Research Area E - Publications 2013

2013, published on 20.12.2013

 

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Wir wünschen allen ein frohes und gesegnetes Weihnachtsfest, und einen guten Start in das neue Jahr!  

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mAbs, 2013, DOI:10.4161/mabs.27444, Volume 6, Issue 2, published on 09.12.2013
mAbs, online article
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We report on the preparation of a new type of immunotoxin via in vitro ligation of the αHer2 antigen binding fragment (Fab) of the clinically-validated antibody trastuzumab to the plant toxin gelonin, employing catalysis by the bacterial enzyme sortase A (SrtA). The αHer2 Fab was fused with the extended SrtA recognition motif LPET↓GLEH6 at the C-terminus of its ...

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Biochemistry, 2013, DOI: 10.1021/bi4014402, 52 (50), pp 8972–8974 published on 02.12.2013

Biochemistry, online article

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Incorporation of the azobenzene derivative gluazo, a synthetic photochromic ligand, into a kainate receptor allows for the optical control of neuronal activity. The crystal structure of gluazo bound to a dimeric GluK2 ligand-binding domain reveals one monomer in a closed conformation, occupied by gluazo, and the other in an open conformation, with a bound buffer ...

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Chem. Sci., 2013, DOI: 10.1039/C3SC52228H, 5, 1158-1167 published on 21.11.2013
Chem. Sci., online article
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Bacterial pathogenesis is triggered by complex molecular mechanisms that sense bacterial density within an infected host and induce the expression of toxins for overriding the immune response. Virulence is controlled by a set of transcriptional regulators that directly bind to DNA promoter regions of toxin-encoding genes. Here, we identified an ...

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ChemBioChem, 2013, DOI: 10.1002/cbic.201300435, Volume 14, Issue 16, pages 2114–2118 published on 04.11.2013

ChemBioChem, online article

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Three for two: By using a Methanosarcina mazei PylRS triple mutant (Y306G, Y384F, I405R) the incorporation of two new exo-norbornene-containing pyrrolysine analogues was achieved. X-ray crystallographic analysis led to the identification of the crucial structural elements involved in substrate recognition by the evolved synthetase.

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Chem. Commun., 2013, DOI: 10.1039/C3CC46002A, 50, 427-429 published on 30.10.2013
Chem. Commun., online article

β-Sultams are potent electrophiles that modify nucleophilic residues in selected enzyme active sites. We here identify and characterize some of the specific bacterial targets and show a unique inhibition of the azoreductase family.

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ChemBioChem, 2013, DOI: 10.1002/cbic.201300551, Volume 14, Issue 18, pages 2447–2455 published on 25.10.2013

ChemBioChem, online article

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Copper-catalysed alkyne–azide 1,3-dipolar cycloaddition (CuAAC) is the predominantly used bioconjugation method in the field of activity-based protein profiling (ABPP). Several limitations, however, including conversion efficiency, protein denaturation and buffer compatibility, restrict the scope of established procedures. We introduce an ABPP customised click ...

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JACS, 2013, DOI: 10.1021/ja4082793, published on 09.10.2013

JACS.,online article

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Over 100 protease inhibitors are currently used in the clinics, and most of them use blockage of the active site for their mode of inhibition. Among the protease drug targets are several enzymes for which the correct multimeric assembly is crucial to their activity, such as the proteasome and the HIV protease. Here, we present a novel mechanism of protease ...

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Molecular & Cellular Proteomics, 2013, doi: 10.1074/mcp.M113.027599, 12, 2901-2910. published on 01.10.2013

Molecular & Cellular Proteomics, online article

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Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this ...

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Chemistry, 2013, DOI: 10.1002/chem.201301838, Volume 19, Issue 40, pages 13309–13312 published on 27.09.2013

Chemistry, online article

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Significant differences in the reactivity of norbornene derivatives in the inverse electron-demand Diels–Alder reaction with tetrazines were revealed by kinetic studies. Substantial rate enhancement for the exo norbornene isomers was observed (see scheme). Quantum-chemical calculations were used to rationalize and support the observed experimental data.

