Biochemie und Chemie
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Within the framework of the eigenchannel reaction theory above the two-particle thresholdcluster channels are introduced. The eigenchannels of the S-matrix are used, i. e. continuum stateswhich diagonalize both the S-matrix and the nuclear Hamiltonian and represent for each reactionenergy a discrete set of coupled channel wave functions with a common (eigen-) phase. Especiallythe emission of a deuteron is discussed. It is shown that the cluster channels supplement the energy-correlated channels describing the energy partition £1 + e2 = E —Ef and that asymptotic channelorthogonality holds. The characteristic feature of the cluster channels as compared to the energy-correlated channels is that their final state interaction is not limited to a finite matching volumecomparable to nuclear sizes.
In dieser Arbeit wurde der neuronale Glutamattransporter EAAC1 (Excitatory Amino Acid Carrier 1), kloniert aus Rattenretina, in HEK (Human Embryonic Kidney) Zellen transient exprimiert und mit Hilfe der patch clampTechnik elektrophysiologisch untersucht. Der Glutamattransport ist gekoppelt an den Kotransport von drei Natriumionen und einem Proton und den Gegentransport von einem Kaliumion. Damit werden pro Transportzyklus zwei positive Nettoladungen in die Zelle verschoben. Zusätzlich zum Glutamattransport verfügt der EAAC1 über eine Glutamatinduzierte Anionenleitfähigkeit, die nicht thermodynamisch an den Glutamattransport gekoppelt ist und besonders deutlich bei chaotropen Anionen (wie SCN ) in Erscheinung tritt. Eine weitere Funktion des Transporters ist seine Glutamatunabhängige Leckleitfähigkeit. Mit Hilfe von Ganzzellableitungen unter definierten ionalen extra und intrazellulären Bedingungen und bestimmtem Haltepotenzial erfolgte die Charakterisierung des Glutamattransporters von der extrazellulären Seite. Eine hohe Überexpression von EAAC1 in den HEKZellen, mit einer durchschnittlichen Dichte von # 4#10 3 Transporter pro µm 2 Zellmembran, erlaubte zudem die Beschreibung des Transporters von der intrazellulären Seite, durch Messungen am insideout patch. Stationäre Messungen an EAAC1 unter kontrollierten Spannungs und ionalen Bedingungen ließen verschiedene Aussagen zu über 1) die Bindungsreihenfolge von Glutamat und den kotransportierten Ionen an den Transporter, 2) den Anteil der Anionenleitfähigkeit am Glutamatinduzierten Gesamtstrom 3) die Abhängigkeit der Glutamatunabhängigen Leckleitfähigkeit und der Glutamatabhängigen Anionenleitfähigkeit von der Protonen und Natriumkonzentration und 4) die Identifikation des Ladungsträgers beim EAAC1assoziierten Leckstrom. Bei den durchgeführten vorstationären Messungen handelte es sich meist um SubstratsprungExperimente mit Hilfe der LaserpulsPhotolyse von #CNBcaged Glutamat. Damit konnte 1) der geschwindigkeitsbestimmende Schritt im Transportzyklus ermittelt werden, 2) Geschwindigkeitskonstanten verschiedener Teilreaktion im Transportzyklus von EAAC1 abgeschätzt werden und 3) die Spannungsabhängigkeit von Teilreaktionen identifiziert werden. Die Kombination von stationären und vorstationären Messungen mit Hilfe der LaserpulsPhotolyse sowie die Kombination von Ganzzellableitungen und insideout patches ermöglichte damit eine umfassende kinetische Untersuchung der verschiedenen Funktionen von EAAC1 und führten zu dem im folgenden beschriebenen Transportmodell. EAAC1 bindet auf der extrazellulären Seite zunächst ein Natriumion, wobei die Natriumbindungsstelle im elektrischen Feld der Membran liegt (# 25#30 %). Dieser Na beladene Transporterzustand ist assoziiert mit einem Glutamatunabhängigen Leckstrom, der von Anionen getragen ist. Der Na Bindungsreaktion schließt sich eine elektroneutrale Protonenbindung an. Der apparente pKWert des Protonakzeptors in EAAC1 liegt bei # 8, sodass unter physiologischen Bedingungen EAAC1 hauptsächlich in seiner protonierten Form vorliegt. Die nachfolgende Glutamatbindung (KD # 50 µM) ist ebenfalls spannungsunabhängig und erfolgt mit einer Geschwindigkeitskonstanten von # 2#10 7 M #1 s #1 . Sie löst eine elektroneutrale Konformationsänderung