TY - JOUR A1 - Bangalore, Disha M. A1 - Heil, Hannah S. A1 - Mehringer, Christian F. A1 - Hirsch, Lisa A1 - Hemmen, Katharina A1 - Heinze, Katrin G. A1 - Tessmer, Ingrid T1 - Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases JF - Scientific Reports N2 - Base excision repair is the dominant DNA repair pathway of chemical modifications such as deamination, oxidation, or alkylation of DNA bases, which endanger genome integrity due to their high mutagenic potential. Detection and excision of these base lesions is achieved by DNA glycosylases. To investigate the remarkably high efficiency in target site search and recognition by these enzymes, we applied single molecule atomic force microscopy (AFM) imaging to a range of glycosylases with structurally different target lesions. Using a novel, automated, unbiased, high-throughput analysis approach, we were able to resolve subtly different conformational states of these glycosylases during DNA lesion search. Our results lend support to a model of enhanced lesion search efficiency through initial lesion detection based on altered mechanical properties at lesions. Furthermore, its enhanced sensitivity and easy applicability also to other systems recommend our novel analysis tool for investigations of diverse, fundamental biological interactions. KW - atomic-force microscopy KW - base pairs KW - molecular structure KW - crystal structure KW - structural basis KW - repair KW - recognition KW - 8-oxoguanine KW - thymine KW - mismatches Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231338 VL - 10 ER - TY - JOUR A1 - Braunschweig, Holger A1 - Ewing, William C. A1 - Ghosh, Sundargopal A1 - Kramer, Thomas A1 - Mattock, James D. A1 - Östreicher, Sebastian A1 - Vargas, Alfredo A1 - Werner, Christine T1 - Trimetallaborides as starting points for the syntheses of large metal-rich molecular borides and clusters JF - Chemical Science N2 - Treatment of an anionic dimanganaborylene complex ([{Cp(CO)\(_2\)Mn}\(_2\)B]\(^-\)) with coinage metal cations stabilized by a very weakly coordinating Lewis base (SMe\(_2\)) led to the coordination of the incoming metal and subsequent displacement of dimethylsulfide in the formation of hexametalladiborides featuring planar four-membered M\(_2\)B\(_2\) cores (M = Cu, Au) comparable to transition metal clusters constructed around four-membered rings composed solely of coinage metals. The analogies between compounds consisting of B\(_2\)M\(_2\) units and M\(_4\) (M = Cu, Au) units speak to the often overlooked metalloid nature of boron. Treatment of one of these compounds (M = Cu) with a Lewis-basic metal fragment (Pt(PCy\(_3\))\(_2\)) led to the formation of a tetrametallaboride featuring two manganese, one copper and one platinum atom, all bound to boron in a geometry not yet seen for this kind of compound. Computational examination suggests that this geometry is the result of d\(^{10}\)-d\(^{10}\) dispersion interactions between the copper and platinum fragments. KW - anionic dimetalloborylene complexes KW - trimetallaborides KW - tetrametallaborides KW - Boron KW - metallaboranes KW - crystal structure KW - metal borylene complexes Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-191511 VL - 7 IS - 1 ER - TY - JOUR A1 - Braunschweig, Holger A1 - Kramer, T. T1 - Crystal structure of μ-1κC:2(\(η^2\))-carbonyl-carbonyl-1κC-chlorido-2κCl-μ-chloridoborylene-1:2\(κ^2\) B:B-[1(\(η^5\))-pentamethylcyclopentadienyl](tricyclohexylphosphane-2κP)iron(II)platinum(II) benzene monosolvate N2 - In the mol­ecular structure of the dinuclear title compound \([η^5-(C_5(CH_3)_5)(CO)Fe{(μ-BCl)(μ-CO)}PtCl(P(C_6H_{11})_3)]·C_6H_6\), the two metal atoms, iron(II) and platinum(II), are bridged by one carbonyl (μ-CO) and one chlorido­borylene ligand (μ-BCl). The \(Pt^{II}\) atom is additionally bound to a chloride ligand situated trans to the bridging