@article{PengUteschYarmanetal.2015, author = {Peng, Lei and Utesch, Tillmann and Yarman, Aysu and Jeoung, Jae-Hun and Steinborn, Silke and Dobbek, Holger and Mroginski, Maria Andrea and Tanne, Johannes and Wollenberger, Ursula and Scheller, Frieder W.}, title = {Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein}, series = {Chemistry - a European journal}, volume = {21}, journal = {Chemistry - a European journal}, number = {20}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201405932}, pages = {7596 -- 7602}, year = {2015}, abstract = {Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant k(s) values between 0.93 and 2.86 s(-1) and apparent formal potentials E-app(0)' between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH.}, language = {en} } @misc{YokoyamaLeimkuehler2015, author = {Yokoyama, Kenichi and Leimk{\"u}hler, Silke}, title = {The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria}, series = {Biochimica et biophysica acta : Molecular cell research}, volume = {1853}, journal = {Biochimica et biophysica acta : Molecular cell research}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-4889}, doi = {10.1016/j.bbamcr.2014.09.021}, pages = {1335 -- 1349}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{KanzleiterJaehnertSchulzeetal.2015, author = {Kanzleiter, Timo and Jaehnert, Markus and Schulze, Gunnar and Selbig, Joachim and Hallahan, Nicole and Schwenk, Robert Wolfgang and Sch{\"u}rmann, Annette}, title = {Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice}, series = {American journal of physiology : Endocrinology and metabolism}, volume = {308}, journal = {American journal of physiology : Endocrinology and metabolism}, number = {10}, publisher = {American Chemical Society}, address = {Bethesda}, issn = {0193-1849}, doi = {10.1152/ajpendo.00289.2014}, pages = {E912 -- E920}, year = {2015}, abstract = {The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice (n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs (P < 0.05, meth diff >5\%, coverage > 10) in their putative promoter regions. Alignment with gene expression data (n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors (Plexin A2) as well as genes that participate in muscle hypertrophy (Igfbp4) and motor neuron innervation (Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training.}, language = {en} } @article{JetzschmannJagerszkiDechtriratetal.2015, author = {Jetzschmann, Katharina J. and Jagerszki, Gyula and Dechtrirat, Decha and Yarman, Aysu and Gajovic-Eichelmann, Nenad and Gilsing, Hans-Detlev and Schulz, Burkhard and Gyurcsanyi, Robert E. and Scheller, Frieder W.}, title = {Vectorially Imprinted Hybrid Nanofilm for Acetylcholinesterase Recognition}, series = {Advanced functional materials}, volume = {25}, journal = {Advanced functional materials}, number = {32}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1616-301X}, doi = {10.1002/adfm.201501900}, pages = {5178 -- 5183}, year = {2015}, abstract = {Effective recognition of enzymatically active tetrameric acetylcholinesterase (AChE) is accomplished by a hybrid nanofilm composed of a propidium-terminated self-assembled monolayer (Prop-SAM) which binds AChE via its peripheral anionic site (PAS) and an ultrathin electrosynthesized molecularly imprinted polymer (MIP) cover layer of a novel carboxylate-modified derivative of 3,4-propylenedioxythiophene. The rebinding of the AChE to the MIP/Prop-SAM nanofilm covered electrode is detected by measuring in situ the enzymatic activity. The oxidative current of the released thiocholine is dependent on the AChE concentration from approximate to 0.04 x 10(-6) to 0.4 x 10(-6)m. An imprinting factor of 9.9 is obtained for the hybrid MIP, which is among the best values reported for protein imprinting. The dissociation constant characterizing the strength of the MIP-AChE binding is 4.2 x 10(-7)m indicating the dominant role of the PAS-Prop-SAM interaction, while the benefit of the MIP nanofilm covering the Prop-SAM layer is the effective suppression of the cross-reactivity toward competing proteins as compared with the Prop-SAM. The threefold selectivity gain provided by i) the shape-specific MIP filter, ii) the propidium-SAM, iii) signal generation only by the AChE bound to the nanofilm shows promise for assessing AChE activity levels in cerebrospinal fluid.}, language = {en} } @misc{HartmannSchwanholdLeimkuehler2015, author = {Hartmann, Tobias and Schwanhold, Nadine and Leimk{\"u}hler, Silke}, title = {Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria}, series = {Biochimica et biophysica acta : Proteins and proteomics}, volume = {1854}, journal = {Biochimica et biophysica acta : Proteins and proteomics}, number = {9}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2014.12.006}, pages = {1090 -- 1100}, year = {2015}, abstract = {The global carbon cycle depends on the biological transformations of C-1 compounds, which include the reductive incorporation of CO2 into organic molecules (e.g. in photosynthesis and other autotrophic pathways), in addition to the production of CO2 from formate, a reaction that is catalyzed by formate dehydrogenases (FDHs). FDHs catalyze, in general, the oxidation of formate to CO2 and H+. However, selected enzymes were identified to act as CO2 reductases, which are able to reduce CO2 to formate under physiological conditions. This reaction is of interest for the generation of formate as a convenient storage form of H-2 for future applications. Cofactor-containing FDHs are found in anaerobic bacteria and archaea, in addition to facultative anaerobic or aerobic bacteria. These enzymes are highly diverse and employ different cofactors such as the molybdenum cofactor (Moco), FeS clusters and flavins, or cytochromes. Some enzymes include tungsten (W) in place of molybdenum (Mo) at the active site. For catalytic activity, a selenocysteine (SeCys) or cysteine (Cys) ligand at the Mo atom in the active site is essential for the reaction. This review will focus on the characterization of Mo- and W-containing FDHs from bacteria, their active site structure, subunit compositions and its proposed catalytic mechanism. We will give an overview on the different mechanisms of substrate conversion available so far, in addition to providing an outlook on bio-applications of FDHs. