@phdthesis{LiessneeEller2021,
  author    = {Liess [n{\´e}e Eller], Anna Katharina Luise},
  title     = {Understanding the regulation of the ubiquitin-conjugating enzyme UBE2S},
  doi       = {10.25972/OPUS-20419},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204190},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The ubiquitination of proteins serves as molecular signal to control an enormous number of physiological processes and its dysregulation is connected to human diseases like cancer. The versatility of this signal stems from the diverse ways by which ubiquitin can be attached to its targets. Thus, specificity and tight regulation of the ubiquitination are pivotal requirements of ubiquitin signaling. Ubiquitin-conjugating enzymes (E2s) act at the heart of the ubiquitination cascade, transferring ubiquitin from a ubiquitin-activating enzyme (E1) to a ubiquitin ligase (E3) or substrate. When cooperating with a RING-type E3, ubiquitin-conjugating enzymes can determine linkage specificity in ubiquitin chain formation. Our understanding of the regulation of E2 activities is still limited at a structural level. The work described here identifies two regulation mechanisms in UBE2S, a cognate E2 of the human RING-type E3 anaphase-promoting complex/cyclosome (APC/C). UBE2S elongates ubiquitin chains on APC/C substrates in a Lys11 linkage-specific manner, thereby targeting these substrates for degradation and driving mitotic progression. In addition, UBE2S was found to have a role in DNA repair by enhancing non-homologous end-joining (NHEJ) and causing transcriptional arrest at DNA damage sites in homologous recombination (HR). Furthermore, UBE2S overexpression is a characteristic feature of many cancer types and is connected to poor prognosis and diminished response to therapy. The first regulatory mechanism uncovered in this thesis involves the intramolecular auto-ubiquitination of a particular lysine residue (Lys+5) close to the active site cysteine, presumably through conformational flexibility of the active site region. The Lys+5-linked ubiquitin molecule adopts a donor-like, 'closed' orientation towards UBE2S, thereby conferring auto-inhibition. Notably, Lys+5 is a major physiological ubiquitination site in ~25\% of the human E2 enzymes, thus providing regulatory opportunities beyond UBE2S. Besides the active, monomeric state and the auto-inhibited state caused by auto-ubiquitination, I discovered that UBE2S can adopt a dimeric state. The latter also provides an auto-inhibited state, in which ubiquitin transfer is blocked via the obstruction of donor binding. UBE2S dimerization is promoted by its unique C-terminal extension, suppresses auto-ubiquitination and thereby the proteasomal degradation of UBE2S. Taken together, the data provided in this thesis illustrate the intricate ways by which UBE2S activity is fine-tuned and the notion that structurally diverse mechanisms have evolved to restrict the first step in the catalytic cycle of E2 enzymes.},
  subject      = {E2},
  language  = {en}
}
@phdthesis{Kasaragod2022,
  author    = {Kasaragod, Vikram Babu},
  title     = {Biochemical and Structural Basis for the Moonlighting Function of Gephyrin},
  doi       = {10.25972/OPUS-14307},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143077},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Neurons are specialized cells dedicated to transmit the nerve impulses throughout the human body across specialized structures called synapses. At the synaptic terminals, a crosstalk between multiple macromolecules regulates the structure and function of the presynaptic nerve endings and the postsynaptic recipient sites. Gephyrin is the central organizer at inhibitory postsynaptic specializations and plays a crucial role in the organization of these structures by anchoring GABAA receptors (GABAAR) and glycine receptors (GlyR) to the postsynaptic membrane. This 93 kDa protein features an N-terminal G domain and a C-terminal E domain and the latter interacts directly with the intracellular loop between transmembrane helices 3 and 4 of certain subunits of the GlyRs and GABAARs. Biochemical and structural analyses have already provided valuable insights into the gephyrin-GlyR interaction. Interestingly, biochemical studies on the gephyrin-GABAAR interaction demonstrated that the GABAARs also depend on the same binding site as the GlyRs for the interaction with the gephyrin, but the molecular basis for this receptor specific interaction of gephyrin was still unknown. Co-crystal structures of GephE-GABAAR α3- derived peptides with supporting biochemical data presented in this study deciphered the receptor-specific interactions of gephyrin in atomic detail. In its moonlighting function, gephyrin also catalyzes the terminal step of the evolutionarily conserved molybdenum cofactor biosynthesis. Molybdenum, an essential transition element has to be complexed with a pterin-based cofactor resulting in the formation of the molybdenum cofactor (Moco). Moco is an essential component at the active site of all molybdenum-containing enzymes with the exception of nitrogenase. Mutations in enzymes involved in this pathway lead to a rare yet severe disease called Moco deficiency, which manifest itself in severe neurodevelopmental abnormalities and early childhood death. Moco biosynthesis follows a complex multistep pathway, where in the penultimate step, the N-terminal G domain of gephyrin activates the molybdopterin to form an adenylated molybdopterin intermediate. In the terminal step, this intermediate is then transferred to the C-terminal E domain of gephyrin, which catalyzes the metal insertion and deadenylation reaction to form active Moco. Previous biochemical and structural studies provided valuable insights into the penultimate step of the Moco biosynthesis but the terminal step remained elusive. Through the course of my dissertation, I crystallized the C-terminal E domain in the apo-form as well as in complex with ADP and AMP. These structures shed lightonto the deadenylation reaction and the formation of a ternary E-domain-ADP-Mo/W complex and thus provide structural insight into the metal insertion mechanism. Moreover, the structures also provided molecular insights into a mutation leading to Moco deficiency. Finally, ternary complexes of GephE, ADP and receptor-derived peptides provided first clues regarding the integration of gephyrin's dual functionality. In summary, during the course of the dissertation I was able to derive high resolution structural insights into the interactions between gephyrin and GABAARs, which explain the receptor-specific interaction of gephyrin and, furthermore, these studies can be extended in the future to understand GABAAR subunit-specific interactions of gephyrin. Finally, the understanding of Moco biosynthesis shed light on the molecular basis of the fatal Moco deficiency.},
  subject      = {Gephyrin},
  language  = {en}
}
@phdthesis{Carstensen2018,
  author    = {Carstensen, Anne Carola},
