine aminopeptidase
Sergio C Chai, Qi-Zhuang Ye BMC Biochemistry 2009, 10:32 (17 December 2009)
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Biochemical evidence for the tyrosine involvement in cationic intermediate stabilization in mouse β-carotene 15, 15'-monooxygenase
Eugenia Poliakov, Susan Gentleman, Preethi Chander, Francis X Cunningham, Bella L Grigorenko, Alexander V Nemuhin, T Michael Redmond BMC Biochemistry 2009, 10:31 (14 December 2009)
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Ghrelin-like peptide with fatty acid modification and O-glycosylation in the red stingray, Dasyatis akajei
Hiroyuki Kaiya, Shiho Kodama, Koutaro Ishiguro, Kouhei Matsuda, Minoru Uchiyama, Mikiya Miyazato, Kenji Kangawa BMC Biochemistry 2009, 10:30 (14 December 2009)
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Prion protein self-peptides modulate prion interactions and conversion
Alan Rigter, Jan Priem, Drophatie Timmers-Parohi, Jan PM Langeveld, Fred G van Zijderveld, Alex Bossers BMC Biochemistry 2009, 10:29 (30 November 2009)
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Prion peptides are tested for their ability to modulate prion protein self-interactions and conversion to the scrapie isoform, indicating domain-specific roles and the importance of stabilizing PrPC-PrPC and PrPC-PrPSc interactions as a prelude to conversion.
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Purification and characterization of cysteine protease from germinating cotyledons of horse gram
Rajeswari Jinka, Vadde Ramakrishna, Sridhar K Rao, Ramakrishna P Rao BMC Biochemistry 2009, 10:28 (17 November 2009)
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The Cytochrome P450 Engineering Database: integration of biochemical properties
Demet Sirim, Florian Wagner, Andrey Lisitsa, Jürgen Pleiss BMC Biochemistry 2009, 10:27 (12 November 2009)
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Editor’s summary
The new version of the Cytochrome P450 Engineering Database (CYPED) contains information on the sequences of 8613 proteins and the structures of 47 proteins, and has been extended by integrating biochemical information from the Cytochrome P450 Knowledgebase.
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Biosynthesis of the proteasome inhibitor syringolin A: the ureido group joining two amino acids originates from bicarbonate
Christina Ramel, Micha Tobler, Martin Meyer, Laurent Bigler, Marc-Olivier Ebert, Barbara Schellenberg, Robert Dudler BMC Biochemistry 2009, 10:26 (28 October 2009)
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Biosynthesis of the proteosome inhibitor syringolin A is directed by the syl gene cluster of phytopathogenic bacterium Pseudomonas syringae pv. syringae B728a after heterologous transfer, with CO2 being incorporated to form the unusual ureido group.
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Ser170 of Bacillus thuringiensis Cry1Ab δ-endotoxin becomes anchored in a hydrophobic moiety upon insertion of this protein into Manduca sexta brush border membranes
Oscar Alzate, Craig F Hemann, Cristina Osorio, Russ Hille, Donald H Dean BMC Biochemistry 2009, 10:25 (19 October 2009)
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Mapping of protein phosphatase-6 association with its SAPS domain regulatory subunit using a model of helical repeats
Julien Guergnon, Urszula Derewenda, Jessica R Edelson, David L Brautigan BMC Biochemistry 2009, 10:24 (16 October 2009)
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Our understanding of how SAPS-related proteins differentially regulate closely-related Ser/Thr phosphatases is advanced by a study indicating that human PP6R3 forms distinctive helical repeats within its conserved SAPS domain and uses interhelical loops to associate with protein phosphatase 6.
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Monitoring compartment-specific substrate cleavage by cathepsins B, K, L, and S at physiological pH and redox conditions
Silvia Jordans, Saša Jenko-Kokalj, Nicole M Kühl, Sofia Tedelind, Wolfgang Sendt, Dieter Brömme, Dušan Turk, Klaudia Brix BMC Biochemistry 2009, 10:23 (22 September 2009)
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Editor’s summary
Cathepsin cysteine proteases are active under conditions simulating extracellular and intracellular compartments with a range of pHs and redox potentials, as shown by cleavage of the natural substrate thyroglobulin in distinct ways in different physiologic environments.