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{CornettiValenteDunningetal.2015, author = {Cornetti, Luca and Valente, Luis M. and Dunning, Luke T. and Quan, Xueping and Black, Richard A. and Hebert, Olivier and Savolainen, Vincent}, title = {The Genome of the "Great Speciator" Provides Insights into Bird Diversification}, series = {Genome biology and evolution}, volume = {7}, journal = {Genome biology and evolution}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1759-6653}, doi = {10.1093/gbe/evv168}, pages = {2680 -- 2691}, year = {2015}, abstract = {Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.}, language = {en} } @article{ZengLeimkuehlerKoetzetal.2015, author = {Zeng, Ting and Leimk{\"u}hler, Silke and Koetz, Joachim and Wollenberger, Ursula}, title = {Effective Electrochemistry of Human Sulfite Oxidase Immobilized on Quantum-Dots-Modified Indium Tin Oxide Electrode}, series = {ACS applied materials \& interfaces}, volume = {7}, journal = {ACS applied materials \& interfaces}, number = {38}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/acsami.5b06665}, pages = {21487 -- 21494}, year = {2015}, abstract = {The bioelectrocatalytic sulfite oxidation by human sulfite oxidase (hSO) on indium tin oxide (ITO) is reported, which is facilitated by functionalizing of the electrode surface with polyethylenimine (PEI)-entrapped CdS nanoparticles and enzyme. hSO was assembled onto the electrode with a high surface loading of electroactive enzyme. In the presence of sulfite but without additional mediators, a high bioelectrocatalytic current was generated. Reference experiments with only PEI showed direct electron transfer and catalytic activity of hSO, but these were less pronounced. The application of the polyelectrolyte-entrapped quantum dots (QDs) on ITO electrodes provides a compatible surface for enzyme binding with promotion of electron transfer. Variations of the buffer solution conditions, e.g., ionic strength, pH, viscosity, and the effect of oxygen, were studied in order to understand intramolecular and heterogeneous electron transfer from hSO to the electrode. The results are consistent with a model derived for the enzyme by using flash photolysis in solution and spectroelectrochemistry and molecular dynamic simulations of hSO on monolayer-modified gold electrodes. Moreover, for the first time a photoelectrochemical electrode involving immobilized hSO is demonstrated where photoexcitation of the CdS/hSO-modified electrode lead to an enhanced generation of bioelectrocatalytic currents upon sulfite addition. Oxidation starts already at the redox potential of the electron transfer domain of hSO and is greatly increased by application of a small overpotential to the CdS/hSO-modified ITO.}, language = {en} } @article{HahnEngelhardReschkeetal.2015, author = {Hahn, Aaron and Engelhard, Christopher and Reschke, Stefan and Teutloff, Christian and Bittl, Robert and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Structural Insights into the Incorporation of the Mo Cofactor into Sulfite Oxidase from Site-Directed Spin Labeling}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {54}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {40}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201504772}, pages = {11865 -- 11869}, year = {2015}, abstract = {Mononuclear molybdoenzymes catalyze a broad range of redox reactions and are highly conserved in all kingdoms of life. This study addresses the question of how the Mo cofactor (Moco) is incorporated into the apo form of human sulfite oxidase (hSO) by using site-directed spin labeling to determine intramolecular distances in the nanometer range. Comparative measurements of the holo and apo forms of hSO enabled the localization of the corresponding structural changes, which are localized to a short loop (residues 263-273) of the Moco-containing domain. A flap-like movement of the loop provides access to the Moco binding-pocket in the apo form of the protein and explains the earlier studies on the in vitro reconstitution of apo-hSO with Moco. Remarkably, the loop motif can be found in a variety of structurally similar molybdoenzymes among various organisms, thus suggesting a common mechanism of Moco incorporation.}, language = {en} } @article{RiedelsbergerDreyerGonzalez2015, author = {Riedelsberger, Janin and Dreyer, Ingo and Gonzalez, Wendy}, title = {Outward Rectification of Voltage-Gated K+ Channels Evolved at Least Twice in Life History}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {9}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0137600}, pages = {17}, year = {2015}, abstract = {Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories-hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom.}, language = {en} } @article{MazumderBrechunKimetal.2015, author = {Mazumder, Mostafizur and Brechun, Katherine E. and Kim, Yongjoo B. and Hoffmann, Stefan A. and Chen, Yih Yang and Keiski, Carrie-Lynn and Arndt, Katja Maren and McMillen, David R. and Woolley, G. Andrew}, title = {An Escherichia coli system for evolving improved light-controlled DNA-binding proteins}, series = {Protein engineering design \& selection}, volume = {28}, journal = {Protein engineering design \& selection}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzv033}, pages = {293 -- 302}, year = {2015}, abstract = {Light-switchable proteins offer numerous opportunities as tools for manipulating biological systems with exceptional degrees of spatiotemporal control. Most designed light-switchable proteins currently in use have not been optimised using the randomisation and selection/screening approaches that are widely used in other areas of protein engineering. Here we report an approach for screening light-switchable DNA-binding proteins that relies on light-dependent repression of the transcription of a fluorescent reporter. We demonstrate that the method can be used to recover a known light-switchable DNA-binding protein from a random library.}, language = {en} }