26
|
Petrovic S, Roske Y, Heinemann U. Structural basis of ASPL-mediated regulation of p97 methylation by METTL21D. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
27
|
Heinemann U, Garg A, Roske Y, Schütz A. Post-translational regulation of gene expression in the immune system by Roquin/RC3H1 and ribonucleases of the Regnase/ZC3H12/MCPIP family. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
28
|
Roske Y, Diehl A, Ball L, Turgay K, Heinemann U, Akbey Ü, Oschkinat H. Structural insight into protein-aided bacterial biofilm formation. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
29
|
Kunstmann S, Gohlke U, Broeker NK, Roske Y, Heinemann U, Santer M, Barbirz S. Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. J Am Chem Soc 2018; 140:10447-10455. [DOI: 10.1021/jacs.8b03719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
30
|
Garg A, Heinemann U. A novel form of RNA double helix based on G·U and C·A + wobble base pairing. RNA (NEW YORK, N.Y.) 2018; 24:209-218. [PMID: 29122970 PMCID: PMC5769748 DOI: 10.1261/rna.064048.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/05/2017] [Indexed: 05/27/2023]
Abstract
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double-helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A+ wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A+ base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson-Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A+ base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.
Collapse
|
31
|
Jurk CM, Roske Y, Heinemann U. Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130. CROAT CHEM ACTA 2018. [DOI: 10.5562/cca3341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
|
32
|
Heinemann U, Ming Q, Roske Y, Schuetz A, Schmidt-Ott KM. Parsimonious DNA target-site recognition by Grh/CP2 transcription factors. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317092750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
33
|
Garg A, Takeuchi O, Heinemann U. Immune response regulation by paralogous endoribonucleases: ZC3H12C and N4BP1. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
34
|
Roske Y, Diehl A, Heinemann U, Oschkinat H, Turgay K. Structural insight into protein-aided bacterial biofilm formation. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
35
|
Schuetz A, Radusheva V, Krug SM, Heinemann U. Crystal structure of the tricellulin C-terminal coiled-coil domain reveals a unique mode of dimerization. Ann N Y Acad Sci 2017; 1405:147-159. [DOI: 10.1111/nyas.13408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/24/2022]
|
36
|
Jennek S, Mittag S, Reiche J, Westphal JK, Seelk S, Dörfel MJ, Pfirrmann T, Friedrich K, Schütz A, Heinemann U, Huber O. Tricellulin is a target of the ubiquitin ligase Itch. Ann N Y Acad Sci 2017; 1397:157-168. [DOI: 10.1111/nyas.13349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 01/05/2023]
|
37
|
Carter DM, Specker E, Przygodda J, Neuenschwander M, von Kries JP, Heinemann U, Nazaré M, Gohlke U. Identification of a Novel Benzimidazole Pyrazolone Scaffold That Inhibits KDM4 Lysine Demethylases and Reduces Proliferation of Prostate Cancer Cells. SLAS DISCOVERY 2017; 22:801-812. [PMID: 28346812 DOI: 10.1177/2472555217699157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human lysine demethylase (KDM) enzymes (KDM1-7) constitute an emerging class of therapeutic targets, with activities that support growth and development of metastatic disease. By interacting with and co-activating the androgen receptor, the KDM4 subfamily (KDM4A-E) promotes aggressive phenotypes of prostate cancer (PCa). Knockdown of KDM4 expression or inhibition of KDM4 enzyme activity reduces the proliferation of PCa cell lines and highlights inhibition of lysine demethylation as a possible therapeutic method for PCa treatment. To address this possibility, we screened the ChemBioNet small molecule library for inhibitors of the human KDM4E isoform and identified several compounds with IC50 values in the low micromolar range. Two hits, validated as active by an orthogonal enzyme-linked immunosorbent assay, displayed moderate selectivity toward the KDM4 subfamily and exhibited antiproliferative effects in cellular models of PCa. These compounds were further characterized by their ability to maintain the transcriptionally silent histone H3 tri-methyl K9 epigenetic mark at subcytotoxic concentrations. Taken together, these efforts identify and validate a hydroxyquinoline scaffold and a novel benzimidazole pyrazolone scaffold as tractable for entry into hit-to-lead chemical optimization campaigns.
