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Top-down and bottom-up approaches are the general methods used to analyse proteomic samples today, however, the bottom-up approach has been dominant in the last decade. Establishing a bottom-up method involves not only the choice of adequate instruments and the optimisation of the experimental parameters, but also choosing the right experimental conditions and sample preparation steps. LC-ESI MS/MS has widely been used in this field due to its advanced automation. The primary objective of the present study was to establish a sensitive high-throughput nLC-MALDI MS/MS method for the identification and characterisation of proteins in biological samples. The method establishment included optimisation and validation of parameters such as the capillaries in the HPLC systems, gradient slopes, column temperature, spotting frequencies or the MS and MS/MS acquisition methods. The optimisation was performed using two HPLC-systems (Agilent 1100 series and Proxeon Easy nLC system), three spotters and the 4800 MALDI-TOF/TOF analyzer. Furthermore, samples preparation protocols were modified to fit to the established nLCMALDI- TOF/TOF-platform. The potentials of this method was demonstrated by the successful analysis of complex protein samples isolated from lipid particles, pre-adipocytes/adipocytes tissues, membrane proteins and proteins pulled-down from protein-proteins interaction studies. Despite the small amount of proteins in the lipid particles or oil bodies, and the challenges encountered in studying such proteins, 41(6 novel + 14 mammal specific + 21 visceral specific) proteins were added to the already existing proteins of the secretome of human subcutaneous (pre)adipocytes and 6 novel proteins localised in the yeast lipid particles. Protein-protein interaction studies present another area of application. Here the analytical challenges are mostly due to the loss of binding partner upon sample clean-up and to differentiate from non-specific background. Novel interaction partners for AF4•MLL and AF4 protein complex were identified. Furthermore, a novel sample protocol for the analysis of membrane proteins, based on the less specific protease, elastase, was established. Compared to trypsin, a higher sequence coverage and higher coverage of the transmembrane domains were achieved. The use of this enzyme in proteomics has been limited because of its non specific cleavage. However, from the results obtained in these studies, elastase was found to cleave preferentially at the C-terminal site of the amino acids AVLIST. The advantage of the established protocol over conventional protocols is that the same enzyme can be used for shaving of the soluble dormains of intact proteins in membranes and the digestion of the hydrophobic domain after solubilisation. Furthermore, the solvents used are compatible with the nLC-MALDI method setup. In addition, it was also shown that for less specific enzymes, a higher mass accuracy is required to reduce the rate of false positive identifications, since current search engines are not perfectly adapted for these types of enzymes. A brief statistical analysis of the MS/MS data obtained from the LC-MALDI TOF/TOF system showed that for less specific enzymes, under high-energy collision conditions, approximately 43 % of the fragment ions could not be matched to the known y- b type ions and their resultant internal fragments. This limitation greatly influenced the search results. However, this limitation can be overcome by modifying the N-terminal amino acids with basic moieties such as TMT. The use of elastase as a digestion enzyme in proteomic workflow further increased the complexity of the sample. Therefore, orthogonal multidimensional separation was necessary. Offgel-IEF was used as the separation technique for the first dimension. Here peptides are separated according to the pI. However, the acquired samples could not be loaded to the nLC due to the high viscosity of the concentrated samples when using the standard protocol. In order to achieve compatibility of the Offgel-IEF to the nLC-MALDI-TOF/TOF-platform, the separation protocol of the Offgel-IEF was modified by omitting the glycerol, which was the cause of the viscous solution. The novel glycerol free protocol is advantageous over the conventional method because the samples could directly be picked-up and loaded onto the pre-column without resulting in an increase in back pressure or a subsequent pre-column clogging. The glycerol free protocol was then assessed using purple membrane and membrane fraction of C. glutamicum. The results obtained were comparable to those applied in published reports. Therefore, the absence of glycerol did not affect the separation efficiency of the Offgel-IEF. In addition the applicability of elastase and the glycerol free Offgel-IEF for quantitation of membrane proteins was assessed. Most of the unique peptides identified were in the acidic region and 85 % were focused only into one fraction and approximately 95 % in only two fractions. These results are in accordance with previously published results (Lengqvist et al., 2007). When compared with theoretical digests of the proteins identified in this study, it can be concluded that basic moiety (TMT) on the peptide backbone, did not affect the separation efficiency of the Offgel-IEF. In an applied study, changes in the protein content of yeast strain grown in two different media were relatively quantified. For example, prominent