  title     = {Identification of novel N-MYC interacting proteins reveals N-MYC interaction with TFIIIC},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143658},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {N-MYC is a member of the human MYC proto-oncogene family, which comprises three transcription factors (C-, N- and L-MYC) that function in multiple biological processes. Deregulated expression of MYC proteins is linked to tumour initiation, maintenance and progression. For example, a large fraction of neuroblastoma displays high N-MYC levels due to an amplification of the N-MYC encoding gene. MYCN-amplified neuroblastoma depend on high N-MYC protein levels, which are maintained by Aurora-A kinase. Aurora-A interaction with N-MYC interferes with degradation of N-MYC via the E3 ubiquitin ligase SCFFBXW7. However, the underlying mechanism of Aurora-A-mediated stabilisation of N-MYC remains to be elucidated. To identify novel N-MYC interacting proteins, which could be involved in N-MYC stabilisation by Aurora-A, a proteomic analysis of purified N-MYC protein complexes was conducted. Since two alanine mutations in MBI of N-MYC, T58A and S62A (N-MYC mut), disable Aurora-A-mediated stabilisation of N-MYC, N-MYC protein complexes from cells expressing either N-MYC wt or mut were analysed. Proteomic analysis revealed that N-MYC interacts with two deubiquitinating enzymes, USP7 and USP11, which catalyse the removal of ubiquitin chains from target proteins, preventing recognition by the proteasome and subsequent degradation. Although N-MYC interaction with USP7 and USP11 was confirmed in subsequent immunoprecipitation experiments, neither USP7, nor USP11 was shown to be involved in the regulation of N-MYC stability. Besides USP7/11, proteomic analyses identified numerous additional N-MYC interacting proteins that were not described to interact with MYC transcription factors previously. Interestingly, many of the identified N-MYC interaction partners displayed a preference for the interaction with N-MYC wt, suggesting a MBI-dependent interaction. Among these were several proteins, which are involved in three-dimensional organisation of chromatin domains and transcriptional elongation by POL II. Not only the interaction of N-MYC with proteins functioning in elongation, such as the DSIF component SPT5 and the PAF1C components CDC73 and CTR9, was validated in immunoprecipitation experiments, but also with the POL III transcription factor TFIIIC and topoisomerases TOP2A/B. ChIP-sequencing analysis of N-MYC and TFIIIC subunit 5 (TFIIIC5) revealed a large number of joint binding sites in POL II promoters and intergenic regions, which are characterised by the presence of a specific motif that is highly similar to the CTCF motif. Additionally, N-MYC was shown to interact with the ring-shaped cohesin complex that is known to bind to CTCF motifs and to assist the insulator protein CTCF. Importantly, individual ChIP experiments demonstrated that N-MYC, TFIIIC5 and cohesin subunit RAD21 occupy joint binding sites comprising a CTCF motif. Collectively, the results indicate that N-MYC functions in two biological processes that have not been linked to MYC biology previously. Furthermore, the identification of joint binding sites of N-MYC, TFIIIC and cohesin and the confirmation of their interaction with each other suggests a novel function of MYC transcription factors in three-dimensional organisation of chromatin.},
  subject      = {Biologie},
  language  = {en}
}
@phdthesis{ScheideNoeth2021,
  author    = {Scheide-N{\"o}th, Jan-Philipp},
  title     = {Activation of the Interleukin-5 receptor and its inhibition by cyclic peptides},
  doi       = {10.25972/OPUS-18250},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-182504},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The cytokine interleukin-5 (IL-5) is part of the TH2-mediated immune response. As a key regulator of eosinophilic granulocytes (eosinophils), IL-5 controls multiple aspects of eosinophil life. Eosinophils play a pathogenic role in the onset and progression of atopic diseases as well as hypereosinophilic syndrome (HES). Here, cytotoxic proteins and pro-inflammatory mediators stored in intracellular vesicles termed granula are released upon activation thereby causing local inflammation to fight the pathogen. However, if such inflammation persists, tissue damage and organ failure can occur. Due to the close relationship between eosinophils and IL-5 this cytokine has become a major pharmaceutical target for the treatment of atopic diseases or HES. As observed with other cytokines, IL-5 signals by assembling a heterodimeric receptor complex at the cell surface in a stepwise mechanism. In the first step IL-5 binds to its receptor IL-5Rα (CD125). This membrane-located complex then recruits the so-called common beta chain βc (CD131) into a ternary ligand receptor complex, which leads to activation of intracellular signaling cascades. Based on this mechanism various strategies targeting either IL-5 or IL-5Rα have been developed allowing to specifically abrogate IL-5 signaling. In addition to the classical approach of employing neutralizing antibodies against IL 5/IL-5Rα or antagonistic IL-5 variants, two groups comprising small 18 to 30mer peptides have been discovered, that bind to and block IL-5Rα from binding its activating ligand IL-5. Structure-function studies have provided detailed insights into the architecture and interaction of IL-5IL-5Rα and βc. However, structural information for the ternary IL-5 complex as well as IL-5 inhibiting peptides is still lacking. In this thesis three areas were investigated. Firstly, to obtain insights into the second receptor activation step, i.e. formation of the ternary ligand-receptor complex IL-5•IL-5Rα•βc, a high-yield production for the extracellular domain of βc was established to facilitate structure determination of the ternary ligand receptor assembly by either X-ray crystallography or cryo-electron microscopy. In a second project structure analysis of the ectodomain of IL-5Rα in its unbound conformation was attempted. Data on IL-5Rα in its ligand-free state would provide important information as to whether the wrench-like shaped ectodomain of IL-5Rα adopts a fixed preformed conformation or whether it is flexible to adapt to its ligand binding partner upon interaction. While crystallization of free IL-5Rα failed, as the crystals obtained did not diffract X rays to high resolution, functional analysis strongly points towards a selection fit binding mechanism for IL-5Rα instead of a rigid and fixed IL-5Rα structure. Hence IL-5 possibly binds to a partially open architecture, which then closes to the known wrench-like architecture. The latter is then stabilized by interactions within the D1-D2 interface resulting in the tight binding of IL-5. In a third project X-ray structure analysis of a complex of the IL-5 inhibitory peptide AF17121 bound to the ectodomain of IL-5Rα was performed. This novel structure shows how the small cyclic 18mer peptide tightly binds into the wrench-like cleft formed by domains D1 and D2 of IL-5Rα. Due to the partial overlap of its binding site at IL-5Rα with the epitope for IL-5 binding, the peptide blocks IL-5 from access to key residues for binding explaining how the small peptide can effectively compete with the rather large ligand IL-5. While AF17121 and IL-5 seemingly bind to the same site at IL-5Rα, functional studies however showed that recognition and binding of both ligands differ. With the structure for the peptide-receptor complex at hand, peptide design and engineering could be performed to generate AF17121 analogies with enhanced receptor affinity. Several promising positions in the peptide AF17121 could be identified, which could improve inhibition capacity and might serve as a starting point for AF17121-based peptidomimetics that can yield either superior peptide based IL-5 antagonists or small-molecule-based pharmacophores for future therapies of atopic diseases or the hypereosinophilic syndrome.},