Collapse
|
38
|
Consentius P, Loll B, Gohlke U, Alings C, Müller C, Müller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T. Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins. J Phys Chem Lett 2017; 8:1113-1117. [PMID: 28221042 DOI: 10.1021/acs.jpclett.6b02971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.
Collapse
|
39
|
Consentius P, Gohlke U, Loll B, Alings C, Heinemann U, Wahl MC, Risse T. Combining EPR spectroscopy and X-ray crystallography to elucidate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals. Phys Chem Chem Phys 2017; 19:20723-20734. [DOI: 10.1039/c7cp03144k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unraveling structural and dynamic details of spin labeled proteins using a combination of single crystal EPR spectroscopy and X-ray crystallography.
Collapse
|
40
|
Arumughan A, Roske Y, Barth C, Forero LL, Bravo-Rodriguez K, Redel A, Kostova S, McShane E, Opitz R, Faelber K, Rau K, Mielke T, Daumke O, Selbach M, Sanchez-Garcia E, Rocks O, Panáková D, Heinemann U, Wanker EE. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Nat Commun 2016; 7:13047. [PMID: 27762274 PMCID: PMC5080433 DOI: 10.1038/ncomms13047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. The AAA+ ATPase p97 is an essential hexameric protein with multiple protein interaction partners and cellular functions. Here, the authors use interaction mapping to examine partner proteins of this large complex, and assess the effects of these proteins on the disassembly of the p97 complex.
Collapse
|
41
|
Consentius P, Gohlke U, Loll B, Alings C, Müller R, Heinemann U, Kaupp M, Wahl M, Risse T. Tracking Transient Conformational States of T4 Lysozyme at Room Temperature Combining X-ray Crystallography and Site-Directed Spin Labeling. J Am Chem Soc 2016; 138:12868-12875. [DOI: 10.1021/jacs.6b05507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
42
|
Abstract
An evacuable guarded hot plate for thermal conductivity measurements between 200 and 800 C was used to investigate the heat transfer in barley straw. The different thermal transfer mechanisms (solid, gaseous conduction and infrared-radiative heat transfer) as well as coupling effects were separated. The measured thermal conductivities (λ = 0.041 W m−1 K−1) are similar to those of conventional insulation materials such as foams, glass or mineral fibres which are widely used as building insulation materials. Straw from barley or wheat, which is a low-cost, renewable material readily available world-wide, is therefore an interesting alternative to conventional insulation materials.
Collapse
|
43
|
Biedermann A, Kudoke C, Merten A, Minogue E, Rotermund U, Ebert HP, Heinemann U, Fricke J, Seifert H. Analysis of Heat Transfer Mechanisms in Polyurethane Rigid Foam. J CELL PLAST 2016. [DOI: 10.1106/kemu-lh63-v9h2-kfa3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Polyurethane closed cell rigid foams have been widely used as insulants in the building and refrigeration industry and also for district heating pipes. It is the special combination of its excellent insulation performance and the mechanical stability due to the foaming process which makes this material very attractive for these applications. The replacement of CFCs, which have been banned as blowing agents since 1993, by hydrocarbons in Europe caused a decrease in the insulation capability of polyurethane (PU) rigid foams. The additional global requirement to reduce energy losses also adds an incentive to search for potentials which would improve the thermal performance of rigid foams. To overcome this problem, the heat transfer within PU rigid foams via
Collapse
|
44
|
Sparta KM, Mueller U, Heinemann U, Weiss MS. The automated expert processing system XDSAPP. ACTA CRYSTALLOGRAPHICA SECTION A FOUNDATIONS AND ADVANCES 2016. [DOI: 10.1107/s2053273316097151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
45
|
Heinemann U, Ming Q, Roske Y, Schütz A. Klf4 and Grhl1: two distinct ways of achieving DNA target site recognition. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
46
|
Garg A, Takeuchi O, Heinemann U. MCPIP3 (ZC 3H 12C) regulates the innate immune response by acting as a ribonuclease. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
47
|
