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Biomedical subjects

Stefan Becker

Publications and source records attributed to Stefan Becker.

34 records · Page 2Linked to original sources
PubMed2005

A generic system for the Escherichia coli cell-surface display of lipolytic enzymes.

EstA is an outer membrane-anchored esterase from Pseudomonas aeruginosa. An inactive EstA variant was used as an anchoring motif for the Escherichia coli cell-surface display of lipolytic enzymes. Flow cytometry analysis and measurement of lipase activity revealed that Bacillus subtilis lipase LipA, Fusarium solani pisi cutinase and one of the largest lipases presently known, namely Serratia marcescens lipase were all efficiently exported by the EstA autotransporter and also retained their lipolytic activities upon cell surface exposition. EstA provides a useful tool for surface display of lipases including variant libraries generated by directed evolution thereby enabling the identification of novel enzymes with interesting biological and biotechnological ramifications.

Amino Acid Sequence↗
PubMed2005

High-resolution solid-state NMR studies on uniformly [13C,15N]-labeled ubiquitin.

Understanding of the effects of intermolecular interactions, molecular dynamics, and sample preparation on high-resolution magic-angle spinning NMR data is currently limited. Using the example of a uniformly [13C,15N]-labeled sample of ubiquitin, we discuss solid-state NMR methods tailored to the construction of 3D molecular structure and study the influence of solid-phase protein preparation on solid-state NMR spectra. A comparative analysis of 13C', 13Calpha, and 13Cbeta resonance frequencies suggests that 13C chemical-shift variations are most likely to occur in protein regions that exhibit an enhanced degree of molecular mobility. Our results can be refined by additional solid-state NMR techniques and serve as a reference for ongoing efforts to characterize the structure and dynamics of (membrane) proteins, protein complexes, and other biomolecules by high-resolution solid-state NMR.

Carbon Isotopes↗
PubMed2005

3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity considerations.

Two types of 3D MAS NMR experiments are introduced, which combine standard (NC,CC) transfer schemes with (1H,1H) mixing to simultaneously detect connectivities and structural constraints of uniformly 15N,13C-labeled proteins with high spectral resolution. The homonuclear CCHHC and CCC experiments are recorded with one double-quantum evolution dimension in order to avoid a cubic diagonal in the spectrum. Depending on the second transfer step, spin systems or proton-proton contacts can be determined with reduced spectral overlap. The heteronuclear NHHCC experiment encodes NH-HC proton-proton interactions, which are indicative for the backbone conformation of the protein. The third dimension facilitates the identification of the amino acid spin system. Experimental results on U-[15N,13C]valine and U-[15N,13C]ubiquitin demonstrate their usefulness for resonance assignments and for the determination of structural constraints. Furthermore, we give a detailed analysis of alternative multidimensional sampling schemes and their effect on sensitivity and resolution.

Amino Acids↗
PubMed2005

A fusion protein system for the recombinant production of short disulfide bond rich cystine knot peptides using barnase as a purification handle.

The inhibitor cystine knot (ICK) structural motif has been found in several small proteins and peptides from plants, insects, marine molluscs, and also in human. It is defined by a triple beta-sheet that is held together by three intramolecular disulfide bonds built by six conserved cysteine residues that generate a highly rigid and stable fold. We describe a procedure for the production of ICK peptides with correct disulfide bond connectivities via expression in Escherichia coli as fusion proteins with an enzymatically inactive variant of the Bacillus amyloliquefaciens RNAse barnase. Barnase directs the fused peptide to the culture medium and the fusion protein can be isolated by combined cation exchange/reverse-phase chromatography. The ICK peptides are released from the barnase expression and purification handle either by cyanogen bromide or by protease cleavage to give pure and correctly folded cystine knot peptides.

Amino Acid Sequence↗
PubMed2005

Development and evaluation of a standard method for the quantitative determination of elements in float glass samples by LA-ICP-MS.

Forensic analysis of glass samples was performed in different laboratories within the NITE-CRIME (Natural Isotopes and Trace Elements in Criminalistics and Environmental Forensics) European Network, using a variety of Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) systems. The main objective of the interlaboratory tests was to cross-validate the different combinations of laser ablation systems with different ICP-MS instruments. A first study using widely available samples, such as the NIST SRM 610 and NIST SRM 612 reference glasses, led to deviations in the determined concentrations for trace elements amongst the laboratories up to 60%. Extensive discussion among the laboratories and the production of new glass reference standards (FGS 1 and FGS 2) established an improved analytical protocol, which was tested on a well-characterized float glass sample (FG 10-1 from the BKA Wiesbaden collection). Subsequently, interlaboratory tests produced improved results for nearly all elements with a deviation of < 10%, demonstrating that LA-ICP-MS can deliver absolute quantitative measurements on major, minor and trace elements in float glass samples for forensic and other purposes.