  subject      = {Interleukin 5},
  language  = {en}
}
@phdthesis{Sander2014,
  author    = {Sander, Bodo},
  title     = {Structural and biochemical characterization of gephyrin and various gephyrin-ligand complexes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-104212},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {Efficient synaptic neurotransmission requires the exact apposition of presynaptic terminals and matching neurotransmitter receptor clusters on the postsynaptic side. The receptors are embedded in the postsynaptic density, which also contains scaffolding and regulatory proteins that ensure high local receptor concentrations. At inhibitory synapses the cytosolic scaffolding protein gephyrin assumes an essential organizing role within the postsynaptic density by the formation of self-oligomers which provide a high density of binding sites for certain -amino butyric acid type A (GABAA) and the large majority of glycine receptors (GlyR). Gephyrin contains two oligomerization domains: In isolation, the 20 kDa N-terminal G domain (GephG) and the 46 kDa E domain (GephE) trimerize and dimerize, respectively. In the full-length protein the domains are interconnected by a central ~150 amino acid linker, and only GephG trimerization is utilized, whereas GephE dimerization is prevented, thus suggesting the need for a trigger to release GephE autoinhibition, which would pave the way for the formation of higher oligomers and for efficient receptor clustering. The structural basis for this GephE autoinhibition has remained elusive so far, but the linker was reported to be sufficient for autoinhibition. This work dealt with the biochemical and structural characterization of apo-gephyrin and gephyrin in complexes with ligands which are known to promote the formation of synaptic gephyrin clusters (collybistin and neuroligin 2) and reorganize them (dynein light chain 1). For full-length gephyrin no structural information has been available so far. Atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) analyses described in this thesis disclosed that the gephyrin trimer forms a highly flexible assembly, which, due to the long linker, can switch between compact and extended conformational states in solution, with a preference for compact states. This partial compaction and potentially GephE autoinhibition are achieved by interactions of parts of the linker with the G and E domains, as suggested by circular dichroism spectroscopy. However, the linker on its own cannot account for GephE blockage, as size exclusion chromatography experiments coupled with multi angle light scattering detection (SEC-MALS) and SAXS analyses revealed that a gephyrin variant only encompassing the linker and GephE (GephLE) forms dimers and not monomers as suggested by an earlier study. The oligomeric state of GephLE and the observation that several gephyrin variants, in which linker segments of varying length were deleted, predominantly formed trimers, suggested the presence of a linker independent mechanism of GephE dimerization blockade. Taken together, the data indicated that linker-dependent and linker-independent mechanisms mediate gephyrin autoinhibition. In the second project gephyrin's interaction with DYNLL1 (Dynein LC8 Light Chain 1) was characterized. DYNLL1 is a 25 kDa dimer incorporated into the dynein motor and provides two binding sites, each of which can accommodate an octapeptide derived from gephyrin's linker region (referred to as GephDB). Originally, DYNLL1 was regarded as a cargo adaptor, linking gephyrin-GlyR complexes to the dynein motor, thus driving their retrograde transport and leading to a decrease of synaptic gephyrin-GlyR complexes. Building on these studies, this thesis assessed the cargo hypothesis as well as the so far unclear stoichiometry of the gephyrin-DYNLL1 complex. The cargo scenario would require ternary complex formation between gephyrin, DYNLL1 and the dynein intermediate chain (DIC) of the dynein motor. However, such a complex could not be detected by analytical size exclusion chromatography (aSEC) experiments - presumably because gephyrin and DIC competed for a common binding site in DYNLL1. This finding was consistent with a single DYNLL1 dimer capturing two linker segments of a single gephyrin trimer as suggested by a 26 kDa mass increase of the gephyrin species in the presence of DYNLL1 in SEC-MALS experiments. aSEC experiments at even higher concentrations (~20 µM gephyrin and ~80 µM DYNLL1) indicated that the affinity of GephDB was significantly impaired in the context of full-length gephyrin but also in a variant that bears only GephG and the first 39 residues of the linker (GephGL220). Presumably due to avidity effects two linkers stably associated with a single DYNLL1 dimer, whereas the third DYNLL1 binding motif remained predominantly unoccupied unless high concentrations of GephGL220 (50 µM) and DYNLL1 (200 µM) were used. These findings indicate that an interplay between GephG and the N-terminal linker segment mediates the attenuation of GephDB affinity towards DYNLL1 and that preventing DYNLL1 from the induction of higher gephyrin oligomers is either advantageous for DYNLL1-mediated reorganization of gephyrin-GlyR clusters or that DYNLL1 exerts possibly two (concentration-dependent) actions on gephyrin. The gephyrin-collybistin-neuroligin 2 complex was the subject of the third project. Previously, collybistin and gephyrin were observed to mutually trigger their translocation to the postsynaptic membrane, where the disordered cytoplasmic tail of the postsynaptic cell adhesion molecule NL2 (NL2cyt) causes the anchoring of collybistin 2 (CB2) by binding to its SH3 domain, thereby releasing SH3 domain mediated autoinhibiton of CB2 binding to the membrane phospholipid phosphatidylinositol-3-phosphate. Critical for this event is the binding of gephyrin to both CB2 and NL2, presumably via GephE. Following up on these previous studies biochemical data presented in this thesis confirm the formation of the ternary complex. Unexpectedly, analyses by means of native polyacrylamide gel electrophoresis pointed to: (1) The existence of a complex containing NL2cyt and CB2 lacking the SH3 domain and consequently an additional NL2 binding site in CB2. (2) Attenuated gephyrin-collybistin complex formation in the presence of the SH3 domain. (3) A requirement for high NL2cyt concentrations (> 30 µM) during the formation of the ternary complex. This might allow for the regulation by other factors such as additional binding partners or posttranslational modifications. Although of preliminary character, these results provide a starting point for future studies, which will hopefully elucidate the interplay between gephyrin, collybistin, NL2 and certain GABAA receptors.},
  subject      = {Gephyrin},
  language  = {en}
}
@phdthesis{Delto2015,
  author    = {Delto, Carolyn Francesca},
