@phdthesis{İşbilir2022,
  author    = {İ{\c{s}}bilir, Ali},
  title     = {Localization and Trafficking of CXCR4 and CXCR7},
  doi       = {10.25972/OPUS-24937},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249378},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {G protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, and are the master components that translate extracellular stimulus into intracellular signaling, which in turn modulates key physiological and pathophysiological processes. Research within the last three decades suggests that many GPCRs can form complexes with each other via mechanisms that are yet unexplored. Despite a number of functional evidence in favor of GPCR dimers and oligomers, the existence of such complexes remains controversial, as different methods suggest diverse quaternary organizations for individual receptors. Among various methods, high resolution fluorescence microscopy and imagebased fluorescence spectroscopy are state-of-the-art tools to quantify membrane protein oligomerization with high precision. This thesis work describes the use of single molecule fluorescence microscopy and implementation of two confocal microscopy based fluorescence fluctuation spectroscopy based methods for characterizing the quaternary organization of two class A GPCRs that are important clinical targets: the C-X-C type chemokine receptor 4 (CXCR4) and 7 (CXCR7), or recently named as the atypical chemokine receptor 3 (ACKR3). The first part of the results describe that CXCR4 protomers are mainly organized as monomeric entities that can form transient dimers at very low expression levels allowing single molecule resolution. The second part describes the establishment and use of spatial and temporal brightness methods that are based on fluorescence fluctuation spectroscopy. Results from this part suggests that ACKR3 forms clusters and surface localized monomers, while CXCR4 forms increasing amount of dimers as a function of receptor density in cells. Moreover, CXCR4 dimerization can be modulated by its ligands as well as receptor conformations in distinct manners. Further results suggest that antagonists of CXCR4 display distinct binding modes, and the binding mode influences the oligomerization and the basal activity of the receptor: While the ligands that bind to a "minor" subpocket suppress both dimerization and constitutive activity, ligands that bind to a distinct, "major" subpocket only act as neutral antagonists on the receptor, and do not modulate neither the quaternary organization nor the basal signaling of CXCR4. Together, these results link CXCR4 dimerization to its density and to its activity, which may represent a new strategy to target CXCR4.},
  subject      = {G-Protein gekoppelter Rezeptor},
  language  = {en}
}
@phdthesis{Klemm2020,
  author    = {Klemm, Theresa Antonia},
  title     = {Minor differences cause major effects: How differential oligomerization regulates the activities of USP25 and USP28},
  doi       = {10.25972/OPUS-19108},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191080},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Deubiquitinases are regulators of the ubiquitin proteasome system that counteract the ubiquitination cascade by removing ubiquitin from substrates and cleaving ubiquitin chains. Due to their involvment in various important pathways, they are associated with several diseases and may thus present promising drug targets. The two related ubiquitin specific proteases USP25 and USP28 share a highly conserved amino acid sequence but perform distinct biological functions. USP28 plays roles in cell cycle regulation and was also linked to several types of cancer. It adopts oncogenic functions by rescuing the oncoproteins MYC and JUN from proteasomal degradation, which is induced by the E3-ligase SCF (FBW7). Opposingly, USP28 also regulates the stability of the tumor suppressor FBW7 itself. USP25 contributes to a balanced innate immune system by stabilizing TRAF3 and TRAF6 and lately was found to promote Wnt-signaling by deubiquitinating TNKS. Due to the high level of identity of both proteases, a recent attempt to inhibit USP28 led to cross reactivity against USP25. In our study, we characterized both USP25 and USP28 structurally and functionally using x-ray crystallography, biochemical as well as biophysical approaches to determine similarities and differences that can be exploited for the development of specific inhibitors. The crystal structure of the USP28 catalytic domain revealed a cherry-couple like dimer that mediates self-association by an inserted helical subdomain, the USP25/28 catalytic domain inserted domain (UCID). In USP25, the UCID leads to formation of a tetramer composed of two interlinked USP28-like dimers. Structural and functional analysis revealed that the dimeric USP28 is active, whereas the tetrameric