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(pdf) published on 11.04.2013
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The Scientific Oktoberfest will be this years meeting point for some of the internationally most distinguished researchers in the field of Chemistry & Chemical Biology. The CIPSM Scientific Oktoberfest will be held from the 19th to the 20th of September in the Department of Chemistry of the Ludwig-Maximilians-Universität (LMU) München. At the two-day conference, ...

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published on 24.07.2013
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On July 18th CIPSM researchers took part in the 2013 Munich B2run project. We thank them for participating so neonish!  

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ChemMedChem, 2013, DOI: 10.1002/cmdc.201300323, Volume 8, Issue 12, pages 1954–1962 published on 17.09.2013
ChemMedChem, online aticle
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Three analogues of amythiamicin D, which differ in the substitution pattern at the methine group adjacent to C2 of the thiazole ring C, were prepared by de novo total synthesis. In amythiamicin D, this carbon atom is (S)-isopropyl substituted. Two of the new analogues carry a hydroxymethyl in place of the isopropyl group, one at an S- (compound 3 a) and the other ...

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JACS, 2013, DOI: 10.1021/ja403229y, 135 (39), pp 14593–14599 published on 27.08.2013

JACS, online article

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Three new cytosine derived DNA modifications, 5-hydroxymethyl-2′-deoxycytidine (hmdC), 5-formyl-2′-deoxycytidine (fdC) and 5-carboxy-2′-deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation ...

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Nature Methods, 2013, doi:10.1038/nmeth.2610, 10, 989–991 published on 25.08.2013

Nature Methods, online article

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We report that low percentages of dimethylsulfoxide (DMSO) in liquid chromatography solvents lead to a strong enhancement of electrospray ionization of peptides, improving the sensitivity of protein identification in bottom-up proteomics by up to tenfold. The method can be easily implemented on any LC-MS/MS system without modification to hardware or software and ...

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PLOS ONE, 2013, DOI: 10.1371/journal.pone.0072307, Volume 8, Issue 8, e72307 published on 22.08.2013
PLOS ONE, online article
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Rhomboids are intramembrane serine proteases that play diverse biological roles, including some that are of potential therapeutical relevance. Up to date, rhomboid inhibitor assays are based on protein substrate cleavage. Although rhomboids have an overlapping substrate specificity, substrates cannot be used universally. To overcome the need for substrates, we ...

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Cell Reports, 2013, doi:10.1016/j.celrep.2013.07.018, Volume 4, Issue 3, 609-620 published on 08.08.2013

Cell Reports, online article

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The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 ...

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PROTEOMICS, 2013, DOI: 10.1002/pmic.201300076, Volume 13, Issue 17, pages 2552–2562 published on 30.07.2013

PROTEOMICS, online article

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The field of proteomics continues to be driven by improvements in analytical technology, notably in peptide separation, quantitative MS, and informatics. In this study, we have characterized a hybrid linear ion trap high field Orbitrap mass spectrometer (Orbitrap Elite) for proteomic applications. The very high resolution available on this instrument allows 95% ...

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PNAS, 2013, doi: 10.1073/pnas.1219125110, vol. 110 no. 28 11302-11307 published on 09.07.2013

PNAS, online article

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Caseinolytic proteases (ClpPs) are large oligomeric protein complexes that contribute to cell homeostasis as well as virulence regulation in bacteria. Although most organisms possess a single ClpP protein, some organisms encode two or more ClpP isoforms. Here, we elucidated the crystal structures of ClpP1 and ClpP2 from pathogenic Listeria monocytogenes and ...

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Biotechnology and Bioengineering, 2013, DOI: 10.1002/bit.24956, Volume 110, Issue 11, pages 2803–2814 published on 01.07.2013

Biotechnology and Bioengineering, online article

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The NADP+-dependent alcohol dehydrogenase from Ralstonia sp. (RasADH) belongs to the protein superfamily of short-chain dehydrogenases/reductases (SDRs). As an enzyme that accepts different types of substrates—including bulky–bulky as well as small–bulky secondary alcohols or ketones—with high stereoselectivity, it offers potential as a biocatalyst for industrial ...