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Identification of a nuclear localization motif in the serine/arginine protein kinase PSRPK of physarum polycephalum
Shide Liu, Zhuolong Zhou, Ziyang Lin, Qiuling Ouyang, Jianhua Zhang, Shengli Tian, Miao Xing BMC Biochemistry 2009, 10:22 (25 August 2009)
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Contribution of oenocytes and pheromones to courtship behaviour in Drosophila
Claude Wicker-Thomas, Ilhem Guenachi, Youssouf F Keita BMC Biochemistry 2009, 10:21 (11 August 2009)
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Biochemical characterization of malate synthase G of P. aeruginosa
Bart Roucourt, Nikki Minnebo, Patrick Augustijns, Kirsten Hertveldt, Guido Volckaert, Rob Lavigne BMC Biochemistry 2009, 10:20 (24 June 2009)
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Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity
Po-Wen Chang, Amrita Madabushi, A-Lien Lu BMC Biochemistry 2009, 10:19 (12 June 2009)
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Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol
Thirunavukkarasu Annamalai, Neil Dani, Bokun Cheng, Yuk-Ching Tse-Dinh BMC Biochemistry 2009, 10:18 (11 June 2009)
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DNA binding kinetics of two response regulators, PlnC and PlnD, from the bacteriocin regulon of Lactobacillus plantarum C11
Daniel Straume, Rune F Johansen, Magnar Bjørås, Ingolf F Nes, Dzung B Diep BMC Biochemistry 2009, 10:17 (11 June 2009)
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Two response regulators of antibacterial peptide production in Lactobacillus plantarum are highly homologous, co-expressed, and bind to the same promoters but differ in their binding affinity and cooperativity, explaining their opposite functions in gene regulation.
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TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation
Mara E Pitulescu, Martin Teichmann, Lingfei Luo, Michael Kessel BMC Biochemistry 2009, 10:16 (10 June 2009)
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A novel transcriptional regulator, isoform 2 of the TATA-binding protein-like factor-interacting protein (TIPT2), binds to the cell cycle regulatory protein geminin, and together they cooperate with chromatin associated factors and the basal transcription machinery to activate transcription synergistically.
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A novel human NatA Nα-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1)
Thomas Arnesen, Darina Gromyko, Diane Kagabo, Matthew J Betts, Kristian K Starheim, Jan Varhaug, Dave Anderson, Johan R Lillehaug BMC Biochemistry 2009, 10:15 (29 May 2009)
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The endocannabinoid anandamide is a precursor for the signaling lipid N-arachidonoyl glycine by two distinct pathways
Heather B Bradshaw, Neta Rimmerman, Sherry Hu, Valery M Benton, Jordyn M Stuart, Kim Masuda, Benjamin F Cravatt, David K O'Dell, J Michael Walker BMC Biochemistry 2009, 10:14 (21 May 2009)
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Editor’s summary
The lipid signaling molecule N-arachidonyl glycine (NAGly) is produced from the endogenous cannabinoid anandamide (AEA) by two pathways - oxidative metabolism of AEA's ethanolamine moiety, and glycine conjugation to arachidonic acid released during AEA hydrolysis by fatty acid amide hydrolase.
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Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI)
Zuzana Valnickova, Morten Thaysen-Andersen, Peter Højrup, Trine Christensen, Kristian W Sanggaard, Torsten Kristensen, Jan J Enghild BMC Biochemistry 2009, 10:13 (5 May 2009)
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Exploring the functional interaction between POSH and ALIX and the relevance to HIV-1 release
Jörg Votteler, Elena Iavnilovitch, Orit Fingrut, Vivian Shemesh, Daniel Taglicht, Omri Erez, Stefan Sörgel, Torsten Walther, Norbert Bannert, Ulrich Schubert, Yuval Reiss BMC Biochemistry 2009, 10:12 (24 April 2009)
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Both Ca2+ and Zn2+ are essential for S100A12 protein oligomerization and function
Olga V Moroz, Will Burkitt, Helmut Wittkowski, Wei He, Anatoli Ianoul, Vera Novitskaya, Jingjing Xie, Oxana Polyakova, Igor K Lednev, Alexander Shekhtman, Peter J Derrick, Per Bjoerk, Dirk Foell, Igor B Bronstein BMC Biochemistry 2009, 10:11 (23 April 2009)
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Identification of distinct SET/TAF-Iβ domains required for core histone binding and quantitative characterisation of the interaction