borylene, and a tri­cyclo­hexyl­phosphane ligand \((PCy_3)\) trans to the carbonyl ligand, forming a distorted square-planar structural motif at the \(Pt^{II}\) atom. The \(Fe_{II}\) atom is bound to a penta­methyl­cyclo­penta­dienyl ligand \([η^5-C_5(CH_3)_5]\) and one carbonyl ligand (CO), forming a piano-stool structure. Additionally, one benzene solvent mol­ecule is incorporated into the crystal structure, positioned staggered relative to the penta­methyl­cyclo­penta­dienyl ligand at the \(Fe^{II}\) atom, with a centroid–centroid separation of 3.630 (2) Å. KW - platinum KW - oxidative addition KW - borylene KW - heterodinuclear compound KW - crystal structure Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120120 VL - 70 IS - 11 ER - TY - JOUR A1 - Capra, Valérie A1 - Busnelli, Marta A1 - Perenna, Alessandro A1 - Ambrosio, Manuela A1 - Accomazzo, Maria Rosa A1 - Galés, Celine A1 - Chini, Bice A1 - Rovati, G. Enrico T1 - Full and Partial Agonists of Thromboxane Prostanoid Receptor Unveil Fine Tuning of Receptor Superactive Conformation and G Protein Activation JF - PLoS ONE N2 - The intrahelical salt bridge between \(E/D^{3.49}\) and \(R^{3.50}\) within the E/DRY motif on helix 3 (H3) and the interhelical hydrogen bonding between the E/DRY and residues on H6 are thought to be critical in stabilizing the class A G protein-coupled receptors in their inactive state. Removal of these interactions is expected to generate constitutively active receptors. This study examines how neutralization of \(E^{3.49/6.30}\) in the thromboxane prostanoid (TP) receptor alters ligand binding, basal, and agonist-induced activity and investigates the molecular mechanisms of G protein activation. We demonstrate here that a panel of full and partial agonists showed an increase in affinity and potency for E129V and E240V mutants. Yet, even augmenting the sensitivity to detect constitutive activity (CA) with overexpression of the receptor or the G protein revealed resistance to an increase in basal activity, while retaining fully the ability to cause agonist-induced signaling. However, direct G protein activation measured through bioluminescence resonance energy transfer (BRET) indicates that these mutants more efficiently communicate and/or activate their cognate G proteins. These results suggest the existence of additional constrains governing the shift of TP receptor to its active state, together with an increase propensity of these mutants to agonist-induced signaling, corroborating their definition as superactive mutants. The particular nature of the TP receptor as somehow "resistant" to CA should be examined in the context of its pathophysiological role in the cardiovascular system. Evolutionary forces may have favored regulation mechanisms leading to low basal activity and selected against more highly active phenotypes. KW - coupled receptor KW - ligand binding KW - intracellular loop KW - molecular dynamics KW - Beta(1)-adrenergic receptor KW - ionic look KW - Beta(2)-adrenergic receptor KW - crystal structure KW - constitutive activity Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131013 VL - 8 IS - 3 ER - TY - JOUR A1 - Gessner, Viktoria H. T1 - Diphenyl[(phenylsulfanyl)methyl]-\(λ^5\)-phosphanethione JF - Acta Crystallographica, Section E: Structure Reports N2 - The title compound, \(C_{19}H_{17}PS_2\), results from the direct deprotonation of di­phenyl­methyl­phosphine sulfide and subsequent reaction with diphenyl di­sulfide. The C-P and C-S bond lengths of 1.8242 (18) and 1.8009 (18) Å, respectively, of the central P-C-S linkage are comparable to those found in the sulfonyl analogue, but are considerably longer than those reported for the dimetallated sulfonyl compound. The dihedral angle between the benzene rings of the di­phenyl­methyl moiety is 69.46 (7)°. No distinct inter­molecular inter­actions are present in the