No / D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties. / NIH

Among multiple interconnected pathways for L-Lysine catabolism in pseudomonads, it has been reported that Pseudomonas aeruginosa PAO1 employs the decarboxylase and the transaminase pathways. However, knowledge of several genes involved in operation and regulation of these pathways was still missing. Transcriptome analyses coupled with promoter activity measurements and growth phenotype analyses led us to identify new members in L-Lys and D-Lys catabolism and regulation, including gcdR-gcdHG for glutarate utilization, dpkA, amaR-amaAB and PA2035 for D-Lys catabolism, lysR-lysXE for putative L-Lys efflux and lysP for putative L-Lys uptake. The amaAB operon is induced by L-Lys, D-Lys and pipecolate supporting the convergence of Lys catabolic pathways to pipecolate. Growth on pipecolate was retarded in the gcdG and gcdH mutants, suggesting the importance of glutarate in pipecolate and 2-aminoadipate utilization. Furthermore, this study indicated links in control of interconnected networks of lysine and arginine catabolism in P. aeruginosa. Effect of D-amino acids and the genes involved in their metabolism are of great interest in both bacteria and mammals. D-Arg utilization in PAO1 requires the coupled dehydrogenases DauB and DauA. In this study, DauB was found to use only L-Arg as its substrate unlike its partner dehydrogenase DauA with wide substrate specificity. However, evidence from this study and previous studies suggest that the coupled enzymes DauB and DauA are unique for D-Arg catabolism. The three D-amino acid dehydrogenases DguA, DadA and DauA were found to have somewhat limited in vivo substrate specificity compared to that found in vitro tested using purified enzymes. Many studies showed that D-amino acids are toxic to bacteria. The ΔdguA, ΔdadA and ΔdauA triple mutant had two-fold lower minimum inhibition concentration of carbenicillin and tetracycline compared to wild-type PAO1. Both in the wild-type PAO1 and the triple mutant, synergy was observed between gentamicin or tetracycline (at concentrations below the MIC) and D-amino acids resulting in growth inhibition or reduction, respectively. However, no special synergistic or antagonistic effects were observed specifically in the ΔdguA, ΔdadA and ΔdauA triple mutant as compared to the wild-type PAO1 when D-amino acids were given in combination with antibiotics.

Biofouling is a major issue in applying nanofiltration and reverse osmosis technologies for wastewater treatment. Biofilm formed on the surface of membranes will severely decline the flux and cause energy waste. In this study, a novel biofouling control method that applies D-amino acids to inhibit biofilm formation was investigated. The D-amino acids previously reported to inhibit biofilm formation and disrupt existing biofilm – D-tyrosine and the mixture of D-tyrosine, D-tryptophan, D-leucine and D-methionine were tested. Pseudomonas aeruginosa and Bacillus subtilis were used as model Gram-negative and Gram-positive bacteria, respectively. D-amino acids have little effect and some effect on inhibition of biofilm formation and disruption of exiting biofilm to Pseudomonas aeruginosa, but have good effect to Bacillus subtilis. A commonly used microtiter plate assay for quantitative biofilm measurement was systematically evaluated and optimized for screening biofilm control agents. The effect of D-tyrosine on inhibition of organic fouling and P. aeruginosa biofouling on NF90 membrane surface in bench scale dead end filtration experiment was examined, which shows that D-tyrosine can effectively inhibit organic fouling and P. aeruginosa biofouling on NF90 membrane surface.

The covalent attachment of poly(ethylene glycol) (PEG) to a protein surface (known as PEGylation), has been demonstrated to increase the serum half-life of therapeutic proteins by reducing kidney clearance and immunogenicity and by protecting against proteolysis. Theses beneficial effects could be further enhanced if PEGylation consistently increased protein conformational stability (i.e. the difference in free energy between the folded and unfolded states). However, the effects of PEGylation on protein conformational stability are unpredictable; PEGylation has been reported to increase, decrease, or have no effect on the conformational stability of medicinal proteins.This thesis details the results of two studies aimed at discovering the structural determinants which influence the thermodynamic impact of PEGylation on the WW domain, a small model protein. Chapter 1 is a brief introduction to protein therapeutics and protein PEGylation. Chapter 2 describes a study which demonstrates that the thermodynamic impact of PEGylation is strongly dependent on the site to which PEG is conjugated. The studies described in Chapter 3 elaborate on this site dependence, and demonstrate that PEG stabilizes the WW domain through interactions with the surface of the folded peptide, and that two factors – the orientation of the PEG chain (relative to the protein surface) and the identity of nearby side chains – play a critical role in determining the thermodynamic impact of PEGylation.