aus, die in einem Zeitbereich von 0,5#1 Millisekunde stattfindet und damit langsam ist im Vergleich zu den anschließenden elektrogenen Na Bindungsreaktionen. Der vollständig beladene Transporters transloziert in einem spannungsabhängigen Prozess (# 60#65 % des elektrischen Felds) Glutamat über die Membran mit einer Geschwindigkeitskonstanten von # 800 s #1 bei einem physiologischen Membranpotenzial von #80 mV. Der GlutamatTransportprozess ist mit der Glutamatinduzierten Anionenleitfähigkeit assoziiert, wobei sich beim GlutamatEinwärtstransport ein Verhältnis zwischen Transport und Anionenstrom (von SCN # ) von 1 zu 4 ergab, während es beim GlutamatAuswärtstransport bei 1 zu 1,5 lag. Die Dissoziationsfolge auf der intrazellulären Seite wurde nur für den Protonen-GlutamatKotransport bestimmt und war in umgekehrter Reihenfolge zur extrazellulären Seite. Verschiedene Mechanismen fördern auf der zytosolischen Seite die Dissoziation des Glutamates, bzw. verhindern den GlutamatAuswärtstransport. So führt die Änderung der Zugänglichkeit des Protonakzeptors zur zytosolischen Seite zu einer Verschiebung des apparenten pKWertes zu # 6,5. Damit liegt EAAC1 unter physiologischen Bedingungen auf der intrazellulären Seite hauptsächlich deprotoniert vor, was die Glutamatdissoziation fördert. Ebenso ist die Affinität mit einem 45fach erhöhten K M Wert im Vergleich zur extrazellulären Seite stark herabgesetzt. Die Relokation des Transporters erfolgt nach der Bindung eines Kaliumions und stellt mit einer Geschwindigkeitskonstanten von # 100 s #1 (bei einem Membranpotenzial von #80 mV) den hauptsächlich geschwindigkeitsbestimmenden Schritt im Transportzyklus dar. Bei der Relokation handelt es sich um einen elektrogenen Prozess (# 70#75 % des elektrischen Felds), wobei negative Ladungsträger über die Membran verschoben werden. Daher muss der Transporter über eine Eigenladung von < #1 verfügen. Daraus ergibt sich, dass die zu transportierende Nettoladung von zwei positiven Ladungen pro Transportzyklus auf zwei Reaktionsschritte verteilt ist. Der neuronale Glutamattransporter EAAC1 verfügt damit über verschiedene Mechanismen, den Transportprozess in Richtung Glutamataufnahme in die postsynaptische Nervenzelle zu fördern, entsprechend seiner physiologischen Aufgabe, die Glutamatkonzentration im synaptischen Spalt gering zu halten.
Corneal topometric, aberrometric and biomechanical parameters in mucopolysaccharidosis patients
(2019)
Aims: To report corneal topometric and aberrometric values in mucopolysaccharidosis (MPS) and to investigate their correlation with biomechanical corneal parameters.
Methods: One randomly chosen eye of 20 MPS patients with no to moderate corneal clouding and one eye of 23 healthy controls with comparable age were prospectively included into this study. Corneal surface regularity was assessed by index of surface variance (ISV), -vertical asymmetry (IVA), -height asymmetry (IHA), -height decentration (IHD); keratoconus index (KI), central keratoconus index (CKI) and Zernike indices of anterior and posterior corneal surface using Scheimpflug imaging (Pentacam). Corneal resistance factor (CRF) and corneal hysteresis (CH) were assessed by Ocular Response Analyzer. Statistical analyses were performed using Mann-Whitney-Test and Spearman Correlation Coefficients.
Results: IVA, ISV, IHD, IHA, but not KI and CKI were significantly higher in MPS patients compared to age matched healthy controls. Spherical aberration and asphericity coefficients either at the anterior or at the posterior corneal surface differed significantly between both groups. The grade of the MPS-associated corneal opacity correlated significantly with ISV (rho = 0.52), IVA (rho = 0.54), IHA (rho = 0.57) and IHD (rho = 0.48). Density of the MPS-affected corneas correlated significantly with ISV (rho = 0.52), IVA (rho = 0.72), IHA (rho = 0.57), IHD (rho = 0.69), 3rd order horizontal trefoil aberration at the posterior (rho = 0.62) and anterior surface (rho = 0.48) as well as with CH (rho = 0.55) and CRF (rho = 0.57). Spherical aberration at the back surface correlated with CRF and CH in MPS and in healthy controls.