proteins, such as the hexose tranporter proteins responsible for transporting glucose accross the membrane, were successfully quantified. Last but not least, the nLC-MALDI-TOF/TOF platform also served as a basis for the development of a high-throughput method for the identification of protein phosphorylation. The establishment of such a method using MALDI has been challenging due to the lack of sensitive matrices, such as CHCA for non-modified peptides, which exhibit a homogenous crystallisation and thus yield stable signal intensity over a long period of time in an automated setup. The first step of this method was the establishment of a matrix/matrix mixture with better crystal morphology and higher analyte signal intensity than the matrix of choice, i.e. DHB. From MS and MS/MS measurements of standard phosphopeptides, a combination of FCCA and CHAC in a 3:1 ratio and 3 mM NH4H2PO4 facilitated high analyte signal intensities and good fragmentation behaviour. Combining a custom-packed biphasic column for the enrichment of phosphopeptides, the applicability of the matrix mixture was assessed in anautomated phosphopeptide analysis using standard phosphopeptides spiked to a 20-fold excess BSA digest. These analyses showed that this method is reproducibile and both flow throughs can be analysed. Applying the method to the analysis of 2 standard phosphoproteins, alpha/beta-casein, and a leukemia related protein, ENL, 13 phosphopeptides from both alpha/beta-Casein and 13 phosphopeptides with 6 phosphorylation sites from the ENL were identified. As a general conclusion, it can be stated that the nLC-MALDI-TOF/TOF method established here in various modifications for different analytical purposes is a robust platform for proteomic analyses.
Development of a computational method for reaction-driven de novo design of druglike compounds
(2010)
A new method for computer-based de novo design of drug candidate structures is proposed. DOGS (Design of Genuine Structures) features a ligand-based strategy to suggest new molecular structures. The quality of designed compounds is assessed by a graph kernel method measuring the distance of designed molecules to a known reference ligand. Two graph representations of molecules (molecular graph and reduced graph) are implemented to feature different levels of abstraction from the molecular structure. A fully deterministic construction procedure explicitly designed to facilitate synthesizability of proposed structures is realized: DOGS uses readily available synthesis building blocks and established reaction schemes to assemble new molecules. This approach enables the software to propose not only the final compounds, but also to give suggestions for synthesis routes to generate them at the bench. The set of synthesis schemes comprises about 83 chemical reactions. Special focus was put on ring closure reactions forming drug-like substructures. The library of building blocks consists of about 25,000 readily available synthesis building blocks. DOGS builds up new structures in a stepwise process. Each virtual synthesis step adds a fragment to the growing molecule until a stop criterion (upper threshold for molecular mass or number of synthesis steps) is fulfilled. In a theoretical evaluation, a set of ~1,800 molecules proposed by DOGS is analyzed for critical properties of de novo designed compounds. The software is able to suggest drug-like molecules (79% violate less than two of Lipinski’s ‘rule of five’). In addition, a trained classifier for drug-likeness assigns a score >0.8 to 51% of the designed molecules (with 1.0 being the top score). In addition, most of the DOGS molecules are deemed to be synthesizable by a retro-synthesis descriptor (77% of molecules score in the top 10% of the decriptor’s value range). Calculated logP(o/w) values of constructed molecules resemble a unimodal distribution centred close to the mean of logP(o/w) values calculated for the reference compounds. A structural analysis of selected designs reveals that DOGS is capable of constructing molecules reflecting the overall topological arrangement of pharmacophoric features found in the reference ligands. At the same time, the DOGS designs represent innovative compounds being structurally distinct from the references. Synthesis routes for these examples are short and seem feasible in most cases. Some reaction steps might need modification by using protecting groups to avoid unwanted side reactions. Plausible bioisosters for known privileged fragments addressing the S1 pocket of trypsin were proposed by DOGS in a case study. Three of them can be found in known trypsin inhibitors as S1-adressing side chains. The software was also tested in two prospective case studies to design bioactive compounds. DOGS was applied to design ligands for human gamma-secretase and human histamine receptor subtype 4 (hH4R). Two selected designs for gamma-secretase were readily synthesizable as suggested by the software in one-step reactions. Both compounds represent inverse modulators of the target molecule. In a second case study, a ligand candidate selected for hH4R was synthesized exactly following the three-step synthesis plan suggested by DOGS. This compound showed low activity on the target structure. The concept of DOGS is able to deliver synthesizable and bioactive compounds. Suggested synthesis plans of selected compounds were readily pursuable. DOGS can therefore serve as a valuable idea generator for the design of new pharmacological active compounds.