D-amino acids (D-AAs) are the α-carbon enantiomers of L-amino acids (L- AAs), the building blocks of proteins in known organisms. It was largely believed that D-AAs are unnatural and must be toxic to most organisms, as they would compete with the L-counterparts for protein synthesis. Recently, new methods have been developed that allow scientists to chromatographically separate the two AA stereoisomers. Since that time, it has been discovered that D-AAs are vital molecules and they have been detected in many organisms. The work of this dissertation focuses on their place in bacterial metabolism. This specific area was selected due to the abundance of D-AAs in bacteria-rich environments and the knowledge of their part in several processes, such as peptidoglycan synthesis, biofilm disassembly, and sporulation. We focused on the bacterium Pseudomonas putida KT2440 which inhabits the densely populated plant rhizosphere. Due to its versatility and cosmopolitan character, this bacterium has provided an excellent system to study D-AA metabolism. In the first chapter, we have developed a new approach to identify specific genes encoding enzymes acting on D-AAs, collectively known as amino acid racemases. Using this novel method, we identified three amino acid racemases encoded by the genome of P. putida KT2440. All of the enzymes were subsequently cloned and purified to homogeneity, followed by a complete biochemical characterization. The aim of the second chapter was to understand the specific role of the peculiar broad-spectrum amino acid racemase Alr identified in chapter one. After constructing a markerless deletion of the cognate gene, we conducted a variety of phenotypic assays that led to a model for a novel catabolic pathway that involves D-ornithine as an intermediate. The work in chapter three identifies for the first time numerous rhizosphere-dwelling bacteria capable of catabolizing D-AAs. Overall, the work in this dissertation contributes a novel understanding of D-AA catabolism in bacteria and aims to stimulate future efforts in this research area.

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In dieser Arbeit wurde die Induktion spezifischer, immunologischer T-Zelltoleranz als therapeutische Strategie bei Autoimmunerkrankungen im Mausmodell untersucht. Da davon ausgegangen werden muss, dass viele der Autoimmunkrankheiten durch T-Zellen vermittelt sind, ist die Induktion spezifischer T-Zelltoleranz eine besonders interessante Therapiestrategie. Spezifische T-Zelltoleranz kann mittels Injektion des entsprechenden Peptidantigens induziert werden. Insgesamt sind zur Induktion einer solchen Toleranz, zumindest beim Menschen, relativ hohe Dosen an Peptidantigen notwendig. Die Produktion dieser Peptidantigene ist teuer. Bei unvorsichtiger Gabe kann es zur Anaphylaxie kommen. Es sollte also von Vorteil sein, die zu applizierende Menge an Peptid möglichst gering, dabei aber effizient zu halten. Vermutlich werden Antigene in Form von Peptiden schnell von unspezifischen Peptidasen und Proteasen in nicht-immunogene Fragmente gespalten und ausgeschieden, was wiederum eine hohe Dosierung erforderlich macht. Im Anfang der vorliegenden Arbeit stand die Hypothese, dass eine Stabilisierung des zu applizierenden Antigens zum Schutz vor Fragmentierung (und damit Wirkungsverlust) eine geeignete Methode sein könnte, Toleranzinduktion effektiver bzw. kostengünstiger zu gestalten. Bezüglich einer Stabilisierung von Peptiden zeigte sich, dass Peptide, welche aus rechtsdrehenden (D-)Aminosäuren zusammengesetzt sind, nur verzögert durch Proteasen/Peptidasen abgebaut werden. Wir setzten deshalb in dieser Arbeit D-Aninosäuren-substituierte Peptid-Varianten des Ovalbumin323-339-Peptidepitops (OVA323-339) ein und betrachteten die Wirkung dieser Peptide in vitro sowie in vivo auf spezifische DO11.10 T-Zellen. Basierend auf dem Peptidantigen OVA323-339, wurde zunächst ein minimales Epitop definiert, welches bei etwa gleicher Potenz um 6 Aminosäuren