Conclusions: This is the first study analyzing shape of the corneal surface in MPS patients. Topometric indices of corneal asymmetry are significantly increased and correlate with MPS-related corneal opacity and density. Spherical aberration and asphericity coefficient at the front and at the back corneal surface differ significantly between MPS and healthy controls.
The full-length translation-regulating add adenine riboswitch (Asw) from Vibrio vulnificus has a more complex conformational space than its isolated aptamer domain. In addition to the predicted apo (apoA) and holo conformation that feature the conserved three-way junctional purine riboswitch aptamer, it adopts a second apo (apoB) conformation with a fundamentally different secondary structure. Here, we characterized the ligand-dependent conformational dynamics of the full-length add Asw by NMR and by single-molecule FRET (smFRET) spectroscopy. Both methods revealed an adenine-induced secondary structure switch from the apoB-form to the apoA-form that involves no tertiary structural interactions between aptamer and expression platform. This strongly suggests that the add Asw triggers translation by capturing the apoA-form secondary structure in the holo state. Intriguingly, NMR indicated a homogenous, docked aptamer kissing loop fold for apoA and holo, while smFRET showed persistent aptamer kissing loop docking dynamics between comparably stable, undocked and docked substates of the apoA and the holo conformation. Unraveling the folding of large junctional riboswitches thus requires the integration of complementary solution structural techniques such as NMR and smFRET.
Biophysical studies of the translation-regulating add adenine riboswitch from Vibrio vulnificus
(2017)
Bacterial gene expression can be regulated at mRNA level by cis-acting mRNA elements termed riboswitches. Riboswitches operate by conformational switching between a ligand-free and a ligand-bound state with different structures that either activate or inhibit gene expression. This PhD thesis contributes to the molecular level understanding of full-length purine riboswitches. It presents biophysical investigations on the ligand-dependent folding of the full-length translation-regulating add adenine riboswitch from the gram-negative human pathogenic marine bacterium Vibrio vulnificus (Asw). Asw has the typical bipartite riboswitch architecture with a 5’ ligand-sensing aptamer domain and a 3’ regulatory domain termed expression platform. According to the working hypothesis, Asw employs a unique thermodynamically-controlled 3-state conformational switching mechanism between an apoB, an apoA and a holo conformation to regulate translation initiation in a temperature-compensated manner. The two apo conformations are the putative translation-OFF states and the holo conformation is the putative translation-ON state of Asw. In the main project of this PhD thesis, an integrated nuclear magnetic resonance (NMR) and smFRET spectroscopic study of the full-length 112-nucleotide Asw (112Asw) was performed. The adenine-dependent folding of 112Asw was monitored at the level of base pairing interactions by NMR of the RNA imino protons, and at the level of three long-range intramolecular distances by smFRET of immobilized molecules. The integrated NMR and smFRET spectroscopic study of 112Asw yielded two major findings. First, NMR and smFRET both revealed that adenine binding to 112Asw impedes apoB formation by stabilizing the apoA secondary structure in the holo conformation without modulating tertiary structural interactions between the two riboswitch domains. This highlights the central role of competitive P1 and P4 helix formation at the interface of the aptamer and the expression platform for switching the accessibility of the ribosome binding site of 112Asw. Moreover, it strongly corroborates the hypothesis that purine riboswitches in general operate according to the key principle of a spatially decoupled secondary structural allosteric switch that proceeds without ligand-induced tertiary structural interactions between the aptamer domain and the expression platform. Second, it was uncovered by smFRET that the apoA and the holo conformation of 112Asw do not adopt a single folding state at near-physiological Mg2+ concentration. Instead, apoA and holo exhibit a persistent dynamic equilibrium between substates with an undocked (U), a short-lived docked (D1; ~s) and a Mg2+-bound long-lived docked (D2; ~10 s) aptamer kissing loop motif. In the holo conformation, the fractional population of the long-lived docked substate is ~2-fold increased compared to the apoA conformation, but undocked and docked substates are still comparably stable. The here described multiple folding states of the apoA and the holo conformation might have regulatory properties that are in between the apoB translation-OFF state and the holo-D2 translation-ON state. Additonally, an integrated NMR and smFRET analysis of 127-nucleotide Asw (127Asw) is presented. Compared to 112Asw, 127Asw is 3’-elongated by 15 nucleotides of the adenosine deaminase encoding sequence of the add gene from Vibrio vulnificus. 127Asw was chosen as mRNA template for future investigations of the interaction between Asw and the 30S ribosomal subunit. The NMR spectra of 127Asw demonstrated that 127Asw has the same overall secondary structure as 112Asw. Like for 112Asw, the combined NMR and smFRET analysis of 127Asw showed that adenine binding impedes apoB formation and stabilizes a long-lived docked aptamer kissing loop fold. However, compared to 112Asw, 127Asw has a destabilized aptamer kissing loop motif and a stabilized P4 helix in the expression platform. Finally, ligand-observed studies of the transient encounter complex between Asw and the near-cognate ligand hypoxanthine are described. By competition binding WaterLOGSY NMR experiments with hypoxanthine and the adenine analogue 2,6-diaminopurine, it could be shown that hypoxanthine binds to the same binding site of 112Asw as the cognate ligand adenine. The hypoxanthine binding constant measured with the WaterLOGSY method is in the low mM range (1.8 mM) and substantially exceeds the physiological hypoxanthine concentration in E. coli (~0.3 mM), thus ruling out that hypoxanthine binding can significantly impact the translational regulation of Asw in vivo. Also, preliminary FTIR difference spectra of 13C,15N-labelled and unlabelled hypoxanthine in complex with the pbuE adenine riboswitch aptamer and the xpt guanine riboswitch aptamer are discussed. These spectra showed a pattern of multiple IR bands that appeared to be characteristic for the respective complex.
