Axel Scheidig - Academia.edu (original) (raw)

Papers by Axel Scheidig

Hepatology Communications

ABSTRACTWHIRLY1 in barley was shown to be a major architect of plastid nucleoids. Its accumulatio... more ABSTRACTWHIRLY1 in barley was shown to be a major architect of plastid nucleoids. Its accumulation in cells of E. coli coincided with an induction of nucleoid compaction and growth retardation. While WHIRLY1 of maize had similar effects on E. coli cells, WHIRLY1 proteins of Arabidopsis and potato a well as WHIRLY2 proteins had no impact on nucleoid compaction in E. coli. By mutagenesis of HvWHIRLY1 the PRAPP motif at the N-terminus preceding the highly conserved WHIRLY domain was identified to be responsible for the nucleoid compacting activity of HvWHIRLY1 in bacteria. This motif is found in WHIRLY1 proteins of most members of the Poaceae family, but neither in the WHIRLY2 proteins of the family nor in any WHIRLY protein of eudicot species such as Arabidopsis thaliana. This finding indicates that a subset of the monocot WHIRLY1 proteins has acquired a specific function as nucleoid compacters by sequence variation in the N-terminal part preceding the conserved WHIRLY domain and that...

Journal of Medicinal Chemistry, 2019

For the development of new drugs, the investigation of their metabolism is of central importance.... more For the development of new drugs, the investigation of their metabolism is of central importance. In the past, the focus was mostly on the consideration of established enzymes leading to oxidations such as cytochrome P450. However, reductive metabolism by the mARC enzyme system can play an important role in particular for nitrogen containing functional groups. A rapid test was established to give developers of new drugs in the preclinical stage the opportunity to test the metabolism by mARC. In order to demonstrate the relevance and validity of the new test system, known and potential substrates were applied to this new assay. All known substrates could be detected by the system. Furthermore, several new substrates were found including long-established drugs such as hydroxyurea and new compounds in development such as epacdadostat.

Marine Drugs, 2019

Formulas derived from theoretical physics provide important insights about the nematocyst dischar... more Formulas derived from theoretical physics provide important insights about the nematocyst discharge process of Cnidaria (Hydra, jellyfishes, box-jellyfishes and sea-anemones). Our model description of the fastest process in living nature raises and answers questions related to the material properties of the cell- and tubule-walls of nematocysts including their polysialic acid (polySia) dependent target function. Since a number of tumor-cells, especially brain-tumor cells such as neuroblastoma tissues carry the polysaccharide chain polySia in similar concentration as fish eggs or fish skin, it makes sense to use these findings for new diagnostic and therapeutic approaches in the field of nanomedicine. Therefore, the nematocyst discharge process can be considered as a bionic blue-print for future nanomedical devices in cancer diagnostics and therapies. This approach is promising because the physical background of this process can be described in a sufficient way with formulas presente...

Proceedings of the National Academy of Sciences, 2018

Significance The involvement of biotransformation enzymes in drug metabolism is one of the most c... more Significance The involvement of biotransformation enzymes in drug metabolism is one of the most crucial objectives during preclinical research, since they ultimately determine the bioavailability of medicinal drugs. The mARC N-reductive enzyme system was found to be a highly effective counterpart to one of the most prominent biotransformation enzymes, CYP450, and is involved in activation of amidoxime prodrugs as well as inactivation of other drugs containing N-hydroxylated functional groups. Owing to its potent N-reductive capacity toward a broad range of compounds, including mutagenic N-oxygenated nucleobase analogs, mARC plays a crucial role in pharmacology. Our crystal structure of human mARC forms the basis for predictions on the metabolism of drug candidates and structure–activity relationships. Moreover, it indicates the evolutionary development of different molybdoenzyme families.

Quarterly reviews of biophysics, 2017

Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumonia... more Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies rec...