Journal Article↗
PubMed2004

A dynamic zinc redox switch.

The crystal structures of glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans, which catalyzes the formation of S-hydroxymethylglutathione from formaldehyde and glutathione, and its complex with glutathione (Gfa-GTT) have been determined. Gfa has a new fold with two zinc-sulfur centers, one that is structural (zinc tetracoordinated) and one catalytic (zinc apparently tricoordinated). In Gfa-GTT, the catalytic zinc is displaced due to disulfide bond formation of glutathione with one of the zinc-coordinating cysteines. Soaking crystals of Gfa-GTT with formaldehyde restores the holoenzyme. Accordingly, the displaced zinc forms a complex by scavenging formaldehyde and glutathione. The activation of formaldehyde and of glutathione in this zinc complex favors the final nucleophilic addition, followed by relocation of zinc in the catalytic site. Therefore, the structures of Gfa and Gfa-GTT draw the critical association between a dynamic zinc redox switch and a nucleophilic addition as a new facet of the redox activity of zinc-sulfur sites.

Carbon-Sulfur Ligases↗
PubMed2004

Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.

Enterococcus faecalis is one of the major causes for hospital-acquired antibiotic-resistant infections. It produces an exotoxin, called cytolysin, which is lethal for a wide range of Gram-positive bacteria and is toxic to higher organisms. Recently, the regulation of the cytolysin operon was connected to autoinduction by a quorum-sensing mechanism involving the CylR1/CylR2 two-component regulatory system. We report here the crystal structure of CylR2 and its properties in solution as determined by heteronuclear NMR spectroscopy. The structure reveals a rigid dimer containing a helix-turn-helix DNA-binding motif as part of a five-helix bundle that is extended by an antiparallel beta-sheet. We show that CylR2 is a DNA-binding protein that binds specifically to a 22 bp fragment of the cytolysin promoter region. NMR chemical shift perturbation experiments identify surfaces involved in DNA binding and are in agreement with a model for the CylR2/DNA complex that attributes binding specificity to a complex network of CylR2/DNA interactions. Our results propose a mechanism where repression is achieved by CylR2 obstruction of the promoter preventing biosynthesis of the cytolysin operon transcript.

Bacterial Proteins↗
PubMed2004

Structural basis for the inhibitory role of tomosyn in exocytosis.

Upon Ca2+ influx synaptic vesicles fuse with the plasma membrane and release their neurotransmitter cargo into the synaptic cleft. Key players during this process are the Q-SNAREs syntaxin 1a and SNAP-25 and the R-SNARE synaptobrevin 2. It is thought that these membrane proteins gradually assemble into a tight trans-SNARE complex between vesicular and plasma membrane, ultimately leading to membrane fusion. Tomosyn is a soluble protein of 130 kDa that contains a COOH-terminal R-SNARE motif but lacks a transmembrane anchor. Its R-SNARE motif forms a stable core SNARE complex with syntaxin 1a and SNAP-25. Here we present the crystal structure of this core tomosyn SNARE complex at 2.0-A resolution. It consists of a four-helical bundle very similar to that of the SNARE complex containing synaptobrevin. Most differences are found on the surface, where they prevented tight binding of complexin. Both complexes form with similar rates as assessed by CD spectroscopy. In addition, synaptobrevin cannot displace the tomosyn helix from the tight complex and vice versa, indicating that both SNARE complexes represent end products. Moreover, data bank searches revealed that the R-SNARE motif of tomosyn is highly conserved throughout all eukaryotic kingdoms. This suggests that the formation of a tight SNARE complex is important for the function of tomosyn.

Adaptor Proteins, Vesicular Transport↗
PubMed2004

Expression, purification, crystallization and preliminary crystallographic studies of the Enterococcus faecalis cytolysin repressor CylR2.

The expression of an exotoxin called cytolysin contributes to the virulence of Enterococcus faecalis, one of the organisms responsible for antibiotic resistant infections acquired in hospitals. The DNA-binding protein CylR2 is a transcriptional repressor of cytolysin. At a specific cell density, cytolysin triggers signaling events, which result in the dissociation of CylR2 from its DNA-binding site. CylR2 was overexpressed in Escherichia coli and purified and crystals diffracting to 1.9 A were obtained in two different crystal forms. One crystal form belongs to space group P4(1), with unit-cell parameters a = 63.7, b = 63.7, c = 41.2 A, alpha = beta = gamma = 90 degrees, and the other belongs to space group P1, with unit-cell parameters a = 36.9, b = 45.0, c = 47.7 A, alpha = 67, beta = 90, gamma = 66 degrees.