crystal structure. KW - crystal structure Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120174 VL - 70 IS - 3 ER - TY - JOUR A1 - Hanft, Anna A1 - Lichtenberg, Crispin T1 - Dimerization of 2-[(2-((2-aminophenyl)thio)phenyl)amino]-cyclohepta-2,4,6-trien-1-one through hydrogen bonding, C\(_{19}\)H\(_{16}\)N\(_2\)OS JF - Zeitschrift für Kristallographie - New Crystal Structures N2 - C\(_{19}\)H\(_{16}\)N\(_2\)OS, triclinic, P (1) over bar (no. 2), a= 8.1510(3) angstrom, b = 8.8021(3) angstrom, c =11.3953(5) angstrom, alpha =72.546(2)degrees, beta=84.568(2)degrees, gamma =80.760(2)degrees, V =768.86(5) angstrom(3), Z =2, R\(_{gt}\)(F) = 0.0491, WR\(_{ref}\)(F-2) = 0.1494, T =100 K. KW - crystal structure KW - complexes KW - ligands KW - tropocoronands KW - mononuclear KW - chemistry Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229482 VL - 235 IS - 4 ER - TY - JOUR A1 - Klammert, Uwe A1 - Müller, Thomas D. A1 - Hellmann, Tina V. A1 - Wuerzler, Kristian K. A1 - Kotzsch, Alexander A1 - Schliermann, Anna A1 - Schmitz, Werner A1 - Kuebler, Alexander C. A1 - Sebald, Walter A1 - Nickel, Joachim T1 - GDF-5 can act as a context-dependent BMP-2 antagonist JF - BMC Biology N2 - Background Bone morphogenetic protein (BMP)-2 and growth and differentiation factor (GDF)-5 are two related transforming growth factor (TGF)-β family members with important functions in embryonic development and tissue homeostasis. BMP-2 is best known for its osteoinductive properties whereas GDF-5—as evident from its alternative name, cartilage derived morphogenetic protein 1—plays an important role in the formation of cartilage. In spite of these differences both factors signal by binding to the same subset of BMP receptors, raising the question how these different functionalities are generated. The largest difference in receptor binding is observed in the interaction with the type I receptor BMPR-IA. GDF-5, in contrast to BMP-2, shows preferential binding to the isoform BMPR-IB, which is abrogated by a single amino acid (A57R) substitution. The resulting variant, GDF-5 R57A, represents a “BMP-2 mimic” with respect to BMP receptor binding. In this study we thus wanted to analyze whether the two growth factors can induce distinct signals via an identically composed receptor. Results Unexpectedly and dependent on the cellular context, GDF-5 R57A showed clear differences in its activity compared to BMP-2. In ATDC-5 cells, both ligands induced alkaline phosphatase (ALP) expression with similar potency. But in C2C12 cells, the BMP-2 mimic GDF-5 R57A (and also wild-type GDF-5) clearly antagonized BMP-2-mediated ALP expression, despite signaling in both cell lines occurring solely via BMPR-IA. The BMP-2- antagonizing properties of GDF-5 and GDF-5 R57A could also be observed in vivo when implanting BMP-2 and either one of the two GDF-5 ligands simultaneously at heterotopic sites. Conclusions Although comparison of the crystal structures of the GDF-5 R57A:BMPR-IAEC- and BMP-2:BMPR-IAEC complex revealed small ligand-specific differences, these cannot account for the different signaling characteristics because the complexes seem identical in both differently reacting cell lines. We thus predict an additional component, most likely a not yet identified GDF-5-specific co-receptor, which alters the output of the signaling complexes. Hence the presence or absence of this component then switches GDF-5′s signaling capabilities to act either similar to BMP-2 or as a BMP-2 antagonist. These findings might shed new light on the role of GDF-5, e.g., in cartilage maintenance and/or limb development in that it might act as an inhibitor of signaling events initiated by other BMPs. KW - growth and differentiation factor 5 KW - ligand-receptor complex KW - crystal structure KW - antagonist Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125550 VL - 13 IS - 77 