Biodegradation and elimination of industrial wastewater in the context of whole effluent assessment
(2010)
The focus of this thesis is on the assessment of the degradability of indirectly discharged wastewater in municipal treatment plants and on assessing indirectly discharged effluents by coupling the Zahn-Wellens test with effect-based bioassays. With this approach persistent toxicity of an indirectly discharged effluent can be detected and attributed to the respective emission source. In the first study 8 wastewater samples from different industrial sectors were analysed according to the “Whole-Effluent Assessment“ (WEA) approach developed by OSPAR. In another study this concept has been applied with 20 wastewater samples each from paper manufacturing and metal surface treating industry. In the first study generally low to moderate ecotoxic effects of wastewater samples have been determined. One textile wastewater sample was mutagenic in the Ames test and genotoxic in the umu test. The source of these effects could not be identified. After treatment in the Zahn-Wellens test the mutagenicity in the Ames test was eliminated completely while in the umu test genotoxicity could still be observed. Another wastewater sample from chemical industry was mutagenic in the Ames test. The mutagenicity with this wastewater sample was investigated by additional chemical analysis and backtracking. A nitro-aromatic compound (2-methoxy-4-nitroaniline) used for batchwise azo dye synthesis and its transformation products are the probable cause for the mutagenic effects analysed. Testing the mother liquor from dye production confirmed that this partial wastewater stream was mutagenic in the Ames test. The wasteweater samples from paper manufacturing industry of the second study were not toxic or genotoxic in the acute Daphnia test, fish egg test and umu test. In the luminescent bacteria test, moderate toxicity was observed. Wastewater of four paper mills demonstrated elevated or high algae toxicity, which was in line with the results of the Lemna test, which mostly was less sensitive than the algae test. The colouration of the wastewater samples in the visible band did not correlate with algae toxicity and thus is not considered as its primary origin. The algae toxicity in wastewater of the respective paper factory could also not be explained with the thermomechanically produced groundwood pulp (TMP) partial stream. Presumably other raw materials such as biocides might be the source of algae toxicity. In the algae test, often flat dose–response relationships and growth promotion at higher dilution factors have been observed, indicating that several effects are overlapping. The wastewater samples from the printed circuit board and electroplating industries (all indirectly discharged) were biologically pre-treated for 7 days in the Zahn–Wellens test before ecotoxicity testing. Thus, persistent toxicity could be discriminated from non-persistent toxicity caused, e.g. by ammonium or readily biodegradable compounds. With respect to the metal concentrations, all samples were not heavily polluted. The maximum conductivity of the samples was 43,700 micro S cm -1 and indicates that salts might contribute to the overall toxicity. Half of the wastewater samples proved to be biologically well treatable in the Zahn–Wellens test with COD elimination above 80%, whilst the others were insufficiently biodegraded (COD elimination 28–74%). After the pre-treatment in the Zahn–Wellens test, wastewater samples from four companies were extremely ecotoxic especially to algae. Three wastewater samples were genotoxic in the umu test. Applying the rules for salt correction to the test results following the German Wastewater Ordinance, only a small part of toxicity could be attributed to salts. In one factory, the origin of ecotoxicity has been attributed to the organosulphide dimethyldithiocarbamate (DMDTC) used as a water treatment chemical for metal precipitation. The assumption, based on rough calculation of input of the organosulphide into the wastewater, was confirmed in practice by testing its ecotoxicity at the corresponding dilution ratio after pre-treatment in the Zahn–Wellens test. The results show that bioassays are a suitable tool for assessing the ecotoxicological relevance of these complex organic mixtures. The combination of the Zahn–Wellens test followed by the performance of ecotoxicity tests turned out to be a cost-efficient suitable instrument for the evaluation of indirect dischargers and considers the requirements of the IPPC Directive.