Bacterial Proteins↗
PubMed2004

Crystallization and preliminary crystallographic studies of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain.

Signal transducer and activator of transcription 6 (STAT6) regulates transcriptional activation in response to interleukin-4 (IL-4) by direct interaction with coactivators. Among them, NCoA-1, a member of the p160/steroid receptor coactivator (SRC) family, has been found to bind to STAT6 with the region B of its putative Per-Arnt-Sim (PAS) domain. STAT6 interacts specifically with NCoA-1 via an LXXLL motif in its transactivation domain. Crystals of the NCoA-1(257-385) domain in complex with the STAT6(794-814) LXXLL motif were obtained in two hexagonal space groups. The crystals in space group P6(1), with unit-cell parameters a = 61.7, b = 61.7, c = 146.5 A, alpha = beta = 90, gamma = 120 degrees, diffract to 2.8 A at a home source. Crystals belonging to space group P6(2), with unit-cell parameters a = 62.0, b = 62.0, c = 73.6 A, alpha = beta = 90, gamma = 120 degrees, diffract to 1.8 A at a synchrotron source.

Crystallization↗
PubMed2004

Structure of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain.

Signal transducer and activator of transcription 6 (STAT6) regulates transcriptional activation in response to interleukin-4 (IL-4) by direct interaction with coactivators. The CREB-binding protein (p300/CBP) and the nuclear coactivator 1 (NCoA-1), a member of the p160/steroid receptor coactivator family, bind independently to specific regions of the STAT6 transactivation domain and act as coactivators. The interaction between STAT6 and NCoA-1 is mediated by an LXXLL motif in the transactivation domain of STAT6. To define the mechanism of coactivator recognition, we determined the crystal structure of the NCoA-1 PAS-B domain in complex with the STAT6 LXXLL motif. The amphipathic, alpha-helical STAT6 LXXLL motif binds mostly through specific hydrophobic interactions to NCoA-1. A single amino acid of the NCoA-1 PAS-B domain establishes hydrophilic interactions with the STAT6 peptide. STAT6 interacts only with the PAS-B domain of NCoA-1 but not with the homologous regions of NCoA-2 and NCoA-3. The residues involved in binding the STAT6 peptide are strongly conserved between the different NCoA family members. Therefore surface complementarity between the hydrophobic faces of the STAT6 fragment and of the NCoA-1 PAS-B domain almost exclusively defines the binding specificity between the two proteins.

Amino Acid Motifs↗
PubMed2004

Ultra-high-throughput screening based on cell-surface display and fluorescence-activated cell sorting for the identification of novel biocatalysts.

Enzyme libraries displayed on the surface of microbial cells or microbeads can be screened with fluorogenic substrates that provide a physical linkage of the reaction product to the corresponding enzyme. Libraries exceeding 10(9) different variants can be quantitatively analysed and screened by flow cytometry at a rate of 30 000 cells/second. The promise of screening methods based on fluorescence-activated cell sorting for directed enzyme evolution is being realized and significantly improved enzymes have been reported recently.

Bacteria↗
PubMed2003

Attaching perylene dyes to polyfluorene: three simple, efficient methods for facile color tuning of light-emitting polymers.

The emission color of fluorene-based polymers can be facilely tuned across the whole visible spectrum by copolymerization with perylene dyes. Methods are demonstrated for incorporation of the dyes in the polymer mainchain, at the chain termini, or as side chains. Efficient energy transfer causes the emission to come solely from the dye units. Efficient LEDs have been made from the copolymers with dyes in the mainchain.

Journal Article↗
PubMed2002

Crystal structure of the endosomal SNARE complex reveals common structural principles of all SNAREs.

SNARE proteins are crucial for intracellular membrane fusion in all eukaryotes. These proteins assemble into tight complexes that connect membranes and may induce fusion. The crystal structure of the neuronal core complex is represented by an unusually long bundle of four alpha-helices connected by 16 layers of mostly hydrophobic amino acids. Here we report the 1.9 A resolution crystal structure of an endosomal SNARE core complex containing four SNAREs: syntaxin 7, syntaxin 8, vti1b and endobrevin/VAMP-8. Despite limited sequence homology, the helix alignment and the layer structure of the endosomal complex are remarkably similar to those of the neuronal complex. However, subtle variations are evident that characterize different SNARE subfamilies. We conclude that the structure of the SNARE core complex is an evolutionarily conserved hallmark of all SNARE complexes and is intimately associated with the general role of SNAREs in membrane fusion.

Amino Acid Sequence↗