  title     = {Structural and Biochemical Characterization of the GABA(A) Receptor Interacting Protein Muskelin},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115922},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {In a study from 2011, the protein muskelin was described as a central coordinator of the retrograde transport of GABA(A) receptors in neurons. As muskelin governs the transport along actin filaments as well as microtubules, it might be the first representative of a novel class of regulators, which coordinate cargo transport across the borders of these two independent systems of transport paths and their associated motorproteins. To establish a basis for understanding the mode of operation of muskelin, the aim of this thesis was an in-depth biochemical and structural characterization of muskelin and its interaction with the GABA(A) receptor. One focus of the work was the analysis of the oligomerization of muskelin. As could be demonstrated, the oligomerization is based on two independent interactions mediated by different domains of the protein: a known interaction of the N-terminal discoidin domain with the C-terminal portion, termed head-to-tail interaction, and a dimerization of the LisH motif in muskelin that was so far neglected in the literature. For the detailed studies of both binding events, the solution of a crystal structure of a fragment of muskelin, comprising the Discoidin domain and the LisH motif, was an important basis. The fragment crystallized as a dimer, with dimerization being mediated solely by the LisH motif. Biochemical analysis corroborated that the LisH motif in muskelin serves as a dimerization element, and, moreover, showed that the C-terminal domain of the protein substantially stabilizes this dimerization. In addition, the crystal structure revealed the molecular composition of the surface of the head in the head-to-tail interaction, namely the discoidin domain. This information enabled to map the amino acids contributing to binding, which showed that the binding site of the head-to-tail interaction coincides with the generic ligand binding site of the discoidin domain. As part of the analyses, residues that are critical for LisH-dimerization and the head-to-tail binding, respectively, were identified, whose mutation specifically interfered with each of the interactions separately. These mutations allowed to investigate the interplay of these interactions during oligomerization. It could be shown that recombinant muskelin assembles into a tetramer to which both interactions, the LisH-dimerization and the head-to-tail binding, contribute independently. When one of the two interactions was disturbed, only a dimer mediated via the respective other interaction could be formed; when both interactions were disturbed, the protein was present as monomer. Furthermore, Frank Heisler in the group of Matthias Kneussel was able to show the drastic impact of an impaired LisH-dimerization on muskelin in cells using these mutations. Disturbing the LisH-dimerization led to a complete redistribution of the originally cytoplasmic muskelin to the nucleus which was accompanied by a severe impairment of its function during GABA(A) receptor transport. Following up on these results in an analysis of muskelin variants, for which alterations of the subcellular localization had been published earlier, the crucial influence of LisH-dimerization to the subcellular localization and thereby the role of muskelin in the cell was confirmed. The biochemical studies of the interaction of muskelin and the alpha1 subunit of the GABA(A) receptor demonstrated a direct binding with an affinity in the low micromolar range, which is mediated primarily by the kelch repeat domain in muskelin. For the binding site on the GABA(A) receptor, it was confirmed that the thirteen most C-terminal residues of the intracellular domain are critical for the binding of muskelin. In accordance with the strong conservation of these residues among the alpha subunits of the GABA(A) receptor, it could be shown that an interaction with muskelin in vitro is also possible for the alpha2 and alpha5 subunits. Based on the comparison of the binding sites between the homologous subunits, tentative conclusions can be drawn about the details of the binding, which may serve as a starting point for follow-up studies. This thesis thereby makes valuable contributions to the understanding of muskelin, in particular the significance of its oligomerization. It furthermore provides an experimental framework for future studies that address related topics, such as the characterization of other muskelin interaction partners, or the questions raised in this work.},
  subject      = {Oligomerisation},
  language  = {en}
}
@phdthesis{Ganesan2014,
  author    = {Ganesan, Jayavarshni},
  title     = {The role of microRNA-378 in cardiac hypertrophy},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-100918},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {MicroRNAs are endogenous ≈22 nt long non coding RNA molecules that modulate gene expression at the post transcriptional level by targeting mRNAs for cleavage or translational repression. MicroRNA-mRNA interaction involves a contiguous and perfect pairing within complementary sites usually in the 3' UTR of the target mRNA. Heart failure is associated with myocyte hypertrophy and death, due to compensatory pathological remodeling and minimal functional repair along with microRNA deregulation. In this study, we identified candidate microRNAs based on their expression strength in cardiomyocytes and by their ability to regulate hypertrophy. Expression profiling from early and late stages of heart failure showed several deregulated microRNAs. Of these microRNAs, miR-378 emerged as a potentially interesting microRNA that was highly expressed in the mouse heart and downregulated in the failing heart. Antihypertrophic activity of miR-378 was first observed by screening a synthetic miR library for morphologic effects on cardiomyocytes, and validated in vitro proving the tight control of hypertrophy by this miR. We combined bioinformatic target prediction analysis and microarray analysis to identify the targets of miR-378. These analyses suggested that factors of the MAP kinase pathway were enriched among miR-378 targets, namely MAPK1 itself (also termed ERK2), the insulin-like growth factor receptor 1 (IGF1R), growth factor receptor bound protein 2 (GRB2) and kinase suppressor of ras 1 (KSR1). Regulation of these targets by miR-378 was then confirmed by mRNA and protein expression analysis. The use of luciferase reporter constructs with natural or mutated miR-378 binding sites further validated these four proteins as direct targets of miR-378. RNA interference with MAPK1 and the other three targets prevented the prohypertrophic effect of antimiR-378, suggesting that they functionally relate to miR-378. In vivo restoration of disease induced loss of miR-378 in a pressure overload mouse model of hypertrophy using adeno associated virus resulted in partial attenuation cardiac hypertrophy and significant improvement in cardiac function along with reduced expression of the four targets in heart. We conclude from these findings that miR-378 is an antihypertrophic microRNA in cardiomyocytes, and the main mechanism underlying this effect is the suppression of the MAP kinase-signaling pathway on four distinct levels. Restoration of disease-associated loss of miR-378 through cardiomyocyte-targeted AAV-miR-378 may prove as an effective therapeutic strategy in myocardial disease.},
  subject      = {Hypertrophie},
  language  = {en}
}
@phdthesis{Bothe2021,
  author    = {Bothe, Sebastian Helmut},
