Katja Schmitz

Technische Universität Darmstadt | TU · Clemens Schöpf-Institute of Chemistry and Biochemistry

Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its ac...

Receptor‐derived peptides have played an important role in elucidating chemokine‐receptor interactions. For the inflammatory chemokine CXCL8, a site II‐mimetic peptide has been derived from parts of extracellular loops 2 and 3 and adjacent transmembrane helices of its receptor CXCR1 (Helmer et al., RSC Adv., 2015, 5, 25657). The peptide sequence wi...

To prevent surgical site infections, antibiotics can be released from carriers made of biomaterials, such as collagen, that support the healing process and are slowly degraded in the body. In our labs we have developed collagen laminates that can be easily assembled and bonded on-site, according to medical needs. As shown previously, the asymmetric...

The controlled release of antibiotics prevents the spread of pathogens and thereby improves healing processes in regenerative medicine. However, high concentrations may interfere with healing processes. It is therefore advantageous to use biodegradable materials for a controlled release. In particular, multilayer materials enable differential relea...

Collagen is one of the most important biomaterials for tissue engineering approaches. Despite its excellent biocompatibility, it shows the non-negligible disadvantage of poor mechanical stability. Photochemical crosslinking with rose bengal and green light (RGX) is an appropriate method to improve this property. The development of collagen laminate...

Chemokines play an important role in various diseases as signaling molecules for immune cells. Therefore, the inhibition of the chemokine-receptor interaction and the characterization of potential inhibitors are important steps in the development of new therapies. Here, we present a new cell-based assay for chemokine-receptor interaction, using che...

The release of inflammatory chemokines leads to the formation of chemokine gradients that result in the directed migration of immune cells to the site of injury. In this process, cells respond to soluble gradients (chemotaxis) as well as to immobilised gradients (haptotaxis). Surface-bound chemokine gradients are mostly presented by endothelial cel...

For medical application, easily accessible biomaterials with tailored properties are desirable. Collagen type I represents a biomaterial of choice for regenerative medicine and tissue engineering. Here, we present a simple method to modify the properties of collagen and to generate collagen laminates. We selected three commercially available collag...

To prevent infections local delivery of antibiotics is a useful tool. Especially in bone fractures, vancomycin impregnated bone cements are often used allowing high concentrations of antibiotics at the infection side without high serum concentrations. However, besides potential pathogens, cells involved in tissue regeneration may also be affected b...

The polypeptide chemokine Interleukin-8 (IL8) plays a crucial role in inflammatory processes in humans. IL8 is involved in chronic inflammatory lung diseases, rheumatoid arthritis, and cancer. Previous studies have shown that the interaction of IL8 with its natural receptors CXCR1 and CXCR2 is critical in these diseases. Antibodies have been used t...

The ubiquitin‐proteasome system (UPS) is an established therapeutic target for approved drugs to treat selected hematologic malignancies. While drug discovery targeting the UPS focuses on irreversibly binding epoxyketones and slowly‐reversibly binding boronates, optimization of novel covalent‐reversibly binding warheads remains largely unattended....

div>Spectroscopic evidence is presented to show that NADH in aqueous solution does not exist as a folded/unfolded equilibrium but as a single state. The molecule is folded but without base stacking between dihydronicotinamide and adenine. </div

The use of covalent irreversible binding inhibitors is an established concept for drug development. Usually the discovery of new irreversible kinase inhibitors occurs serendipitously showing that efficient rational approaches for the rapid discovery of new drugs are needed. Herein, we report a virtual screening strategy that led to the discovery of...

Peptoids that bind to protein targets can be selected from one‐bead‐one‐compound libraries. Macrocyclization has been often used to increase conformational rigidity and binding affinity in both peptides and peptoids. Here we describe a combined strategy to label and cyclize hexameric peptoid sequences previously identified in a screen against the i...

Correction for ‘Rational design of a peptide capture agent for CXCL8 based on a model of the CXCL8:CXCR1 complex’ by Dorothea Helmer et al. , RSC Adv. , 2015, 5 , 25657–25668.

The Fusarium solani cutinase (FsC) is a promising candidate for the enzymatic degradation of the synthetic polyester polyethylene terephthalate (PET) but still suffers from a lack of activity. Using atomic MD simulations with different concentrations of cleavage product ethylene glycol (EG), we show influences of EG on the dynamic of FsC. We observ...