verkürzt werden konnte. Anschließend wurde eine Substitutionsanalyse durchgeführt, in der die ursprüngliche Aminosäuresequenz durch Austausch einiger L-Aminosäuren mittels D-Aminosäuren verändert wurde. Diese neu synthetisierten Peptide wurden zunächst auf ihre Fähigkeit überprüft, die OVA323-339 spezifischen DO11.10 T-Zellen in vitro zu aktivieren. Parallel konnte gezeigt werden, dass diese synthetisierten Peptidepitope in vitro eine deutlich verlängerte Serumhalbwertszeit aufwiesen. Im Weiteren wurde versucht, durch systemische Injektion von 300µg D-Peptid-Varianten in BABLB/c Mäusen T-Zelltoleranz zu induzieren. Die ex vivo restimulierten Lymphknoten-Zellen dieser Mäuse präsentierten je nach appliziertem Peptid eine reduzierte Proliferationsbereitschaft und IL-2 Sekretion. Die hier induzierte Toleranz konnte bis zu 60 Tagen post injectionem sowohl für das OVA323-339 als auch für einige der eingesetzten D-Peptide nachgewiesen werden. Auch nach Reduktion der Peptiddosis auf nur 100µg/Maus, waren die verkürzten und D-Aminosäuren-substituierten Peptide immer noch in der Lage sicher Toleranz zu induzieren. Die induzierte Toleranz durch D-Peptide war dabei der durch das Ausgangspeptid OVA323-339 induzierten Toleranz vergleichbar stark. Mit der Hilfe eines Transfermodells in unmanipulierte Mäuse, wurde das Verhalten der spezifischen T-Zellpopulation in vivo beobachtet. Durch den Transfer konnten in den Empfängermäusen (Balb/c) definierte T-Zellpopulationen bekannter Größe erzeugt werden. Mit dem Antikörper KJ1-26.1, der spezifisch den DO11.10-T-Zellrezeptor erkennt, konnten die transferierten Zellen in Geweben der Empfängermaus per FACS-Analyse nachgewiesen und deren Verhalten ex vivo studiert werden. Die intravenöse Injektion der serumstabilisierten Peptidanaloge führte in den transferierten Mäusen je nach Peptid zu einer funktionellen Nichtreaktivität (Anergie) als auch zur Deletion der für das Ausgangs(L-)Peptid spezifischen DO11.10 T-Zellen. In den oben genannten Versuchen ergaben sich Hinweise dafür, dass die D-Peptide ebenso effektiv sind wie das wesentlich längere Ausgangspeptid OVA323-339. Zukünftige Experimente werden weitere Aufschlüsse über einen möglichen Vorteil des Einsatzes von D-Peptiden in der Toleranzinduktion erbringen. / Induction of antigen-specific peripheral T cell tolerance in autoimmune diseases is an interesting therapeutically strategy. It can be induced by systemic injection of high-dose antigen. Investigations in induction of peripheral T cell tolerance in autoimmune mouse models revealed promising results. But it was also shown that the induced T cell tolerance spontaneously reverses after a period of time. This is probably due to a short in vivo half-life of the administrated peptide antigens. Since durable tolerance is required for this strategy to be of therapeutic value the administrated antigen-dose has to be of a very high and has to be injected repeatedly, and therefore bears an increased risk of anaphylactic reactions or exacerbation of the autoimmune disease. Because of these restrictions and also the high costs of peptide-production and purification, it is not surprising that this therapy didn t really find its way in to the clinical practice. The discovery that Peptides assembled partly or totally from D-amino acids are much more stable to proteolysis then natural L-peptides and therefore show an increased stability, lead to a wide interest of pharmacologists and immunologists. In former investigations it was shown that D-peptides used as vaccines elicited high levels of neutralizing antibodies so that there is no doubt about their immunogenic potency in vivo. It is also known that a single T cell receptor recognizes a wide range of peptide analogues that closely mimic the natural antigen. These observations led to our hypothesis, that the induction of peripheral T cell tolerance by systemic administration of D-Peptide substituted antigen variants should be possible and could be much