N-Allyltetramethylpiperidine is readily isomerized to the corresponding enamine by treatment with catalytic amounts of B(C6F5)3. It adds HB(C6F5)2 at the nucleophilic enamine carbon atom to form a C/B Lewis adduct. This reacts with two molar equivalents of carbon monoxide by selective head to tail coupling to give a five-membered C2O2B heterocycle. In contrast the enamine/HB(C6F5)2 Lewis pair reacts with two molar equiv. of nitric oxide by head to head coupling. This reaction probably proceeds via equilibrium with the corresponding vicinal N/B Lewis pair. Most products were characterized by X-ray diffraction.
The ion-molecule reactions of thiothionylfluoride have been studied by ion cyclotron resonance spectrometry. The major secondary ions are S2F3+ , S3F+ , and S3F2+. In a consecutive reaction of S3F2+ the tertiary ion S4F2+ is formed. The rate constant of the IMR with the greatest yield S2F2+ + SSF2 → S3F2+ + SF was estimated to k = 2 · 10-9 cm 3 molecule -1 sec -1 . The results were compared with the mass spectrum of thiothionylfluoride. They permit conclusions on chemical reactions of lower sulphurfluorides.
The low temperature IR stretching vibrations of difluorodisulfane (FSSF) and thiothionylfluoride (SSF2), in the solid phase and in a cyclohexane matrix, of the mixtures FSSF -SSF2, FSSF-OSF2 and SSF, -OSF2, and of solid difluorotrisulfane (FS3F) have been investigated. While SSF, forms no distinct oligomers, a dimer with absorption bands at 635 and 682 cm-1 has been detected in the case of FSSF. These differences between FSSF and SSF, are rationalized by the different S-F bond lengths. A structure of the FSSF dimer similar to that of the sulfur tetrafluoride dimer is proposed. The low temperature spectrum of FS3F shows 3 bands in the frequency range between 460 and 1000 cm-1: 590, 605 and 680 cm-1, due to associated molecules. FS3F decomposes on warming. The main decomposition products containing fluorine are FSSF and SSF2. Mechanisms for the rearrangement and decomposition of the three compounds studied are discussed.
The mass spectra and the ion molecule reactions of methylphosphine, dimethylphosphine and dimethyldeuterophosphine have been studied by ion cyclotron resonance spectrometry. About 50 ion molecule reaction are observed for each compound. The product ions can be classified as ions with two phosphorus atoms: P2R5+, P2R3+, P2R2+ and P2R+ (R = CH3 or H), as phosphonium and phosphinium ions and ions resulting from collision dissociations and charge exchange reactions. Tertiary ions with three phosphorus atoms like CH3P3H2+ (from CH3PH2) and (CH3)4P3H2 (from (CH3)2PH) have also been detected. The mechanisms of the ion molecule reactions, rearrangements, P -H- and C-H-reactivities and product ion structures are discussed, using in the case of dimethylphosphine the results obtained with the deuterated compound. Rate constants of formation of the more abundant product ions from the molecular ion and the CH3P+ ion, both odd electron particles, have been determined. The reactions with dimethylphosphine have much smaller rate constants than the reactions with methylphosphine.
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different length, linkage-type and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying length, as well as, homotypic and heterotypic branched chains of the two most abundant linkage types – K48- and K63-linked Ub. We identified some of the first K48/K63 branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4 and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50 and p97-adaptor FAF1. Crucially, we compared datasets collected using two common DUB inhibitors – Chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.