Protein-protein interactions are governed by relatively few amino acid residues at the binding interface. Peptides derived from these protein regions may serve as mimics of one of the interaction partners in structural studies or as inhibitors to disrupt the respective interaction and investigate its biological consequences. Inhibitory peptides may...

The split-synthesis approach offers a quick and easy method for producing a large diversity of substances for the discovery of novel protein ligands. Screening of the resulting one-bead-one-compound (OBOC) libraries with fluorescently labelled proteins is not trivial, however, since the resin beads can display significant autofluorescence. Here we...

The attachment of neutrophils to the endothelial surface and their migration towards the site of inflammation following chemokine gradients play an essential role in the innate immune response. Chemokines adhere to glycosaminoglycans on the endothelial surface to be detected by leukocytes and trigger their movement along surface- bound gradients in...

β-keto esters are used as precursors for the synthesis of β-amino acids, which are building blocks for some classes of pharmaceuticals. Here we describe the comparison of screening procedures for hydrolases to be used for the hydrolysis of β-keto esters, the first step in the preparation of β-amino acids. Two of the tested high throughput screening...

pNB-Est13 esterase compared by SDS-PAGE. Equal volumes with the same protein concentration were analyzed. The separation was carried in in a 12.5% SDS- polyacrylamide-gel at 200 V. Crude pNB-Est13 esterase was used after osmotic shock with TES-buffer and ddH2O. (TIF)

Contour plot to optimize the luminescence assay. The ethanol concentration (0 to 2.5 mM) was plotted against the HRP concentration (0 to 0.87 U/mL),AOX concentration (0 to 18.5 mU/mL)and luminol concentration (0 μM;37.5 μM;75 μM). Was scaled Contrasting the activity. A) luminescence slope per s: blue = high activity; red = low / no activity. (B) av...

Structural investigation of RML and CRL. a) Surface representation of CRL open (grey, 1CRL) and closed (blue, 1THG) state. Structural alignment of CRL open (grey, 1CRL) and closed (blue, 1THG). b) Surface representation of RML open (grey, 4TGL) and closed (blue, 3TGL) state. Structural alignment of RML open (grey, 4TGL) and closed (blue, 3TGL). c)...

Calibration of HTS-assays. The error bars show standard deviation. (a) Spectrometric ethanol assay (Pearson: 0.998, p-value = 1.64 ⋅ 10−8) (b) pH-indicator assay at 620 nm (Pearson: -0.999, p-value = 2.47 ⋅ 10−8). (c) Mean Luminescence ethanol assay (Pearson: 0.967, p-value = 8.15 ⋅ 103) a) and b) were measured in triplicate. The assays are describ...

First step optimization of the luminescence assay, by varying the concentration of luminol/ethanol (a) and luminol/hydrogen peroxide (b) against the average luminescence intensity over the time. The surface model plot was created by Modde 10.1. (TIF)

The complex activity of the transglutaminase factor XIII (FXIII) comprises central functions in secondary hemostasis. Congenital or acquired FXIII deficiencies may be associated with habitual abortions, impaired wound healing, coagulopathy and fatal hemorrhage. The present review describes physiological functions of FXIII, as well as pathophysiolog...

Molekulare Signale steuern, wohin die Zellen des Immunsystems wandern, wenn sie Pathogene und Entzündungen bekämpfen. Dabei beeinflussen Proteinmuster die patrouillierenden Zellen. Die Frage ist nur: Wie?

The migration of leukocytes in response to chemokine gradients is an important process in the homeostasis of the human immune system and inflammation. In vivo the migration takes place on the surface of the endothelium to which the chemokine gradient is immobilized via interaction with glycosaminoglycans. To study leukocyte migration in response to...

Protein-capture agents are widely used for the detection, immobilization and isolation of proteins and are the foundation for the development of in vitro diagnostic chips. The chemokine CXCL8 is an interesting protein target due to its involvement in the human inflammatory response. We constructed a novel structural model of CXCL8 interaction with...

Protein-protein interactions are governed by relatively few amino acid residues at the binding interface. Peptides derived from these protein regions may serve as mimics of one of the interaction partners in structural studies or as inhibitors to disrupt the respective interaction and investigate its biological consequences. Inhibitory peptides may...