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Angewandte Chemie, 2013, DOI: 10.1002/anie.201208941, Volume 52, Issue 27, pages 6921–6925 published on 01.07.2013

Angewandte Chemie, online article

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Duocarmycin-derived seco-cyclopropabenzindole (CBI) drugs have been shown to bind DNA and an aldehyde dehydrogenase (ALDH1A1) in lung cancer cells. The removal of the DNA-binding indole moiety results in a CBI compound that does not bind to DNA in whole cells but still exhibits remarkable cytotoxicity. This CBI compound has an increased affinity for ALDH1A1. ...

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Angewandte Chemie, 2013, DOI: 10.1002/anie.201208941, Volume 52, Issue 27, pages 6921–6925 published on 01.07.2013

Angewandte Chemie, online article

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Duocarmycin-derived seco-cyclopropabenzindole (CBI) drugs have been shown to bind DNA and an aldehyde dehydrogenase (ALDH1A1) in lung cancer cells. The removal of the DNA-binding indole moiety results in a CBI compound that does not bind to DNA in whole cells but still exhibits remarkable cytotoxicity. This CBI compound has an increased affinity for ALDH1A1. ...

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Nature, 2013, (pdf) published on 27.06.2013

Nature, online article

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We are happy that Nature notes: „One goal of the Excellence Initiative is to create research clusters that integrate university laboratories more closely with local non-university institutes such as Max Planck and Helmholtz centres. The clusters are also intended to form a conduit between academia and business, a sector which funds and conducts two-thirds of ...

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J. Proteome Res., 2013, DOI: 10.1021/pr400455j, 12 (8), pp 3792–3800 published on 25.06.2013

J. Proteome Res., online article

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Protein kinases are key regulators of cellular processes, and aberrant function is often associated with human disease. Consequently, kinases represent an important class of therapeutic targets and about 20 kinase inhibitors (KIs) are in clinical use today. Detailed knowledge about the selectivity of KIs is important for the correct interpretation of their ...

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J. Proteome Res., 2013, DOI: 10.1021/pr400098r, 12 (8), pp 3586–3598 published on 17.06.2013

J. Proteome Res., online article

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Isobaric mass tagging (e.g., TMT and iTRAQ) is a precise and sensitive multiplexed peptide/protein quantification technique in mass spectrometry. However, accurate quantification of complex proteomic samples is impaired by cofragmentation of peptides, leading to systematic underestimation of quantitative ratios. Label-free quantification strategies do not suffer ...

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Protein Engineering, Design and Selection, 2013, doi: 10.1093/protein/gzt023, 26 (8): 489-501 published on 10.06.2013

Protein Engineering,Design and Selection, online article

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A major limitation of biopharmaceutical proteins is their fast clearance from circulation via kidney filtration, which strongly hampers efficacy both in animal studies and in human therapy. We have developed conformationally disordered polypeptide chains with expanded hydrodynamic volume comprising the small residues Pro, Ala and Ser (PAS). PAS sequences are ...

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European Journal of Organic Chemistry, 2013, DOI: 10.1002/ejoc.201300586, Volume 2013, Issue 21, pages 4483–4485 published on 07.06.2013

European Journal of Organic Chemistry, online article

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Queuosine is one of the most strongly modified nucleosides found in transferRNA (tRNA) of almost all species. Queuosine is found exclusively in the wooble position of the anticodon loop of several tRNA, where it is involved in tRNAAsp, tRNAAsn tRNAHis, and tRNATyr. The biosynthesis of queuosine is performed by prokaryotes, and eukaryotes are fully dependent on ...

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Nature Chemical Biology, 2013, doi:10.1038/nchembio.1254, published on 19.05.2013

Nature Chemical Biology, online article

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8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1′ glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming ...