ER - TY - JOUR A1 - Lorenz, Sonja A1 - Bhattacharyya, Moitrayee A1 - Feiler, Christian A1 - Rape, Michael A1 - Kuriyan, John T1 - Crystal Structure of a Ube2S-Ubiquitin Conjugate JF - PLoS ONE N2 - Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. KW - crystal structure KW - protein ubiquitination KW - Ubiquitin-conjugating (E2) enzymes KW - Ube2S Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-167265 VL - 11 IS - 2 ER - TY - JOUR A1 - Merget, Benjamin A1 - Sotriffer, Christoph A. T1 - Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations JF - PLoS One N2 - An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant koff. For the essential antimycobacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular dynamics (MD) simulations with a total sampling time of 3.0 µs were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2'-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade substituent in 5'-position of the diphenyl ether B-ring. KW - crystal structure KW - ethers KW - oxygen KW - cofactors (biochemistry) KW - binding analysis KW - biochemical simulations KW - hydrogen bonding mycobacterium tuberculosis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125607 VL - 10 IS - 5 ER - TY - JOUR A1 - Rakette, Sonja A1 - Donat, Stefanie A1 - Ohlsen, Knut A1 - Stehle, Thilo T1 - Structural Analysis of Staphylococcus aureus Serine/Threonine Kinase PknB JF - PLoS One N2 - Effective treatment of infections caused by the bacterium Staphylococcus aureus remains a worldwide challenge, in part due to the constant emergence of new strains that are resistant to antibiotics. The serine/threonine kinase PknB is of particular relevance to the life cycle of S. aureus as it is involved in the regulation of purine biosynthesis, autolysis, and other central metabolic processes of the bacterium. We have determined the crystal structure of the kinase domain of PknB in complex with a non-hydrolyzable analog of the substrate ATP at 3.0 angstrom resolution. Although the purified PknB kinase is active in solution, it crystallized in an inactive, autoinhibited state. Comparison with other bacterial kinases provides insights into the determinants of catalysis, interactions of PknB with ligands, and the pathway of activation. KW - SER/THR kinase KW - domain KW - subunit KW - dependent protein-kinase KW - mycobacterium-tuberculosis KW - activation mechanism KW - crystal structure KW - antibiotic resistance KW - catalytic KW - methicillin KW - inhibitor Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-135369 VL - 7 IS - 6 ER - TY - JOUR A1 - Riad, Noura M. A1 - Zlotos, Darius P. A1 - Holzgrabe, Ulrike T1 - Crystal structure of 5,11-dihydropyrido[2,3-b][1,4]benzodiazepin-6-one. JF - Acta Crystallographica Section E Crystallographic Communications N2 - The title compound, C\(_{12}\)H\(_{9}\)N\(_{3}\)O, is an inter­mediate in the synthesis of the muscarinic M2 receptor antagonist AFDX-384. The seven-membered ring adopts a boat conformation and the dihedral angle between the planes of the aromatic rings is 41.51 (9)°. In the crystal, mol­ecules are linked into [001] chains of alternating inversion dimers formed by pairs of N-H・・・O hydrogen bonds and pairs of N-H・・・N hydrogen bonds. In both cases, R\(_{2}\)\(^{2}\)(8) loops are generated. KW - crystal structure KW - pyridobenzodiazepine KW - boat conformation KW - hydrogen bonding Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149627 VL - E71 ER - TY - JOUR A1 - Schmitt, Dominik R. A1 - Kuper, Jochen A1 - Elias, Agnes A1 - Kisker, Caroline T1 - The Structure of the TFIIH p34 Subunit Reveals a Von Willebrand Factor A Like Fold JF - PLoS ONE N2 - RNA polymerase II dependent transcription and nucleotide excision repair are mediated by a multifaceted interplay of subunits within the general transcription factor II H (TFIIH). A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these