USP25 is auto inhibited. Disruption of the tetramer by a cancer-associated mutation or a deletion-variant activates USP25 through dimer formation in in vitro assays and leads to an increased stability of TNKS in cell studies. Furthermore, in vitro data showed that neither ubiquitin nor substrate binding led to the activation of the USP25 tetramer construct. With the structure of the C-terminal domain of USP25, we determined the last unknown region in the enzyme as a separately folded domain that mediates substrate interactions. Combined the structures of the USP25 and USP28 catalytic domains and the functional characterization of both enzymes provide novel insights into the regulation of USPs by oligomerization. Furthermore, we identified individual features of each protease that might be explored for the development of specific small molecule inhibitors.},
  subject      = {Oligomerisation},
  language  = {en}
}
@phdthesis{Mueller2009,
  author    = {M{\"u}ller, Nicole},
  title     = {Entwicklung antigenabh{\"a}ngig aktivierbarer TNF-Ligand-Fusionsproteine},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-36489},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Von TRAIL, FasL und APRIL, drei Mitgliedern der TNF-Liganden-Familie, ist bekannt, dass Trimerstabilit{\"a}t und Oligomerisierungsstatus maßgeblich das Rezeptoraktivierungspotential dieser Liganden beeinflussen. F{\"u}r die immunstimulatorischen TNF-Liganden CD27L, CD40L, OX40L, 41BBL und GITRL war hingegen vor der Durchf{\"u}hrung dieser Arbeit praktisch nicht bekannt, inwieweit Trimerbildung, Stabilisierung und Oligomerisierung wichtig f{\"u}r deren Aktitvit{\"a}t sind. Dies wurde in dieser Arbeit systematisch untersucht. CD40L besaß bereits als trimeres Molek{\"u}l eine hohe Aktivit{\"a}t, die durch sekund{\"a}re Oligomerisierung nur wenig gesteigert wurde. Die spezifische Aktivit{\"a}t konnte durch Stabilisierung mit Hilfe der Tenascin-C (TNC)-Trimerisierungsdom{\"a}ne nur geringf{\"u}gig gesteigert werden. CD27L war als l{\"o}sliches Flag-markiertes sowie als hexameres Fc-Protein selbst nach Quervernetzen nicht in der Lage, seinen Rezeptor CD27 zu binden und zu aktivieren. Die TNC-stabilisierte trimere Form des CD27L hingegen induzierte nach Oligomerisierung mit einem anti-Flag-Antik{\"o}rper ein starkes Signal. Trimerer OX40L und trimerer 41BBL konnten nur in oligomerisierter Form ihre Rezeptoren aktivieren, wobei die Aktivit{\"a}t der TNC-stabilisierten Form signifikant st{\"a}rker ausgepr{\"a}gt war. GITRL aktivierte seinen Rezeptor bereits als stabilisiertes Trimer und Hexamer, die Aktivit{\"a}t konnte durch Quervernetzen nur gering gesteigert werden. Zusammenfassend kann man sagen, dass CD27L, OX40L und 41BBL zu der Untergruppe der TNF-Ligandenfamilie geh{\"o}rt, f{\"u}r die eine Stabilisierung des trimeren Molek{\"u}ls und dessen Oligomerisierung n{\"o}tig sind, um eine starke Rezeptoraktivierung zu erm{\"o}glichen. Im Gegensatz dazu zeigten CD40L und GITRL bereits oligomerisierungsunabh{\"a}ngig eine hohe Aktivit{\"a}t. GITRL ben{\"o}tigte allerdings die Stabilisierung des trimeren Molek{\"u}ls durch die TNC-Dom{\"a}ne, um gute Aktivit{\"a}t zu zeigen. Im Weiteren wurden Antik{\"o}rperfragment (scFv-)-TNF-Ligand-Fusionsproteine konstruiert und untersucht, die ein Zelloberfl{\"a}chenantigen binden. Eine starke Zelloberfl{\"a}chenantigen-spezifische Aktivierung des jeweiligen Rezeptors konnte f{\"u}r scFv-41BBL und f{\"u}r scFv-OX40L gezeigt werden, wohingegen scFv-CD40L und scFv-GITRL bereits auf antigennegativen Zellen stark aktiv waren. scFv-CD27L war selbst auf antigenpositiven Zellen inaktiv. Verwendet man an Stelle des Antik{\"o}rperfragments eine extrazellul{\"a}re Proteinbindedom{\"a}ne, z.B. die eines TNF-Rezeptors, erh{\"a}lt man Fusionsproteine, die zum einen eine selektive Aktivierung der TNF-Ligandendom{\"a}ne und somit die Aktivierung des korrespondierenden Rezeptors auf der Zielzelle erm{\"o}glichen, zum anderen aber durch die Bindung an den membranst{\"a}ndigen Liganden dessen Aktitv{\"a}t neutralisieren k{\"o}nnen. F{\"u}r CD40-, RANK- und B7-2-FasL konnte der immobilisationabh{\"a}ngige Aktivierungseffekt auf entsprechenden Zelloberfl{\"a}chenmolek{\"u}l-exprimierenden Zellen gezeigt werden. Anhand von T47D-Zellen, die durch eine autokrine CD40L-CD40-Signalschleife vor Apoptose gesch{\"u}tzt sind, konnte gezeigt werden, dass durch die Bindung von CD40-FasL an membranst{\"a}ndigen CD40L die CD40L-CD40-Interaktion gest{\"o}rt und gleichzeitig Apoptose verst{\"a}rkt induziert werden kann. Das Prinzip der antigenabh{\"a}ngigen Aktivierung von TNF-Liganden k{\"o}nnte Anwendung in der Tumortherapie finden, da bei Verwendung entsprechender selektiv exprimierter Marker eine lokale Rezeptoraktivierung erreicht und so Nebenwirkungen minimiert werden k{\"o}nnen.},
  subject      = {Rekombinantes Protein},
  language  = {de}
}