  title     = {Fragmentbasiertes Design von p97-Liganden: Identifizierung von Startstrukturen zur Entwicklung von Protein-Protein-Interaktionsinhibitoren f{\"u}r die SHP-Bindestelle der AAA+ ATPase p97},
  doi       = {10.25972/OPUS-23911},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239112},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Die AAA+ ATPase p97 ist ein essenzielles Protein, das an einer Vielzahl zellul{\"a}rer Prozesse beteiligt ist und eine Schl{\"u}sselrolle in der Protein-Hom{\"o}ostase spielt. Die funktionale Diversit{\"a}t von p97 beruht auf der Interaktion zahlreicher unterschiedlicher Kofaktoren, die vorwiegend an die N-Dom{\"a}ne von p97 binden. Aufgrund seiner Bedeutung in der Regulierung diverser physiologischer und pathologischer Prozesse stellt p97 eine interessante Zielstruktur f{\"u}r die Entwicklung neuer Wirkstoffe dar, die insbesondere in der Krebstherapie von Bedeutung sein k{\"o}nnte. Bekannte p97-Inhibitoren greifen vor allem die ATPase-Funktion des Proteins an. Ein neuer pharmakologischer Ansatz stellt die Inhibierung der Kofaktorbindung an die N-Dom{\"a}ne dar. Ein solcher Protein-Protein-Interaktionsinhibitor w{\"a}re nicht nur von therapeutischem Interesse, sondern h{\"a}tte auch einen besonderen Nutzen f{\"u}r die Entschl{\"u}sselung molekularer und zellul{\"a}rer Funktionen von p97-Kofaktoren. In dieser Arbeit wurde ein fragmentbasierter Ansatz f{\"u}r die Identifizierung von chemischen Startstrukturen f{\"u}r die Entwicklung eines Protein-Protein- Interaktionsinhibitors verfolgt. Als Zielstruktur wurde die SHP-Bindestelle in der N-Dom{\"a}ne gew{\"a}hlt. Die Identifizierung von Liganden erfolgte sowohl durch computergest{\"u}tzte Methoden (insbesondere virtuelles Screening und Molekulardynamik-Simulationen) als auch experimentell durch biophysikalische Techniken (wie Biolayer-Interferometrie, R{\"o}ntgenstrukturanalyse und ligandbasierte NMR-Techniken). Die Grundlage des computerbasierten Designs stellte eine Analyse der bekannten Kristallstrukturen der p97-Komplexe mit den SHP-Motiven der Kofaktoren UFD1 und Derlin-1 dar. Dar{\"u}ber hinaus dienten Molekulardynamik-Simulationen der Analyse der Wassereigenschaften innerhalb der SHP-Bindestelle. Darauf aufbauend wurden verschiedene Pharmakophormodelle entwickelt, die die Grundlage des im Anschluss durchgef{\"u}hrten virtuellen Screenings und Dockings bildeten. Anhand der Ergebnisse von Molekulardynamik-Simulationen wurden zehn Verbindungen f{\"u}r die experimentelle Validierung ausgew{\"a}hlt. Hiervon konnten zwei Fragmente in STD-NMR- und Biolayer-Interferometrie-Experimenten als Liganden best{\"a}tigt werden. In einem parallel durchgef{\"u}hrten biophysikalischen Fragmentscreening mittels Biolayer-Interferometrie wurden unter mehr als 650 Verbindungen 22 identifiziert, die an die N-Dom{\"a}ne binden. 15 dieser Fragmente wurden durch einen orthogonalen STD-NMR-Assay best{\"a}tigt. F{\"u}nf dieser Verbindungen zeigten Affinit{\"a}ten mit KD-Werten kleiner 500μMund g{\"u}nstigen Ligandeffizienzen. Des Weiteren konnte die Bindungskinetik und Affinit{\"a}t des in der Literatur als p97-Inhibitor berichteten Naturstoffes Xanthohumol bestimmt und eine Bindung an die N-Dom{\"a}ne best{\"a}tigt werden. Zur Identifizierung m{\"o}glicher Bindestellen dieser f{\"u}nf Fragmente wurden mixed-solvent Molekulardynamik-Simulationen durchgef{\"u}hrt. Diese ergaben, dass alle Verbindungen die SHP-Bindestelle in der N-Dom{\"a}ne adressieren. Die Regionen fielen mit hot spots der Kofaktorwechselwirkungen zusammen und stellen somit m{\"o}gliche Ankerpunkte f{\"u}r die Weiterentwicklung dar. F{\"u}r zwei Fragmente konnten die postulierten Bindestellen mittels R{\"o}ntgenstrukturanalyse bzw. STD-NMR-Messungen an p97-Alanin-Mutanten best{\"a}tigt werden. Die erhaltene R{\"o}ntgenstruktur ist die erste p97-Struktur, die ein gebundenes Fragment an der N-Dom{\"a}ne zeigt.},
  subject      = {Arzneimitteldesign},
  language  = {de}
}
@phdthesis{TrujilloViera2022,
  author    = {Trujillo Viera, Jonathan},
  title     = {Protein kinase D2 drives chylomicron-mediate lipid transport in the intestine and promotes obesity},
  doi       = {10.25972/OPUS-26509},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-265095},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Obesity and associated metabolic syndrome are growing concerns in modern society due to the negative consequences for human health and well-being. Cardiovascular diseases and type 2 diabetes are only some of the pathologies associated to overweight. Among the main causes are decreased physical activity and food availability and composition. Diets with high content of fat are energy-dense and their overconsumption leads to an energy imbalance, which ultimately promotes energy storage as fat and obesity. Aberrant activation of signalling cascades and hormonal imbalances are characteristic of this disease and members of the Protein Kinase D (PKD) family have been found to be involved in several mechanisms mediating metabolic homeostasis. Therefore, we aimed to investigate the role of Protein Kinase D2 (PKD2) in the regulation of metabolism. Our investigation initiated with a mice model for global PKD2 inactivation, which allowed us to prove a direct involvement of this kinase in lipids homeostasis and obesity. Inactivation of PKD2 protected the mice from high-fat diet-induced obesity and improved their response to glucose, insulin and lipids. Furthermore, the results indicated that, even though there were no changes in energy intake or expenditure, inactivation of PKD2 limited the absorption of fat from the intestine and promoted energy excretion in feces. These results were verified in a mice model for specific deletion of intestinal PKD2. These mice not only displayed an improved metabolic fitness but also a healthier gut microbiome profile. In addition, we made use of a small-molecule inhibitor of PKD in order to prove that local inhibition of PKD2 in the intestine was sufficient to inhibit lipid absorption. The usage of the inhibitor not only protected the mice from obesity but also was efficient in avoiding additional body-weight gain after obesity was pre-established in mice. Mechanistically, we determined that PKD2 regulates lipids uptake in enterocytes by phosphorylation of Apolipoprotein A4 (APOA4) and regulation of chylomicron-mediated triglyceride absorption. PKD2 deletion or inactivation increased abundance of APOA4 and decreased the size of chylomicrons and therefore lipids absorption from the diet. Moreover, intestinal activation of PKD2 in human obese patients correlated with higher levels of triglycerides in circulation and a detrimental blood profile. In conclusion, we demonstrated that PKD2 is a key regulator of dietary fat absorption in murine and human context, and its inhibition might contribute to the treatment of obesity.},
  subject      = {Chylomicrons},
  language  = {en}
}
@phdthesis{Zink2023,
  author    = {Zink, Christoph},
  title     = {Biochemische und strukturbiologische Charakterisierung der Inhibition der Pyridoxal 5´-Phosphat Phosphatase durch 7,8-Dihydroxyflavon},