vital cellular processes. The importance of this complex becomes further evident in the context of severe diseases like xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy, that arise from single point mutations in TFIIH subunits. Here we describe the structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum. The structure revealed that p34 contains a von Willebrand Factor A (vWA) like domain, a fold which is generally known to be involved in protein-protein interactions. Within TFIIH p34 strongly interacts with p44, a positive regulator of the helicase XPD. Putative protein-protein interfaces are analyzed and possible binding sites for the p34-p44 interaction suggested. KW - sequence motif analysis KW - iodides KW - protein-protein interactions KW - protein domains KW - molecular structure KW - electron density KW - protein structure KW - crystal structure Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-119471 SN - 1932-6203 VL - 9 IS - 7 ER - TY - JOUR A1 - Schäfer, Nadine A1 - Friedrich, Maximilian A1 - Jørgensen, Morten Egevang A1 - Kollert, Sina A1 - Koepsell, Hermann A1 - Wischmeyer, Erhard A1 - Lesch, Klaus-Peter A1 - Geiger, Dietmar A1 - Döring, Frank T1 - Functional analysis of a triplet deletion in the gene encoding the sodium glucose transporter 3, a potential risk factor for ADHD JF - PLoS ONE N2 - Sodium-glucose transporters (SGLT) belong to the solute carrier 5 family, which is characterized by sodium dependent transport of sugars and other solutes. In contrast, the human SGLT3 (hSGLT3) isoform, encoded by SLC5A4, acts as a glucose sensor that does not transport sugar but induces membrane depolarization by Na\(^{+}\) currents upon ligand binding. Whole-exome sequencing (WES) of several extended pedigrees with high density of attention-deficit/hyperactivity disorder (ADHD) identified a triplet ATG deletion in SLC5A4 leading to a single amino acid loss (ΔM500) in the hSGLT3 protein imperfectly co-segregating with the clinical phenotype of ADHD. Since mutations in homologous domains of hSGLT1 and hSGLT2 were found to affect intestinal and renal function, respectively, we analyzed the functional properties of hSGLT3[wt] and [ΔM500] by voltage clamp and current clamp recordings from cRNA-injected Xenopus laevis oocytes. The cation conductance of hSGLT3[wt] was activated by application of glucose or the specific agonist 1-desoxynojirimycin (DNJ) as revealed by inward currents in the voltage clamp configuration and cell depolarization in the current clamp mode. Almost no currents and changes in membrane potential were observed when glucose or DNJ were applied to hSGLT3[ΔM500]-injected oocytes, demonstrating a loss of function by this amino acid deletion in hSGLT3. To monitor membrane targeting of wt and mutant hSGLT3, fusion constructs with YFP were generated, heterologously expressed in Xenopus laevis oocytes and analyzed for membrane fluorescence by confocal microscopy. In comparison to hSGLT3[wt] the fluorescent signal of mutant [ΔM500] was reduced by 43% indicating that the mutant phenotype might mainly result from inaccurate membrane targeting. As revealed by homology modeling, residue M500 is located in TM11 suggesting that in addition to the core structure (TM1-TM10) of the transporter, the surrounding TMs are equally crucial for transport/sensor function. In conclusion, our findings indicate that the deletion [ΔM500] in hSGLT3 inhibits membrane targeting and thus largely disrupts glucose-induced sodium conductance, which may, in interaction with other ADHD risk-related gene variants, influence the risk for ADHD in deletion carriers. KW - Xenopus laevis oocytes KW - ADHD KW - glucose KW - cell membranes KW - membrane proteins KW - membrane potential KW - crystal structure KW - amino acid analysis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176495 VL - 13 IS - 10 ER -