Rösner J, Liotta A, Angamo EA, Spies C, Heinemann U, Kovács R. Minimizing photodecomposition of flavin adenine dinucleotide fluorescence by the use of pulsed LEDs. J Microsc 2016; 264:215-223. [PMID: 27368071 DOI: 10.1111/jmi.12436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/27/2016] [Accepted: 05/30/2016] [Indexed: 01/08/2023]
Abstract
Dynamic alterations in flavin adenine dinucleotide (FAD) fluorescence permit insight into energy metabolism-dependent changes of intramitochondrial redox potential. Monitoring FAD fluorescence in living tissue is impeded by photobleaching, restricting the length of microfluorimetric recordings. In addition, photodecomposition of these essential electron carriers negatively interferes with energy metabolism and viability of the biological specimen. Taking advantage of pulsed LED illumination, here we determined the optimal excitation settings giving the largest fluorescence yield with the lowest photobleaching and interference with metabolism in hippocampal brain slices. The effects of FAD bleaching on energy metabolism and viability were studied by monitoring tissue pO2 , field potentials and changes in extracellular potassium concentration ([K+ ]o ). Photobleaching with continuous illumination consisted of an initial exponential decrease followed by a nearly linear decay. The exponential decay was significantly decelerated with pulsed illumination. Pulse length of 5 ms was sufficient to reach a fluorescence output comparable to continuous illumination, whereas further increasing duration increased photobleaching. Similarly, photobleaching increased with shortening of the interpulse interval. Photobleaching was partially reversible indicating the existence of a transient nonfluorescent flavin derivative. Pulsed illumination decreased FAD photodecomposition, improved slice viability and reproducibility of stimulus-induced FAD, field potential, [K+ ]o and pO2 changes as compared to continuous illumination.
Collapse
|
48
|
Kowenz-Leutz E, Schuetz A, Liu Q, Knoblich M, Heinemann U, Leutz A. Functional interaction of CCAAT/enhancer-binding-protein-α basic region mutants with E2F transcription factors and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:841-7. [PMID: 27131901 DOI: 10.1016/j.bbagrm.2016.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 11/28/2022]
Abstract
The transcription factor CCAAT/enhancer-binding protein α (C/EBPα) regulates cell cycle arrest and terminal differentiation of neutrophils and adipocytes. Mutations in the basic leucine zipper domain (bZip) of C/EBPα are associated with acute myeloid leukemia. A widely used murine transforming C/EBPα basic region mutant (BRM2) entails two bZip point mutations (I294A/R297A). BRM2 has been discordantly described as defective for DNA binding or defective for interaction with E2F. We have separated the two BRM2 mutations to shed light on the intertwined reciprocity between C/EBPα-E2F-DNA interactions. Both, C/EBPα I294A and R297A retain transactivation capacity and interaction with E2F-DP. The C/EBPα R297A mutation destabilized DNA binding, whereas the C/EBPα I294A mutation enhanced binding to DNA. The C/EBPα R297A mutant, like BRM2, displayed enhanced interaction with E2F-DP but failed to repress E2F-dependent transactivation although both mutants were readily suppressed by E2F1 for transcription through C/EBP cis-regulatory sites. In contrast, the DNA binding enhanced C/EBPα I294A mutant displayed increased repression of E2F-DP mediated transactivation and resisted E2F-DP mediated repression. Thus, the efficient repression of E2F dependent S-phase genes and the activation of differentiation genes reside in the balanced DNA binding capacity of C/EBPα.
Collapse
|
49
|
Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016; 138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
50
|
Abstract
XDSAPPis an expert system and graphical user interface (GUI) for the automated processing of diffraction images using theXDSprogram suite and other programs. The latest major update and the extension of the program are presented here. The update includes new features, as well as improvements in the GUI and the underlying decision-making system.XDSAPPis freely available for academic users.
Collapse
|