  doi       = {10.25972/OPUS-25151},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251511},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Die Pyridoxal-5'-Phosphat Phosphatase (PDXP), auch bekannt als Chronophin (CIN), ist eine HAD-Phosphatase, die beim Menschen ubiquit{\"a}r exprimiert wird und eine entscheidende Rolle im zellul{\"a}ren Vitamin-B6-Metabolismus einnimmt. PDXP ist in der Lage Pyridoxal-5'-Phosphat (PLP), die co-enzymatisch aktive Form von Vitamin B6, zu dephosphorylieren. In-vivo Studien mit M{\"a}usen zeigten, dass die Abwesenheit von PDXP mit verbesserten kognitiven Leistungen und einem verringerten Wachstum von Hirntumoren assoziiert ist. Dies begr{\"u}ndet die gezielte Suche nach einem pharmakologischen Inhibitor f{\"u}r PDXP. Ein Hochdurchsatz-Screen legte nahe, dass 7,8-Dihydroxyflavon (7,8-DHF) hierf{\"u}r ein potenzieller Kandidat ist. Zahlreiche Studien beschreiben bereits vielf{\"a}ltige positive neurologische Effekte nach in-vivo Administration von 7,8-DHF, allerdings bleibt der genaue Wirkmechanismus umstritten und wird bis dato nicht mit PDXP in Zusammenhang gebracht. Ziel dieser Arbeit ist es, die Inhibition von PDXP durch 7,8-DHF n{\"a}her zu charakterisieren und damit einen Beitrag zur Beantwortung der Frage zu leisten, ob PDXP an den 7,8-DHF-induzierten Effekten beteiligt ist. Hierzu wurde der Effekt von 7,8-DHF auf die enzymatische Aktivit{\"a}t von rekombinant hergestelltem, gereinigtem PDXP in in-vitro Phosphatase-Assays charakterisiert. Um die Selektivit{\"a}t von 7,8-DHF gegen{\"u}ber PDXP zu untersuchen, wurden f{\"u}nf weitere HAD-Phosphatasen getestet. Unter den analysierten Phosphatasen zeigte einzig die dem PDXP nah verwandte Phosphoglykolat Phosphatase (PGP) eine geringer ausgepr{\"a}gte Sensitivit{\"a}t gegen 7,8-DHF. Ein Vergleich von 7,8-DHF mit sechs strukturell verwandten, hydroxylierten Flavonen zeigte, dass 7,8-DHF unter den getesteten Substanzen die h{\"o}chste Potenz und Effektivit{\"a}t aufwies. Außerdem wurde eine Co-Kristallisation von PDXP mit 7,8-DHF durchgef{\"u}hrt, deren Struktur bis zu einer Aufl{\"o}sung von 2,0 {\AA} verfeinert werden konnte. Die in der Kristallstruktur identifizierte Bindungsstelle von 7,8-DHF an PDXP wurde mittels verschiedener, neu generierter PDXP-Mutanten enzymkinetisch best{\"a}tigt. Zusammenfassend zeigen die hier beschriebenen Ergebnisse, dass 7,8-DHF ein direkter, selektiver und vorwiegend kompetitiver Inhibitor der PDXP-Aktivit{\"a}t ist, mit einer IC50 im submikromolaren Bereich. Die Ergebnisse dieser in-vitro Untersuchungen motivieren zu weiterer Forschung bez{\"u}glich der 7,8-DHF-vermittelten Inhibition der PDXP-Aktivit{\"a}t in Zellen, um die Frage beantworten zu k{\"o}nnen, ob PDXP auch in-vivo ein relevantes Target f{\"u}r 7,8-DHF darstellt.},
  subject      = {Pyridoxalphosphat},
  language  = {de}
}
@phdthesis{Truongvan2023,
  author    = {Truongvan, Ngoc},
  title     = {Understanding the dual specificity of UBA6},
  doi       = {10.25972/OPUS-24457},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-244579},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Ubiquitylation is a protein post translational modification, in which ubiquitin is covalently attached to target protein substrates resulting in diverse cellular outcomes. Besides ubiquitin, various ubiquitin-like proteins including FAT10 exist, which are also conjugated to target proteins. The underlying modification mechanisms are conserved. In the initial step, ubiquitin or a ubiquitin-like protein is thioester-linked to a catalytic cysteine in the E1activating enzyme in an ATP-dependent manner. The respective protein modifier is then transferred to an E2 conjugating enzyme in a transthioesterification reaction. Finally, an E3 ubiquitin ligase E3 catalyzes the covalent attachment of the protein modifier to a substrate. In the case of ubiquitin, multiple ubiquitin molecules can be attached to a substrate in the form of either linear or branched polyubiquitin chains but also as single ubiquitin modifications. Depending on the nature of the ubiquitin chain, the substrates are destined to various cellular processes such as their targeted destruction by the proteasome but also non-degradative outcomes may occur. As stated above FAT10 is a ubiquitin-like protein modifier which typically targets proteins for proteasomal degradation. It consists of two ubiquitin-like domains and is mainly expressed in cells of the human immune system. The reported involvement of FAT10 modifications in cancers and other diseases has caught the attention of the scientific community as an inhibition of the FAT10ylation process may provide avenues for novel therapeutic approaches. UBA6 is the E1 activating enzyme that resides at the apex of the FAT10 proteasomal degradation pathway. UBA6 not only recognizes FAT10 but can also activate ubiquitin as efficiently as the ubiquitin specific E1 UBA1. The dual specificity of UBA6 may complicate the inhibition FAT10ylation since targeting the active site of UBA6 will also inhibit the UBA6-catalyzed ubiquitin activation. Therefore, it is important to understand the underlying principles for the dual specificity of UBA6 prior to the development of compounds interfering with FAT10ylation. In this thesis important novel insights into the structure and function of UBA6 were derived by X-ray crystallography and biochemical methods. The first crystal structure of UBA6 reveals the multidomain architecture of this enzyme in atomic detail. The enzyme is composed of a rigid core including its active and inactive adenylation domains as well as a 4 helix bundle. Overall, the molecule adopts a "Y" shape architecture with the core at the base and the first and second catalytic half domains forming one arm of the "Y" and the ubiquitin fold domain constituting the other arm. While UBA6 shares the same domain architecture as UBA1, substantial differences were revealed by the crystal structure. In particular, the first catalytic half domain undergoes a significant shift to a position more distal from the core. This rigid body movement is assumed to generate room to accommodate the second ubiquitin-like domain of FAT10. Differences are also observed in a hydrophobic platform between the core and the first catalytic half domain and the adenylation active site in the core, which together from the binding sites for ubiquitin and FAT10. Site directed mutagenesis of key residues in these areas altered the UBA6-catalyzed activation of ubiquitin and FAT10. UBA6 variants were generated with the goal of trying to block the activation of FAT10 while still maintaining that of ubiquitin activation, in order to fully explain the dual specificity of UBA6. However, none of these mutations could block the activation of FAT10, while some of these UBA6 variants blocked ubiquitin activation. Preliminary inhibition assays with a group of E1 inhibitors belonging to the adenosyl sulfamate family demonstrated potent inhibition of FAT10ylation for two compounds. The dual specificity of UBA6 hence needs to be further examined by biochemical and structural methods. In particular, the structure of a complex between UBA6 and ubiquitin or FAT10 would provide key insights for further biochemical studies, ultimately allowing the targeted inhibition of the FAT10ylation machinery.},
  language  = {en}
}
@phdthesis{PaciosMichelena2023,
  author    = {Pacios Michelena, Anabel},
  title     = {Molecular insights into the complex formed by the actin cytoskeleton related protein VASP and the inhibitory postsynaptic scaffolding protein gephyrin},