Zoe Karetsou, Anastasia Emmanouilidou, Ioannis Sanidas, Stamatis Liokatis, Eleni Nikolakaki, Anastasia S Politou, Thomais Papamarcaki BMC Biochemistry 2009, 10:10 (9 April 2009)
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alpha-Sarcin catalytic activity is not required for cytotoxicity
Spencer C Alford, Joel D Pearson, Amanda Carette, Robert J Ingham, Perry L Howard BMC Biochemistry 2009, 10:9 (3 April 2009)
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Characterisation of the paralytic shellfish toxin biosynthesis gene clusters in Anabaena circinalis AWQC131C and Aphanizomenon sp. NH-5
Troco K Mihali, Ralf Kellmann, Brett A Neilan BMC Biochemistry 2009, 10:8 (30 March 2009)
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The roles of aldehyde dehydrogenases (ALDHs) in the PDH bypass of Arabidopsis
Yanling Wei, Ming Lin, David J Oliver, Patrick S Schnable BMC Biochemistry 2009, 10:7 (25 March 2009)
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A novel method for screening the glutathione transferase inhibitors
Zhijun Wang, Li Jin, Grzegorz Węgrzyn, Alicja Węgrzyn BMC Biochemistry 2009, 10:6 (16 March 2009)
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Transmembrane voltage regulates binding of annexin V and lactadherin to cells with exposed phosphatidylserine
Christina Smith, Donald F Gibson, Jonathan F Tait BMC Biochemistry 2009, 10:5 (17 February 2009)
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Dictyostelium cells bind a secreted autocrine factor that represses cell proliferation
Jonathan M Choe, Deenadayalan Bakthavatsalam, Jonathan E Phillips, Richard H Gomer BMC Biochemistry 2009, 10:4 (2 February 2009)
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Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein
Gustavo P Riboldi, Hugo Verli, Jeverson Frazzon BMC Biochemistry 2009, 10:3 (2 February 2009)
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Human Rad51 mediated DNA unwinding is facilitated by conditions that favour Rad51-dsDNA aggregation
Kamakshi Balakrishnan, Neeraja M Krishnan, Anagha Kulkarni, Basuthkar J Rao BMC Biochemistry 2009, 10:2 (9 January 2009)
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Editor’s summary
The unwinding of double-stranded DNA in humans as mediated by hRad51, the RecA homolog, is stimulated by the protein hRad52, which possibly acts as a scaffold to bring DNA and hRad51 together.
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Redox biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide
Saurabh Garg, Md Suhail Alam, Richa Bajpai, KV Radha Kishan, Pushpa Agrawal BMC Biochemistry 2009, 10:1 (5 January 2009)
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Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF
Catherine Paradis-Bleau, Adrian Lloyd, François Sanschagrin, Tom Clarke, Ann Blewett, Timothy DH Bugg, Roger C Levesque BMC Biochemistry 2008, 9:33 (19 December 2008)
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Modification of carbonic anhydrase II with acetaldehyde, the first metabolite of ethanol, leads to decreased enzyme activity
Fatemeh Bootorabi, Janne Jänis, Jarkko Valjakka, Sari Isoniemi, Pirjo Vainiotalo, Daniela Vullo, Claudiu T Supuran, Abdul Waheed, William S Sly, Onni Niemelä, Seppo Parkkila BMC Biochemistry 2008, 9:32 (27 November 2008)
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Editor’s summary
Acetaldehyde, a metabolite of ethanol, forms a Schiff base with one of the amino groups of carbonic anhydrase II, and its inhibition of this enzyme by covalent modification may help explain the toxicity of ethanol in human tissues.
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Lipid bilayer composition influences small multidrug transporters
Kalypso Charalambous, David Miller, Paul Curnow, Paula J Booth BMC Biochemistry 2008, 9:31 (25 November 2008)
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The activity of two bacterial multidrug transporters increases in membrane bilayers containing phosphatidylethanolamine, with EmrE from Escherichia coli and TBsmr from Mycobacterium tuberculosis also becoming more active in the presence of phosphatidylglycerol and phosphatidylinositol, respectively.
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An earthworm protease cleaving serum fibronectin and decreasing HBeAg in HepG2.2.15 cells
Xue-Qing Wang, Lan Chen, Rong Pan, Jing Zhao, Ying Liu, Rong-Qiao He BMC Biochemistry 2008, 9:30 (24 November 2008)
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The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71
Claudia Ester, Peter Uetz BMC Biochemistry 2008, 9:29 (11 November 2008)
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