Purpose of the Study: The purpose of the current study was to evaluate the role of radiofrequency (RF) and microwave (MW) ablation in the treatment of pulmonary neoplasms. Materials and Methods: From March 2004 to January 2009, 164 patients (92 males, 72 females; mean age 59.7 years, SD: 10.2) underwent computed tomography (CT)-guided percutaneous RFA of pulmonary malignancies. RFA was performed on 248 lung lesions (20 primary lesions and 228 metastatic lesions) in 248 sessions (one lesion per session). Tumors were pathologically proven and were classified as primary lung neoplasms in 20 patients (non-small cell lung cancer) and as metastatic lung neoplasms in 144 patients. RFA was performed using: a) CelonProSurge bipolar internally cooled applicator b) RITA®StarburstTMXL. From December 2007 to October 2009, 80 patients (30 males, 50 females; mean age 59.7 years, range: 48-68, SD: 6.4) underwent computed tomography (CT) guided percutaneous MW ablation of pulmonary metastases from variable histopathological primaries. MW was performed on 130 lung lesions in 130 sessions (one lesion per session) using Valleylab TM system. Results: The overall success rate of RFA was 67.7% (168/248 lesions), with overall failure rate either due to tumor residue or recurrence on follow up in 32.3% (80/248) with mean time to tumor progress was 5.6 months SD: 2.99 (Range:1-18 months). Complete successful ablation was achieved in patients treated by MWA in 73.1% (95/130 lesions), with failure rate either due to tumor residue or recurrence on follow up in 26.9% (35/130) with mean time to tumor progress 6 months SD: 2.83 (Range:1-12months). Correlation of the histopathological type of the lesion and the end result of ablation therapy revealed insignificant correlation in both RFA and MWA (p > 0.1). The preablation tumor size was one of the most significant factors that determined the end result of ablation. In RFA successful tumor ablation was significant statistically for lesions with maximal axial diameter up to 2.5 cm (110/140) in comparison to lesions of more than 2.5 cm in maximal axial diameter (58/108) (Fisher’s exact test: p < 0.0001). While in MW ablated lesions successful tumor ablation was significant statistically for lesions with maximal axial diameter up to 3 cm (90/110) in comparison to lesions of more than 3 cm in maximal axial diameter (5/20) (Fisher’s exact test: p < 0.001). The location of the lesion was another important factor that determined the end result of ablation. In both RFA and MWA successful ablation was significantly more correlated to peripheral lesions (RFA: 120/160, 80% / MWA: 80/100, 80%) than centrally located lesions (RFA: 48/88, 50%; MWA: 15/30, 50%) (Fisher’s Exact Test: p > 0.001). For successfully RFA ablated cases mean preablation tumor volumes 1.9 cc SD: 0.9 (range: 0.3 - 4.25 cc) while for failed cases the mean tumor volume was 3.7 SD: 2.4 (range: 0.8 – 6.8cc). For successfully MW ablated cases the mean preablation tumor volume: 2.4 cc SD: 2.2 (range: 0.25-8.2 cc) while for failed cases the mean tumor volume was 3.5 SD: 2.6 (range: 0.3 – 7.1 cc). In RFA the survival rates at 12, 24 and 36 months were 90%, 78% and 68% respectively while in MWA treated patients the survival rate within 12 months follow up period was 96% while at 20 month the survival rate was 77%. Complications associated with the ablation therapy were: a) procedure related mortality: 0.4% (1/248) in RFA due to massive pulmonary hemorrhage versus 0% (0/130) in MWA, b) pneumothorax: 11.3% (28/240) in RFA versus 8.5% (11/130) in MWA, c) pulmonary Hemorrhage: 17.7% (44 of 248 sessions) of which one patient had massive uncontrolled bleeding and immediate death versus 6.2% (8/130) in MWA, d) pleural effusion: 3.2 % (8 of 248 sessions) in RFA versus 3.8 % (6/130) in MWA, e) hemoptysis: 4% (10/248) in RFA versus 4.6% (6/130) in MWA ranging from mild tinged sputum to frank bleeding, f) infection: 0.4% (1/248) in RFA, versus 0% in MWA, and g) post ablation pain: 10% (25/248) in RFA versus 9.2% (12/130) in MWA. Pain was generally adequately controlled by analgesics. Conclusion: Radiofrequency and microwave ablation are effective minimally invasive tools and may be safely applied for management of lung malignancy. The success of ablation therapy is significantly correlated to the preablation tumor size, volume and tumor location.