Cancer Research, 2017

Objectives. Human IgG3 differs from other antibody isotypes by its extended hinge region and by i... more Objectives. Human IgG3 differs from other antibody isotypes by its extended hinge region and by its higher affinity for C1q. The ability of complement to promote lysis of antibody-opsonized cells is well-established and may represent a main mechanism in antibody mediated tumor therapy. The aim of this project was to investigate effector mechanisms of tumor- directed IgG3 antibodies in more detail. Experimental procedures. Therapeutic antibodies against EGFR (cetuximab, 225) and CD20 (rituximab, C2B8) were produced as IgG1 and IgG3 isotype variants by co-transfecting CHO cells with the respective de novo synthesized VH and VL domains fused to the respective heavy chain containing vectors. A Fab fragment of C2B8-IgG3 was crystallized and analyzed by X-ray structure analysis at PETRA III (DESY, Hamburg, Germany). Based on the resolved structure selected mutations were introduced into the CH1 domain of IgG3 aiming to improve or abolish CDC. Purified antibodies were assessed for compleme...

ChemMedChem, 2016

Figure 1. Illustration of a sialic acid tetramer consisting of four a2,8-linked Neu5Ac residues.

GBM Annual Fall meeting M�nster 2004, 2004

Novartis Foundation Symposia, 2007

Ras (or p21) is the product of the ras proto-oncogene and is believed to be involved in growth-pr... more Ras (or p21) is the product of the ras proto-oncogene and is believed to be involved in growth-promoting signal transduction. The structure of the guanine nucleotide-binding domain of H-Ras (or p21H-ras) in the triphosphate conformation was determined at very high resolution (1.4 A). All the binding interactions between protein and Gpp[NH]p and Mg2+ can be resolved in great detail. The region around amino acids 61-65 is flexible and exists in two conformations, one of which seems to be important for catalysis. The properties and structures of several oncogenic and non-oncogenic mutant forms of Ras have also been determined. Since the structure of the GDP-bound form is also known, the nature of the conformational change from the GTP-bound to the GDP-bound form can be inferred from the 3-D structure. A mechanism for the intrinsic GTP hydrolysis has been proposed. Its implications for the GAP-stimulated GTPase reaction is discussed in the light of recent kinetic and mutational experiments.

Journal of Neuroscience Research, 2014

The Superfamily of ras-Related Genes, 1991

The three-dimensional crystal structure of the catalytically active, GTP-analogue containing comp... more The three-dimensional crystal structure of the catalytically active, GTP-analogue containing complex of H-ras encoded p21 (aa 1–166) has been determined at 1.35 A resolution. It has the same topology as the G-binding domain of elongation factor Tu. The structure analysis revealed the binding sites of the nucleotide and of the essential cofactor Mg2+ in great detail and made it possible to propose a mechanism for GTP hydrolysis. In addition to the wild-type protein, the structures of several p21 mutants have been solved. While the overall structures of these proteins are not perturbed, there are small, but significant differences at the positions of the mutated amino acids. In the oncogenic mutants (Gly-12→Arg, Gly-12→Val, Gln-61→Leu, Gln-61→His), these mutations interfere with the proposed mechanism of catalysis and thus lead to a reduced rate of GTP hydrolysis.

Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 1992

Current knowledge of the structure of H-ras p21 is reviewed with particular emphasis on the inter... more Current knowledge of the structure of H-ras p21 is reviewed with particular emphasis on the interaction between guanine nucleotides and the active site of the protein. The nature of the conformational change induced by GTP hydrolysis is discussed. The major change is seen in the region known as the effector loop (loop 2), with significant but less well-defined changes occurring in loop 4, which is implicated in the GTPase reaction. Other evidence concerning the mechanism of GTP hydrolysis and its activation by GAP (GTPase-activating protein) is also discussed. Evidence regarding the rate limiting step in the p21 GTPase reaction, and the manner in which this and possibly other steps are accelerated by GAP, is inconclusive.

Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences, 1992

We describe here the results obtained to date on a project aimed at characterizing the changes oc... more We describe here the results obtained to date on a project aimed at characterizing the changes occurring in the protein product (p21) of the H-ras proto-oncogene during and as a result of hydrolysis of GTP at its active site. The approach used involves crystallization of p21 with a photosensitive precursor of GTP (caged GTP) at the active site followed by generation of GTP by photolysis and collection of X-ray diffraction data using the Laue method at a synchrotron source. The structure of p21 complexed with a single diastereomer of caged GTP is presented here. In contrast to crystals obtained with mixed diastereomers, the nucleotide appears to bind in a manner which is very similar to that of other guanine nucleotides (GDP, GTP, GppNHp). The current state of time resolved structural experiments using these crystals is presented.