  doi       = {10.25972/OPUS-21337},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213373},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Gephyrin is a 93 kDa moonlighting protein, which is involved in the last two steps of the molybdenum cofactor (Moco) biosynthesis pathway while at the same time playing a central role in the anchoring, clustering and stabilization of glycine receptors (GlyRs) ...},
  language  = {en}
}
@phdthesis{Misra2020,
  author    = {Misra, Mohit},
  title     = {Knowing then defeating: The Ubiquitin activating enzyme, a promising target for cancer therapy},
  doi       = {10.25972/OPUS-16722},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167227},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Ubiquitin is a 76 amino acid long polypeptide, which is present throughout eukaryotes in a highly conserved fashion. Ubiquitin can modify proteins by becoming covalently attached to them. Eukaryotic cells employ ubiquitin to maintain and regulate fundamental cellular processes like protein degradation, the immune response and transcriptional and translational regulation. Transfer of ubiquitin to the substrate is achieved by the catalysis of three classes of enzymes namely E1, E2 and E3. Together these enzymes form a pyramidal hierarchy, where E1 stands at the apex and E3 enzymes form the base of the pathway. The ubiquitin activating enzyme 1 (UBA1) plays a major role in ubiquitylation being the ubiquitin-dedicated E1 enzyme. In addition, it is the only enzyme in this pathway to use ATP as an energy source to catalyze two important reactions. The products of these reactions, ubiquitin adenylate and ubiquitin thioester, are the essential intermediate states of ubiquitin, for being conjugated to the target protein. With the help of X-ray crystallography and biochemical approaches, snapshots of multiple catalytic states of UBA1, where it is bound to Mg-ATP, ubiquitin and the E2 Ubc13 as substrates could be captured. With the help of these high-resolution crystal structures, deeper insights into the enzymatic mechanism of UBA1 could be attained. The resulting insights into the catalytic cycle were further validated by biochemical assays. It could be shown that ATP acts as a molecular switch to induce the enzyme's open conformation. Ubiquitin-binding to the enzyme leads to domain rotations, which facilitate the recruitment of a cognate E2 enzyme. The interdomain communication as well as the cross-talk with the substrates and the products fuel the enzymatic cycle of UBA1. Due to the proven efficacy of proteasome inhibitors for cancer treatment, which block degradation of proteins labeled with ubiquitin, enzymes participating in the ubiquitylation cascade have been targeted by researchers for the development of novel anti-cancer therapeutics. UBA1 inhibition has been shown to preferentially induce cell death in malignant cells, and it can also be used as a strategy to overcome resistance against proteasome inhibitors. MLN7243, an adenosyl sulfamate inhibitor developed by Millenium Pharmaceutical to specifically target UBA1, is currently in Phase-I clinical trials for the treatment of solid tumors. UBA1 could be crystallized in complex with three adenosyl sulfamate inhibitors covalently linked to ubiquitin, which are promising drug candidates for cancer therapy. The inhibitors employed, MLN7243, MLN4924 and ABPA3, show distinct specificities towards different E1 enzymes. With the help of crystal structures the specificity determinants of these inhibitors could be deciphered, which were further confirmed by inhibition assays as well as molecular dynamics simulations. Together these crystal structures provide a starting point for developing E1-specific inhibitors, which, besides their potential for medicinal purposes, are important tools to better understand the function of the ubiquitin system as well as the action of ubiquitin-like proteins.},
  subject      = {Ubiquitin-aktivierende Enzym 1},
  language  = {en}
}
@phdthesis{Diebold2023,
  author    = {Diebold, Mathias},
  title     = {Virtuelles Screening und Entwicklung selektiver Liganden des Aurora-A - MYCN Komplexes und computergest{\"u}tzte Methoden zur Analyse und Design von PROTACs},
  doi       = {10.25972/OPUS-31759},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-317594},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Die Interaktion des onkogenen Transkriptionsfaktors MYCN mit der Ser/Thr Kinase Aurora-A verhindert dessen Abbau {\"u}ber das Ubiquitin Proteasomsystem indem die Rekrutierung des SCF FbxW7 Komplexes verhindert wird. Die Kinase nimmt mit der Bindung an MYCN eine aktive Konformation ein und erh{\"a}lt somit die F{\"a}higkeit zur Kinaseaktivit{\"a}t ohne die sonst notwendige Phosphorylierung von Thr288 oder die Anwesenheit eines Aktivators wie TPX2. Da hohe MYCN Konzentrationen Tumore wie Neuroblastome antreiben, ist die St{\"o}rung der Komplexbildung mit Aurora-A eine valide Strategie zur Entwicklung von Chemotherapeutika. Einige Inhibitoren von Aurora-A wie Alisertib (MLN8237) sind in der Lage, eine Konformations{\"a}nderung in der Kinase zu verursachen, die mit der Bindung von MYCN inkompatibel ist und auf diese Weise den Abbau des Transkriptionsfaktors induziert. Da Aurora-A wichtige Funktionen in der Mitose {\"u}bernimmt, k{\"o}nnte eine direkte Adressierung des Komplexes anstelle einer systemischen Inhibition der Kinase vielversprechender sein. Ziel des Projektes war die Identifizierung von Molek{\"u}len, die selektiv an das Interface des Aurora-A - MYCN Komplexes binden und weiter optimiert werden k{\"o}nnen, um einen gezielten Abbau des Transkriptionsfaktors {\"u}ber einen PROTAC Ansatz zu erm{\"o}glichen. Virtuelle Screenings und molekulardynamische Simulationen wurden durchgef{\"u}hrt, um kommerziell erh{\"a}ltliche Verbindungen zu identifizieren, welche mit einer Bindetasche des Komplexes interagieren, die nur zustande kommt, wenn beide Proteine miteinander interagieren. Aus einem ersten Set von zehn potentiellen Liganden wurde f{\"u}r vier eine selektive Interaktion mit dem Protein - Protein Komplex gegen{\"u}ber Aurora-A oder MYCN alleine in STD-NMR Experimenten best{\"a}tigt. Zwei der Hits besaßen ein identisches Grundger{\"u}st und wurden als Ausganspunkt f{\"u}r die Optimierung zu potenteren Liganden genutzt. Das Ger{\"u}st wurde fragmentweise vergr{\"o}ßert und in Richtung besserer in-silico Ergebnisse und Funktionalisierung zur Anbringung von E3-Ligase-Liganden optimiert. Neun dieser Liganden der zweiten Generation wurden synthetisiert. Um quantitative Bindungsdaten zu erhalten, wurde ein kovalent verkn{\"u}pftes Aurora-A - MYCN Konstrukt entworfen. Die strukturelle und funktionale Integrit{\"a}t wurde in STD-NMR und BLI Experimenten mit bekannten Aurora-A Inhibitoren best{\"a}tigt, sowie in NMR-basierten ATPase Assays. Zus{\"a}tzlich konnte die Kristallstruktur des Konstrukts gel{\"o}st und damit die Validit{\"a}t des Designs best{\"a}tigt werden. Quantitative Messungen der synthetisierten Molek{\"u}le identifizierten HD19S als Hit mit einer zehnfach h{\"o}heren Affinit{\"a}t f{\"u}r das Aurora-A - MYCN Konstrukt im Vergleich zu der Kinase allein. Zus{\"a}tzlich wurden in-silico Untersuchungen zu PROTACs der Aurora-A Kinase durchgef{\"u}hrt. Interaktionen zwischen Aurora-A, der E3-Ligase Cereblon und den Liganden wurden modelliert und f{\"u}r die Erkl{\"a}rung unterschiedlicher Aktivit{\"a}ten der eingesetzten PROTACs verwendet. Zudem zeigte das aktivste PROTAC eine hohe Selektivit{\"a}t f{\"u}r Aurora-A gegen{\"u}ber Aurora-B, obwohl die verwendete Erkennungseinheit (Alisertib) an beide Aurora-Proteine bindet. Dieser Umstand konnte durch energetische Analysen von molekulardynamischen Simulationen der tern{\"a}ren Komplexe erkl{\"a}rt werden. Optimierungsm{\"o}glichkeiten f{\"u}r eine effizientere Degradation von Aurora-A durch die PROTACs wurden basierend auf modifizierten Erkennungseinheiten und verbesserten Linkern untersucht.},