G-protein coupled receptors (GPCRs) are the key players in signal perception and transduction and one of the currently most important class of drug targets. An example of high pharmacological relevance is the human endothelin (ET) system comprising two rhodopsin-like GPCRs, the endothelin A (ETA) and the endothelin B (ETB) receptor. Both receptors are major modulators in cardiovascular regulation and show striking diversities in biological responses affecting vasoconstriction and blood pressure regulation as well as many other physiological processes. Numerous disorders are associated with ET dysfunction and ET antagonism is considered an efficient treatment of diseases like heart failure, hypertension, diabetes, artherosclerosis and even cancer. This study exemplifies strategies and approaches for the preparative scale synthesis of GPCRs in individual cell-free (CF) systems based on E. coli, a newly emerging and promising technique for the production of even very difficult membrane proteins. The preparation of high quality samples in sufficient amounts is still a major bottleneck for the structural determination of the ET receptors. Heterologous overexpression has been a challenge now for decades but extensive studies with conventional cell-based systems had only limited success. A central milestone of this study was the development of efficient preparative scale expression protocols of the ETA receptor in qualities sufficient for structural analysis by using individual CF systems. Newly designed optimization strategies, the implementation of a variety of CF expression modes and the development of specific quality control assays finally resulted in the production of several milligrams of ETA receptor per one millilitre of reaction mixture. The versatility of CF expression was extensively used to modulate GPCR sample quality by modification of the solubilization environment with detergents and lipids in a variety of combinations at different stages of the production process. Downstream processing procedures of CF synthesized GPCRs were systematically optimized and sample properties were analysed with respect to homogeneity, protein stability and receptor ligand binding competence. Evaluation was accomplished by an array of complementary and specifically modified techniques. Depending on its hydrophobic environment, CF production of the ETA receptor resulted in non-aggregated, monodisperse forms with sufficient long-term stability and high degrees of secondary structure thermostability. The obtained results document the CF production of the ETA receptor in two different modes as an example of a class A GPCR in ligand-binding competent and non-aggregated form in quantities sufficient for structural approaches. The presented strategy could serve as basic guideline for the production of related receptors in similar systems.
In this work we study compact stars, i.e. neutron stars, as cosmic laboratories for the nuclear matter. With a mass of around 1 - 3 solar masses and a radius of around 10km, compact stars are very dense and, besides nucleons, can contain exotic matter such as hyperons or quark matter. The KaoS collaboration studied nuclear matter for densities up to 2-3 times saturation density by analysing kaon multiplicities from Au+Au and C+C collisions. The results show that nuclear matter in the corresponding density region is very compressible, with a compressibility of <200MeV. For such soft nuclear equations of state the maximum masses of neutron stars are ca. 1.8 - 1.9 solar masses, whereas the central densities are higher than 5 times nuclear saturation density and therefore point towards a possible phase transition to quark matter. If quark matter would be present in the interior of neutron stars, so-called hybrid stars, it could be produced already during their birth in supernova explosions. To study this we implement a quark matter phase transition in a hadronic equation of state which is used in supernova simulations. Supernova simulations of low and intermediate mass progenitors and two different bag constants show a collapse of the proto neutron star due to the softening of the equations of state in the quark-hadron mixed phase. The stiffening of the equation of state for pure quark matter halts the collapse and leads to the production of a second shock wave. The second shock wave is energetic enough to lead to an explosion of the star and produces a neutrino burst when passing the neutrinospheres. Furthermore, first studies of the longtime cooling of hybrid stars show, that colour superconductivity can significantly influence the cooling behaviour of hybrid stars, if all quarks form Cooper Pairs. For the so-called CSL phase (colour-spin locking) with pairing energies of several MeV, the cooling of the quark phase is suppressed and the hybrid star appears as a pure hadronic star.