Peptide based inhibitors of protein-protein interactions are of great interest in proteomics, structural biology and medicinal chemistry. Optimized inhibitors can be designed by experimental approaches or by computational prediction. Ideally, computational models are adjusted to the peptide-protein complex of interest according to experimental data...

The androgen receptor (AR) is a ligand-activated transcription factor that is essential for prostate cancer development. It is activated by androgens through its ligand-binding domain (LBD) that consists predominantly of 11 alpha helices. Upon ligand binding, the last helix is reorganized to an agonist conformation termed activator function-2 (AF-2...

Mimicking the in vivo microenvironment of cells is a challenging task in engineering in vitro cell models. Surface functionalization is one of the key components providing biochemical cues to regulate the interaction between cells and their substrate. In this study, two different approaches yield biofunctional surface patterns on thermoformed polym...

Garland Science (Taylor & Francis), 2012. 504 pp., softcover, £ 48.00.—ISBN 978‐0815342144

MEMS/MOEMS based systems are increasingly applied in the biological and biomedical context, e.g. in form of biosensors or substrates for monitoring biological responses such as cell migration. For such applications, technical surfaces have to be provided with suitable biochemical functionalization. Typical functionalization procedures include wet-c...

The molecular chaperone GRP78/BiP is a key regulator of protein folding in the endoplasmic reticulum, and it plays a pivotal role in cancer cell survival and chemoresistance. Inhibition of its function has therefore been an important strategy for inhibiting tumor cell growth in cancer therapy. Previous efforts to achieve this goal have used peptide...

The Bag-1 peptide does not impair ATPase activity of GRP78. In vitro ATPase activity assay of GRP78. A. ATPase activity was measured with the ATPase assay kit from Innova Bioscience (Cambridge, UK). The reaction mixture contained GRP78 (0.5 µg) increasing amounts of GST purified Bag-1 (continuous line) or Bag-1 peptide (dashed line) up to 1.5 µg. T...

The Bag-1 peptide induces GCN2 phosphorylation. 22Rv.1 cells stably expressing the empty vector control or the Bag-1 peptide were treated with thapsigargin (300 nM) for 16 h and subjected to Western blot analysis using anti-phospho-GCN2, GCN2 and HA-specific antibodies. The filters used in this experiment for the GCN2 signals are the same filters u...

Homology-basded structure prediction of the Bag-1 peptide. (DOCX)

Colocalization of Bag-1 with the endoplasmic reticulum. Immunofluorescence experiment was performed with 22Rv.1 cells fixed with 4% paraformaldehyde. After fixation, cells were permeabilized with a solution of PBS (phosphate buffer saline) containing 0.1% triton-X-100 and blocked with 4% goat serum in PBS. Endogenous Bag-1 (green channel) and the e...

ATF6 expression is upregulated by thapsigargin treatment. A. Real time PCR analysis of ATF6 gene expression following thapsigargin (300 nM) treatment for the indicated time points in 22Rv.1 cell clones with empty vector control (open bars) and peptide-expressing clones (filled bars). The RNA was extracted using PeqGold RNA pure (PeqLab, Germany) ki...

Overexpression of the Bag-1 peptide increases Capase-7 cleavage and JNK expression. 22Rv.1 cells stably transfected with an empty vector control (lane 1–2) or a plasmid encoding an HA-tagged Bag-1 peptide (lane 3–4) were treated with 300 nM thapsigargin (TG) for 24 h and harvested for Western blot anaysis. Specific antibodies against JNK (Cell Sign...

Knock-down of CHOP impairs the Bag-1 peptide-mediated increase in apoptosis. The action of the Bag-1 peptide is dependent on CHOP. Pooled clones of 22Rv.1 expressing an empty expression vector (lane 1 to 4) or an HA-tagged Bag-1 peptide (lane 5 to 8) were transfected with control GFP siRNA (lane 1–2 and 5–6) or CHOP siRNA (lane 3–4 and 7–8). After...

The N-terminal Bag-1 peptide interacts with GRP78(SBD). The N-terminal peptide binds to the SBD of GRP78. GST-pull down assay was performed using 100 µg of cell lysate from HEK 293 cells transfected with a plasmid expressing an HA-tagged N-ter-Bag-1 peptide together with 10 µg of the indicated GST-fused protein. After the pull-down experiment, West...