  subject      = {Arzneimitteldesign},
  language  = {de}
}
@phdthesis{Imam2023,
  author    = {Imam, Nasir},
  title     = {Molecular basis of collybistin conformational activation},
  doi       = {10.25972/OPUS-31145},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311458},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The nervous system relies on an orchestrated assembly of complex cellular entities called neurons, which are specifically committed to information management and transmission. Inter-neuronal communication takes place via synapses, membrane-membrane junctions which ensure efficient signal transfer. Synaptic neurotransmission involves release of presynaptic neurotransmitters and their reception by cognate receptors at postsynaptic terminals. Inhibitory neurotransmission is primarily mediated by the release of neurotransmitters GABA (γ-Aminobutyric acid) and glycine, which are precisely sensed by GABA type-A receptors (GABAARs) and glycine receptors (GlyRs), respectively. GABAAR assembly and maintenance is coordinated by various postsynaptic neuronal factors including the scaffolding protein gephyrin, the neuronal adaptor collybistin (CB) and cell adhesion proteins of the neuroligin (NL) family, specifically NL2 and NL4. At inhibitory postsynaptic specializations, gephyrin has been hypothesized to form extended structures underneath the plasma membrane, where its interaction with the receptors leads to their stabilization and impedes their lateral movement. Gephyrin mutations have been associated with various brain disorders, including autism, schizophrenia, Alzheimer's disease, and epilepsy. Furthermore, gephyrin loss is lethal and causes mice to die within the first post-natal day. Gephyrin recruitment from intracellular deposits to postsynaptic membranes primarily relies on the adaptor protein CB. As a moonlighting protein, CB, a guanine nucleotide exchange factor (GEF), also catalyzes a nucleotide exchange reaction, thereby regenerating the GTP-bound state of the small GTPase Cdc42 from its GDP-bound form. The CB gene undergoes alternative splicing with the majority of CB splice variants featuring an N-terminal SH3 domain followed by tandem Dbl-homology (DH) and pleckstrin-homology (PH) domains. Previous studies demonstrated that the most widely expressed, SH3-domain containing splice variant (CB2SH3+) preferentially adopts a closed conformation, in which the N-terminally located SH3 domain forms intra-molecular interaction with the DH-PH domain tandem. Previous cell-based studies indicated that SH3 domain-encoding CB variants remain untargeted and colocalize with intracellular gephyrin deposits and hence require additional factors which interact with the SH3 domain, thus inducing an open or active conformation. The SH3 domain-deficient CB isoform (CB2SH3-), on the contrary, adopts an open conformation, which possess enhanced postsynaptic gephyrin-clustering and also effectively replenishes the GTP-bound small GTPase-Cdc42 from its GDP-bound state. Despite the fundamental role of CB as a neuronal adaptor protein maintaining the proper function of inhibitory GABAergic synapses, its interactions with the neuronal scaffolding protein gephyrin and other post synaptic neuronal factors remain poorly understood. Moreover, CB interaction studies with the small GTPase Cdc42 and TC10, a closely related member of Cdc42 subfamily, remains poorly characterized. Most importantly, the roles of the neuronal factors and small GTPases in CB conformational activation have not been elucidated. This PhD dissertation primarily focuses on delineating the molecular basis of the interactions between CB and postsynaptic neuronal factors. During the course of my PhD dissertation, I engineered a series of CB FRET (F{\"o}rster Resonance Energy Transfer) sensors to characterize the CB interaction with its binding partners along with outlining their role in CB conformational activation. Through the aid of these CB FRET sensors, I analyzed the gephyrin-CB interaction, which, due to technical limitations remained unaddressed for more than two decades (refer Chapter 2 for more details). Subsequently, I also unraveled the molecular basis of the interactions between CB and the neuronal cell adhesion factor neuroligin 2 (refer chapter 2) and the small GTPases Cdc42 and TC10 (refer chapter 3) and describe how these binding partners induce a conformational activation of CB. In summary, this PhD dissertation provides strong evidence of a closely knit CB communication network with gephyrin, neuroligin and the small GTPase TC10, wherein CB activation from closed/inactive to open/active states is effectively triggered by these ligands.},
  language  = {en}
}
@phdthesis{Kawan2024,
  author    = {Kawan, Mona},
  title     = {The membrane trafficking protein myoferlin is a novel interactor of p97},
  doi       = {10.25972/OPUS-28121},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-281218},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {p97 uses the energy of ATP hydrolysis to unfold and thereby segregate proteins. It is involved in various cellular processes such as proteasomal degradation, DNA damage repair, autophagy, and endo-lysosomal trafficking. The specificity for these processes is controlled by more than 30 regulatory cofactors. Interactions of p97 with cofactors and target proteins are known to be highly dynamic and transient. To identify new interaction partners and to uncover novel cellular functions of p97, the interactome of endogenous p97 was determined by using in cellulo crosslinking followed by immunoprecipitation and mass spectrometry. Myoferlin (MYOF) was identified as a novel interactor of p97 and the interaction was validated in reciprocal immunoprecipitation experiments for different cell lines. The ferlin family member MYOF is a tail-anchored membrane protein containing multiple C2 domains. MYOF is involved in various membrane repair and trafficking processes such as the endocytic recycling of cell surface receptors. The MYOF interactome was determined by mass spectrometry. Among others, the p97 cofactor PLAA, CD71 and Rab14 were identified as common interactors of p97 and MYOF. Immunoprecipitation experiments with PLAA KO cells revealed that the interaction between MYOF and p97 depends on PLAA. Immunofluorescence microscopy showed a co-localization of MYOF with Rab14 and Rab11, which are both involved in endocytic recycling pathways. Furthermore, immunofluoroscence experiments revealed that MYOF and the p97 cofactor PLAA are localized to Rab14- and Rab5-positive endosomal compartments. Using p97 inhibitors and p97 trapping mutants, the presence of p97 at MYOF-positive and Rab14-positive structures could be demonstrated. Consistent with this finding, the endocytic recycling of transferrin was delayed upon inhibition of p97. Taken together, this work identified MYOF as a novel interactor of p97 and suggests a role for p97 in the recycling of endocytic cargo.},
  subject      = {Endosom},
  language  = {en}
}