Vibronic (vibrational-electronic) transition is one of the fundamental processes in molecular physics. Indeed, vibronic transition is essential both in radiative and nonradiative photophysical or photochemical properties of molecules such as absorption, emission, Raman scattering, circular dichroism, electron transfer, internal conversion, etc. A detailed understanding of these transitions in varying systems, especially for (large) biomolecules, is thus of particular interest. Describing vibronic transitions in polyatomic systems with hundreds of atoms is, however, a difficult task due to the large number of coupled degrees of freedom. Even within the relatively crude harmonic approximation, such as for Born-Oppenheimer harmonic potential energy surfaces, the brute-force evaluation of Franck-Condon intensity profiles in a time-independent sum-over-states approach is prohibitive for complex systems owing to the vast number of multi-dimensional Franck-Condon integrals. The main goal of this thesis is to describe a variety of molecular vibronic transitions, with special focus on the development of approaches that are applicable to extended molecular systems. We use various representations of Fermi’s golden rule in frequency, time and phase spaces via coherent states to reduce the computational complexity. Although each representation has benefits and shortcomings in its evaluation, they complement each other. Peak assignment of a spectrum can be made directly after calculation in the frequency domain but this sum-over-states route is usually slow. In contrast, computation is considerably faster in the time domain with Fourier transformation but the peak assignment is not directly available. The representation in phase space does not immediately provide physically-meaningful quantities but it can link frequency and time domains. This has been applied to, herein, for example (non-Condon) absorption spectra of benzene and electron transfer of bacteriochlorophyll in the photosynthetic reaction center at finite temperature. This work is a significant step in the treatment of vibronic structure, allowing for the accurate and efficient treatment of complex systems, and provides a new analysis tool for molecular science.
Succinate:quinone oxidoreductases (SQORs) are integral membrane protein complexes, which couple the two-electron oxidation of succinate to fumarate (succinate → fumarate + 2H+ + 2e-) to the two-electron reduction of quinone to quinol (quinone + 2H+ + 2e- → quinol) as well as catalyzing the opposite reaction, the reduction of fumarate by quinol. In mitochondria and some aerobic bacteria, succinate:ubiquinone reductase, also known as complex II of the aerobic respiratory chain or as succinate dehydrogenase from the tricarboxylic acid (TCA or Krebs) cycle, catalyzes the oxidation of succinate by ubiquinone, which is mildly exergonic under standart conditions and not directly associated with energy storage in the form of a transmembrane electrochemical proton potential (Δp). Gram-positive bacteria do not contain ubiquinone but rather menaquinone, a quinone with significantly lower oxidation-reduction (“redox”) midpoint potential. In these cases, the catalyzed oxidation of succinate by quinone is endergonic under standard conditions. Consequently, these bacteria face a thermodynamic problem in supporting the catalysis of this reaction in vivo. Based on experimental evidence obtained on whole cells and purified membranes, it had previously been proposed that the SQR from Gram-positive bacteria supports this reaction at the expense of the protonmotive force, Δp. Nonetheless, it has been argued that the observed Δp dependence is not associated specifically with the activity of SQR because the occurrence of artifacts in experiments with bacterial membranes and whole cells can not be fully excluded. Clearly, definitive insight into the mechanism of catalysis of this intriguing reaction required a corresponding functional characterization of an isolated, membranebound SQR from a Gram-positive bacterium. The first aim of the present work addresses the question if the general feasibility of the energetically uphill electron transfer from succinate to menaquinone is associated specifically to a single enzyme complex, the SQR. The prerequisite to achieve this goal was stable preparation of this enzyme.
