@article{PeissertSauerGrabarczyketal.2020,
  author    = {Peissert, Stefan and Sauer, Florian and Grabarczyk, Daniel B. and Braun, Cathy and Sander, Gudrun and Poterszman, Arnaud and Egly, Jean-Marc and Kuper, Jochen and Kisker, Caroline},
  title     = {In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair},
  series = {Nature Communications},
  volume    = {11},
  journal   = {Nature Communications},
  number    = {1},
  doi       = {10.1038/s41467-020-15241-9},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229857},
  year      = {2020},
  abstract  = {The XPD helicase is a central component of the general transcription factor TFIIH which plays major roles in transcription and nucleotide excision repair (NER). Here we present the high-resolution crystal structure of the Arch domain of XPD with its interaction partner MAT1, a central component of the CDK activating kinase complex. The analysis of the interface led to the identification of amino acid residues that are crucial for the MAT1-XPD interaction. More importantly, mutagenesis of the Arch domain revealed that these residues are essential for the regulation of (i) NER activity by either impairing XPD helicase activity or the interaction of XPD with XPG; (ii) the phosphorylation of the RNA polymerase II and RNA synthesis. Our results reveal how MAT1 shields these functionally important residues thereby providing insights into how XPD is regulated by MAT1 and defining the Arch domain as a major mechanistic player within the XPD scaffold.},
  language  = {en}
}
@article{LorenzinBenaryBaluapurietal.2016,
  author    = {Lorenzin, Francesca and Benary, Uwe and Baluapuri, Apoorva and Walz, Susanne and Jung, Lisa Anna and von Eyss, Bj{\"o}rn and Kisker, Caroline and Wolf, Jana and Eilers, Martin and Wolf, Elmar},
  title     = {Different promoter affinities account for specificity in MYC-dependent gene regulation},
  series = {eLife},
  volume    = {5},
  journal   = {eLife},
  doi       = {10.7554/eLife.15161},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162913},
  pages     = {e15161},
  year      = {2016},
  abstract  = {Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells.},
  language  = {en}
}
@article{FischerHarrisonRamirezetal.2017,
  author    = {Fischer, Annette and Harrison, Kelly S and Ramirez, Yesid and Auer, Daniela and Chowdhury, Suvagata Roy and Prusty, Bhupesh K and Sauer, Florian and Dimond, Zoe and Kisker, Caroline and Hefty, P Scott and Rudel, Thomas},
  title     = {Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense},
  series = {eLife},
  volume    = {6},
  journal   = {eLife},
  number    = {e21465},
  doi       = {10.7554/eLife.21465},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171073},
  year      = {2017},
  abstract  = {Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound vacuole called inclusion, which serves as a signaling interface with the host cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes in the inclusion membrane and faces the cytosol with the active deubiquitinating enzyme domain. The structure of this domain revealed high similarity to mammalian deubiquitinases with a unique α-helix close to the substrate-binding pocket. We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1 and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1 and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally, inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNγ and impaired infection in mice. Thus, the chlamydial inclusion serves as an enriched site for a deubiquitinating activity exerting a function in selective stabilization of host proteins and protection from host defense.},
  language  = {en}
}
@article{KoelmelKuperKisker2021,
  author    = {Koelmel, Wolfgang and Kuper, Jochen and Kisker, Caroline},
  title     = {Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem},
  series = {Scientific Reports},
  volume    = {11},
  journal   = {Scientific Reports},
  number    = {1},
  doi       = {10.1038/s41598-021-95186-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-261644},
  pages     = {17038},
  year      = {2021},
  abstract  = {Over the last decades the phase problem in macromolecular x-ray crystallography has become more controllable as methods and approaches have diversified and improved. However, solving the phase problem is still one of the biggest obstacles on the way of successfully determining a crystal structure. To overcome this caveat, we have utilized the anomalous scattering properties of the heavy alkali metal cesium. We investigated the introduction of cesium in form of cesium chloride during the three major steps of protein treatment in crystallography: purification, crystallization, and cryo-protection. We derived a step-wise procedure encompassing a "quick-soak"-only approach and a combined approach of CsCl supplement during purification and cryo-protection. This procedure was successfully applied on two different proteins: (i) Lysozyme and (ii) as a proof of principle, a construct consisting of the PH domain of the TFIIH subunit p62 from Chaetomium thermophilum for de novo structure determination. Usage of CsCl thus provides a versatile, general, easy to use, and low cost phasing strategy.},
  language  = {en}
}