Protein patterns of different shapes and densities are useful tools for studies of cell behavior and to create biomaterials that induce specific cellular responses. Up to now the dominant techniques for creating protein patterns are mostly based on serial writing processes or require templates such as photomasks or elastomer stamps. Only a few of t...

Hormone-dependent aggregation of the androgen receptor (AR) with a polyglutamine (polyQ) stretch amplification (>38) is considered to be the causative agent of the neurodegenerative disorder spinal and bulbar muscular atrophy (SBMA), consistent with related neurodegenerative diseases involving polyQ-extended proteins. In spite of the widespread acc...

The screening of new medical drugs needs high throughput test systems to analyze binding interactions, e.g. between test substances and molecular targets occurring in the human body. So called small-molecule microarrays are a means for automatic compound screening and discovery. In comparison to other microarray techniques, small-molecule microarra...

As a response to environmental stress, bacterial cells can enter a physiological state called viable but noncultivable (VBNC). In this state, bacteria fail to grow on routine bacteriological media. Consequently, standard methods of contamination detection based on bacteria cultivation fail. Although they are not growing, the cells are still alive a...

Chemokines, a class of small secreted proteins, direct immune cells to their target sites and play an important role in chronic inflammations and allergies. To study their interactions with their cellular receptors or potential inhibitors large quantities of chemokines are required. Here we present a fast and efficient strategy to purify the human...

Preventing intramolecular cyclization greatly improves 5`-deoxy-5`-thioguanosine monophosphorothioate (GSMP) synthesis and its application as a potent initiator nucleotide for T7 run-off transcription of noncoding RNAs. GSMP was efficiently incorporated into the 5`-end of siRNA sense strands and the resulting thiol-modified siRNA was crosslinked wi...

Modulation of protein-protein interactions by competitive small-molecule binding emerges as a promising avenue for drug discovery. Hot spots, i.e., amino acids with important contributions to the overall interaction energy, provide useful targets within these interfaces. To avoid time-consuming mutagenesis experiments, computational alanine screeni...

Photodynamic therapy: The application of porphyrins in photodynamic therapy has been limited by their low solubility and cellular uptake efficiency. The introduction of a charged polyamine moiety to the lipophilic porphyrin ring can enhance the amphiphilicity of a compound of this class and ultimately lead to greater therapeutic efficacy.

Small-molecule microarrays have been used to discover biologically active small molecules in collections of synthetic compounds. Here we utilize a versatile isocyanate chemistry to immobilize extracts from microorganisms in a microarray format. Specific bioactive small molecules are detected in crude extracts of Streptomyces hygroscopicus, and the...

For many therapeutic applications, it has become more and more important to find synthetic compounds that have the ability to transport a variety of drugs and cargo molecules into cells and tissues. Like arginine-rich cell-penetrating peptides (CPPs), it is already known that peptide mimetics such as beta-peptides and peptoids can also express a tr...

RNA interference (RNAi) is an evolutionarily conserved phenomenon of double-stranded (ds)RNA-mediated mRNA degradation that leads to the posttranscriptional silencing of the corresponding gene. First reports on RNAi emerged in 1998, and since then, it has become one of the most fascinating fields of molecular biology. RNAi has provided important in...

Die Fehlregulation von Genen führt oft zu schweren Störungen in der Entwicklung von Organismen oder zu unkontrolliertem Zellwachstum, etwa bei Krebs. Daher wurden künstliche Transkriptionsfaktoren entwickelt, die die Expression der betroffenen Gene regulieren können, um die normale Zellregulation wieder herzustellen. Dervan et al. synthetisierten m...

For Abstract see ChemInform Abstract in Full Text.

Recently, double-stranded RNA (dsRNA)-mediated RNA interference (RNAi) has rapidly developed to a powerful instrument for specific silencing of gene expression in several organisms, including Caenorhabditis elegans, Drosophila melanogaster, and plants. The finding that synthetic small interfering RNAs (siRNAs) of 21 nt as well as stable, endogenous...

A common method used to investigate the function of glycoproteins and other glycosylated biological molecules is the knockout experiment. For this purpose, the phenotypes of cell and tissue cultures or organisms that lack specific proteins due to mutations or alterations are analyzed. In humans, inherited monogenetic diseases such as glycosphingoli...

The first stable phosphaarene pi-complex of copper displays unusual 31P NMR data that suggest a novel interpretation of 31P coordination shifts in pi-complexes of phosphorus containing multiple bonds.