The glycine receptor (GlyR) is the major inhibitory neurotransmitter receptor in spinal cord and brainstem. Heteropentameric GlyRs are clustered and anchored at inhibitory postsynaptic sites by the binding of the large intracellular loop between transmembrane domains 3 and 4 of the GlyRbeta subunit (GlyRbeta-loop) to the cytoplasmic scaffolding protein gephyrin. GlyRs are also cotransported with gephyrin along microtubules in the anterograde and retrograde direction due to the binding of gephyrin to microtubule-associated motor proteins. Additionally, GlyRs undergo lateral diffusion in the plasma membrane from extrasynaptic to synaptic sites and vice versa. Since its discovery, gephyrin has remained for many years the only binding partner interacting directly with the GlyRbeta subunit. In an attempt to elucidate further mechanisms involved in GlyR function and regulation at inhibitory postsynaptic sites, a proteomic screen for putative binding partners to the GlyRbeta loop was performed. Three proteins were identified as putative interactors. In this thesis, the interaction between these putative binding proteins and the GlyRbeta subunit was analyzed and characterized. Binding studies with glutathione-S-transferase fusion proteins revealed that all putative binding proteins, Syndapin (Sdp), Vacuolar Protein Sorting 35 (Vps35) and Neurobeachin (Nbea), interact specifically with the GlyRbeta loop. The Sdp family of proteins are F-BAR and SH3 domain containing proteins. Inmmunocytochemical experiments showed that SdpI as well as the isoforms SdpII-S and SdpIIL colocalize with the full-length GlyRbeta subunit in a mammalian cell expression system. In cultured spinal cord neurons, a partial colocalization of endogenous SdpI with several excitatory and inhibitory synaptic markers was demonstrated. Mapping experiments using deletion mutants narrowed the SdpI binding site down to 22 amino acids. Peptide competition experiments confirmed the specificity of the interaction between SdpI and this sequence of the GlyRbeta subunit. Point mutation analysis revealed a SH3-proline rich domain dependent interaction between SdpI and the GlyRbeta subunit, respectively. In addition, binding studies in mammalian cells showed that both splice variants of SdpII as well as SdpI interact with the GlyR scaffolding protein gephyrin. Although the SdpI and gephyrin binding sites do not overlap, protein competition studies revealed that interaction of the E-domain of gephyrin with the GlyRbeta loop interferes with SdpI binding. Since SdpI is a dynamin binding protein involved in vesicle endocytosis and recycling pathways, a possible function of SdpI in the regulation of GlyR synaptic distribution was investigated. Co-immunoprecipitation experiments confirmed a SdpI-GlyR association in the vesicle-enriched fraction of rat spinal cord tissue. Immunocytochemical studies of SdpI knock out mice showed that the clustering and distribution of GlyRs in the brain stem is unchanged. However, acute down-regulation of SdpI in rat spinal cord neurons by viral shRNA expression led to a reduction in the number and size of GlyR clusters, an effect that could be rescued upon shRNA-resistant SdpI overexpression. Further immunocytochemical analysis of the localization of gephyrin, the gamma2 subunit of the type A gamma-aminobutyric acid receptor (GABAARgamma2 subunit) and the vesicular inhibitory amino acid transporter (VIAAT) under SdpI knock-down conditions showed that both the number and average size of the gamma2-subunit containing GABAA receptor clusters were significantly reduced in spinal cord neurons. In contrast to GlyR and GABAARgamma2 immunoreactivity, the number and average size of gephyrin and VIAAT clusters were barely reduced upon SdpI downregulation. These results suggest that SdpI has a role in GlyR trafficking that can be compensated by other syndapin isoforms or other trafficking pathways. Furthermore, SdpI might be required for the clusters of GlyRs and gamma2-subunit containing GABAARs in spinal cord and brainstem. Vps35 is the core protein of the retromer complex, which mediates the endosome to Golgi apparatus retrieval of different types of receptors in mammals and yeast. Here, protein-protein interaction assays revealed for the first time that Vps35 interacts directly with the GlyRbeta loop as well as with gephyrin. The generation of specific Vps35 antibodies allowed to determine the distribution of this protein in the central nervous system. Immunocytochemical analyses revealed the presence of Vps35 in the somata and neurites of spinal cord neurons, suggesting a possible interaction of Vps35 with the GlyR under physiological conditions. Nbea is a BEACH domain containing, neuron-specific protein. Binding studies revealed a direct interaction between two regions of Nbea and the GlyRbeta loop. Immunocytochemical experiments confirmed a somatic and synaptic distribution of Nbea in primary cultures. In spinal cord neurons, a partial colocalization of Nbea with excitatory and inhibitory synaptic markers suggests a possible interaction of Nbea with the GlyR at inhibitory synaptic sites.