Journal of the American Chemical Society, 2007

We thank Björn Klink and Yvonne Carius for data collection at the ESRF. We acknowledge the Europe... more We thank Björn Klink and Yvonne Carius for data collection at the ESRF. We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities and we thank the beam line staff for assistance in using beamline ID14-1 and ID14-3. We are grateful to the Scottish Higher Education Funding Council and the Engineering and Physical Sciences Research Council for funding and thank Dr. Steven Magennis for his invaluable assistance in COSMIC. T.L. thanks the Stiftung Stipendien-Fonds des Verbandes der Chemischen Industrie with financial contribution from the BMBF for a Ph.D. fellowship. Data deposition: The coordinates and structure factors for the complexes have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID codes 2IBS and 2IBT). Supporting information: General methods, materials, crystallization conditions, micro handling procedure for fluorescence measurement of small co-crystals, Figure S1 of co-crystals used for time-resolved fluorescence measurement, Figure S2 showing the 3' neighbor thymine shift in more detail, Table S1 of crystallographic data and refinement results, Table S2 comparing r.m.s deviations of M.TaqI backbone atoms in various co-crystal complexes, Tables S3-S10 of detailed fluorescence decay parameters and two files in crystallographic interchange format (cif) describing the two X-ray co-crystal structures.

Journal of Structural Biology, 2005

The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus pantotrophus is composed of... more The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus pantotrophus is composed of several proteins, which together oxidize hydrogen sulfide, sulfur, thiosulfate or sulfite and transfers the gained electrons to the respiratory chain. The hetero-dimeric cytochrome c complex SoxXA functions as heme enzyme and links covalently the sulfur substrate to the thiol of the cysteine-138 residue of the SoxY protein of the SoxYZ complex. Here, we report the crystal structure of the c-type cytochrome complex SoxXA. The structure could be solved by molecular replacement and refined to a resolution of 1.9 Å identifying the axial heme-iron coordination involving an unusual Cys-251 thiolate of heme2. Distance measurements between the three heme groups provide deeper insight into the electron transport inside SoxXA and merge in a better understanding of the initial step of the aerobic sulfur oxidation process in chemotrophic bacteria.

Journal of Molecular Graphics and Modelling, 2007

Flaviviridae are evolutionarily related viruses, comprising the hepatitis C virus (HCV), with the... more Flaviviridae are evolutionarily related viruses, comprising the hepatitis C virus (HCV), with the non-structural protein 4B (NS4B) as one of the least characterized proteins. NS4B is located in the endoplasmic reticulum membrane and is assumed to be a multifunctional protein. However, detailed structure information is missing. The hydrophobic nature of NS4B is a major difficulty for many experimental techniques. We applied bioinformatics methods to analyse structural and functional properties of NS4B in different viruses. We distinguish a central non-globular membrane portion with four to five transmembrane regions from an N-and C-terminal part with non-transmembrane helical elements. We demonstrate high similarity in sequence and structure for the C-terminal part within the flaviviridae family. A palmitoylation site contained in the C-terminal part of HCV is equally conserved in GB virus B. Furthermore, we identify and characterize an N-terminal basic leucine zipper (bZIP) motif in HCV, which is suggestive of a functionally important interaction site. In addition, we model the interaction of the bZIP region with the recently identified interaction partner CREB-RP/ATF6b, a human activating transcription factor involved in ER-stress. In conclusion, the versatile structure, together with functional sites and motifs, possibly enables NS4B to adopt a role as protein hub in the membranous web interaction network of virus and host proteins. Important structural and functional properties of NS4B are predicted with implications for ER-stress response, altered gene expression and replication efficacy.

Journal of Inorganic Biochemistry, 2003

Journal of Biological Chemistry, 2010