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Nature Biotechnology, 2013, doi:10.1038/nbt.2585, 31, 557–564 published on 19.05.2013

Nature Biotechnology, online article

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We present a peptide library and data resource of >100,000 synthetic, unmodified peptides and their phosphorylated counterparts with known sequences and phosphorylation sites. Analysis of the library by mass spectrometry yielded a data set that we used to evaluate the merits of different search engines (Mascot and Andromeda) and fragmentation methods (beam-type ...

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J. Proteome Res., 2013, DOI: 10.1021/pr400215r, 12 (6), pp 2386–2398 published on 30.04.2013

J. Proteome Res., online article

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Protein sequence databases are indispensable tools for life science research including mass spectrometry (MS)-based proteomics. In current database construction processes, sequence similarity clustering is used to reduce redundancies in the source data. Albeit powerful, it ignores the peptide-centric nature of proteomic data and the fact that MS is able to ...

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Chem. Commun., 2013, DOI: 10.1039/C3CC42076K, published on 24.04.2013

Chem. Commun., online article

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Trifunctional biotin reagents incorporating cleavable linkers are evaluated for their usage in protein enrichment. A linker based on the Dde protecting group leads to efficient release of protein targets under mild conditions. It additionally contains a masked trypsin cleavage site, which eliminates the majority of the tag during tryptic digestion.

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JBC, 2013, doi: 10.1074/jbc.M113.453852 jbc.M113.453852., published on 15.04.2013

JBC, online article

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The last step in the biosynthetic pathway of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) is catalyzed by Fragaria x ananassa enone oxidoreductase (FaEO), earlier putatively assigned as quinone oxidoreductase (FaQR). The ripening-induced enzyme catalyzes the reduction of the exocyclic double bond of the highly reactive precursor ...

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PROTEOMICS - Clinical Applications, 2013, DOI: 10.1002/prca.201200046, Volume 7, Issue 3-4, pages 225–233, published on 15.04.2013

PROTEOMICS Clinical Applications, online article

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Archival formalin-fixed and paraffin-embedded clinical samples represent a very diverse source of material for proteomic investigation of diseases, often with follow-up patient information. Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of ...

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J. Proteome Res., 2013, DOI: 10.1021/pr301073j, 12 (4), pp 1723–1731 published on 15.03.2013

J. Proteome Res., online article

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Kinases are involved in the regulation of many cellular processes and aberrant kinase signaling has been implicated in human disease. As a consequence, kinases are attractive drug targets. Assessing kinase function and drug selectivity in a more physiological context is challenging and often hampered by the generally low expression level of kinases and the ...

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Angewandte Chemie, 2013, DOI: 10.1002/ange.201204690, Volume 125, Issue 10, pages 3083–3088 published on 04.03.2013

Angewandte Chemie, online article

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Maintaining homeostasis at the protein level is an important prerequisite for cellular viability for which prokaryotes exhibit several proteolytic machineries, including ClpXP. In 2008, we reported the first small-molecule inhibitor for the proteolytic subunit ClpP and demonstrated that the inhibition of the enzyme in living bacteria significantly attenuates ...

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Journal of Molecular Biology, 2013, http://dx.doi.org/10.1016/j.jmb.2012.12.004, Volume 425, Issue 4, Pages 780–802 published on 22.02.2013

Journal of Molecular Biology, online article

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The oncofetal isoform of the extracellular matrix protein fibronectin (Fn), which carries the extra-domain B (ED-B) and is exclusively expressed in neovasculature, has gained interest for tumor diagnosis and therapy using engineered antibody fragments. We have employed the human lipocalin 2 (Lcn2) as a small and robust non-immunoglobulin scaffold to select ...

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Cell, 2013, http://dx.doi.org/10.1016/j.cell.2013.02.004, Volume 152, Issue 5, 1146-1159, published on 21.02.2013

Cell, online article

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Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and ...