more effective than the induction by the wild-type L-peptide. To verify our hypothesis we have chosen the well known OVA323-339 antigen which is recognized by T cells through the presentation in the I-Ad context. In a first step we performed a truncation analysis of OVA323-339 to identify a minimal epitope in it. We were able to demonstrate that the sequence OVA327-337 is as well potent as the original and 6 amino acids longer OVA323-339 sequence. The potency of new defined epitopes was tested by stimulating the OVA323-339 -specific DO11.10 T cells in vitro. In a stepwise performed substitution analysis we attempted to insert some D-amino acids in this novel peptide epitope. The DO11.10 cells only tolerated a few D-amino acid substitutions into the original sequence with the effect of now showing reduced proliferation. Performing an analysis of their half-life in vitro we identified two peptides as interesting candidates for the in vivo tolerance induction experiments. In the in vivo part of this work we induced peripheral tolerance by injecting the novel peptides into BALB/c mice. To monitor the behaviour of the tolerated T cells we also performed adoptive transfer experiments by transferring DO11.10 cells into naive BALB/c mice. With the help of the KJ26-1 antibody which specifically recognizes the DO11.10 T cell receptor it became possible to detect the transferred T cells ex vivo. Our results demonstrate that induction of peripheral T cell tolerance through injection of D-peptides is possible and long lasting (up to 60 days). Even with a dose reduction we found a stable T cell tolerance under ex vivo restimulation with the original peptide. Summarizing we were able to show that D-peptides are at least as effective as the natural occurring L-peptides inducing tolerance. Much more, the transfer experiments revealed that the kind of induced T cell tolerance (i.e. anergy and/or deletion through activation induced cell death) is antigen dependent and probably differs due to the agonistic potency of the given antigen.

In the present PhD thesis we studied the solid-phase peptide synthesis of antimicrobial peptides derived from the lead peptides BP100 and BPC194. First, peptides derived from BP100 containing D-amino acids at different positions of the sequences were prepared. Moreover, peptidotriazoles derived from BP100 were also synthesized containing the triazole ring at the side-chain of different amino acids. Then, we proceeded to perform studies for the synthesis of multivalent peptides derived from BPC194. To achieve this objective, the synthesis of cyclic peptides containig a triazole ring at amino acids side-chain with different elongations was carried out. Finally, we prepared various carbopeptides containing 2 and 4 units of BP100 and/or its derivatives. The evaluation of the biological activity allowed the identification of active sequences against the economically important phytopathogenic bacteria and fungi and not toxic against eukaryotic cells. / En aquesta tesi doctoral es va estudiar la preparació en fase sòlida de pèptids antimicrobians derivats dels pèptids lead BP100 i BPC194. En primer lloc, es varen preparar derivats del pèptid lineal BP100 incorporant D aminoàcids en diferents posicions de la seqüència. A més, també es varen sintetitzar derivats d'aquest pèptid lead incorporant un anell de triazole a la cadena lateral de diferents aminoàcids. Posteriorment, es va procedir a l'estudi de la síntesi dd pèptids multivalents derivats de BPC194. Per aconseguir aquest objectiu es va portar a terme la síntesi de pèptids cíclics incorporant un anell de triazole a la cadena lateral d’aminoàcids amb diferents allargades de cadena. Finalment, va procedir a la preparació de carbopèptids contenint 2 i 4 unitats de BP100 i/o derivats. L’avaluació de l’activitat biològica dels pèptids sintetitzats va permetre idenficar seqüències actives enfront de bacteris fitopatògens i fongs i poc tòxiques enfront cèl•lules eucariotes.