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Chemistry, 2013, DOI: 10.1002/chem.201204209, Volume 19, Issue 13, pages 4244–4248, published on 18.02.2013

Chemistry, online article

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We report an efficient synthesis of the hypermodified natural tRNA modifications wybutosine (yW) and hydroxywybutosine (OHyW). We also describe the preparation of isotopically labeled analogues for precise quantification of yW and OHyW in different tissues including plant materials. The synthesis involved the formation of the unusual tricyclic ring structure of ...

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Chemical Biology, 2013, http://dx.doi.org/10.1016/j.cbpa.2012.11.024, Volume 17, Issue 1, Pages 102–109 published on 15.02.2013

Chemical Biology, online article

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Covalent chemical probes enable investigation of a desired fraction of the proteome. It is possible to adjust the selectivity of these probes, so they either react with a certain amino acid in all proteins, a class of proteins or only a single protein species. A combination of specific reactive groups with additional recognition elements can fine tune probes to ...

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Journal of Molecular Biology, 2013, http://dx.doi.org/10.1016/j.jmb.2012.11.030, Volume 425, Issue 3, Pages 466–474 published on 08.02.2013

Journal of Molecular Biology, online article

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Hsp70s are molecular chaperones involved in the folding and assembly of proteins. They recognize hydrophobic amino acid stretches in their substrate binding groove. However, a detailed understanding of substrate specificity is still missing. Here, we use the endoplasmic reticulum-resident Hsp70 BiP to identify binding sites in a natural client protein. Two sites ...

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PNAS, 2013, doi: 10.1073/pnas.1215076110, vol. 110 no. 7 2472-2477, published on 28.01.2013

PNAS, online article

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Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. Here, we describe a mass spectrometry-based assay to measure rhomboid substrate cleavage and inhibition. We have ...

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Proteins, 2013, DOI: 10.1002/prot.24233, Volume 81, Issue 5, pages 774–787 published on 15.01.2013

Proteins, online ablage

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Apart from their crucial role in metabolism, pyridoxal 5′-phosphate (PLP)-dependent aminotransferases (ATs) constitute a class of enzymes with increasing application in industrial biotechnology. To provide better insight into the structure-function relationships of ATs with biotechnological potential we performed a fundamental bioinformatics analysis of 330 ...

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J. Proteome Res., 2013, DOI: 10.1021/pr300967y, 12 (2), pp 927–936 published on 09.01.2013

J. Proteome Res., online article

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The post-translational modification of proteins with N-acetylglucosamine (O-GlcNAc) is involved in the regulation of a wide variety of cellular processes and associated with a number of chronic diseases. Despite its emerging biological significance, the systematic identification of O-GlcNAc proteins is still challenging. In the present study, we demonstrate a ...

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Org. Lett., 2013, DOI: 10.1021/ol3033219, 15 (2), pp 366–369 published on 03.01.2013

Org.Lett., online article

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The synthesis of the triphosphates of 5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine and the incorporation of these building blocks into long DNA fragments using the polymerase chain reaction (PCR) are reported. In this way DNA fragments containing multiple hmC, fC, and caC nucleobases are readily accessible.

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European Journal of Organic Chemistry, 2013, DOI: 10.1002/ejoc.201201256, Volume 2013, Issue 1, pages 77–83, published on 01.01.2013

European Journal of Organic Chemistry, online article

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The total syntheses of the natural product 3-O-methylfunicone (1), a member of the funicone class of compounds, and its derivatives is reported. The key reactions in the construction of the biaryl ketone core are a regioselective TMPZnCl·LiCl halogenation and a carbonylative Stille cross-coupling reaction. In addition, the inhibitory activities of the funicones ...

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Chem. Commun., 2013, DOI: 10.1039/C2CC37836A, 49, 379-381, published on 01.01.2013

Chem. Commun., online article

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Recently new lysine modifications were detected in histones and other proteins. Using the pyrrolysine amber suppression system we genetically inserted three of the new amino acids ε-N-propionyl-, ε-N-butyryl-, and ε-N-crotonyl-lysine site specifically into histone H3. The lysine at position 9 (H3 K9), which is known to be highly modified in chromatin, was ...

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