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Trigger Factor (TF) is a prokaryotic chaperone protein that exerts its major chaperone activity while associated with translating ribosomes, assisting de novo folding of the emerging nascent chain. Although much is known about the kinetics behind TF-ribosome binding, most results are based on in vitro experiments which fail to mimic the cellular environment. Single-particle approaches have gained increasing power for studying binding kinetics of biomolecules in living cells. One such method is single-particle tracking by super-resolution fluorescence microscopy, where the position of a fluorescently labelled particle is recorded over time, giving information about the movement of the particle inside the cell. Changes in diffusion behaviour is then used as an indicator of changes in biological activities. In this work, a diffusion model that qualitatively and quantitatively describes TF’s binding to ribosomes is presented. The model was obtained by single-particle tracking of TF labelled with HaloTag. Particle movements were analysed with a Hidden Markov Model-based algorithm that fit the trajectories to a defined set of different diffusion states, where fast diffusion could be related to free TF and slow diffusion to a ribosome-bound state. Moreover, the model could distinguish between two types of ribosome interactions: TF’s stable binding to ribosomes and a faster sampling behaviour. The average time spent stably bound to ribosomes is 670 ms and these interactions account for 53% of TF’s activity. TF is one of many processing proteins that interact with the emerging peptide chain during translation. By using the same approach on more of these factors, the interplay between them and the growing nascent chain can be characterized, giving an increased understanding of the highly complex translation machinery.

The foundational studies of this dissertation concern the characterization of segmented polyurethanes and polyureas synthesized without the use of chain extenders'molecules that are typically used to promote a microphase separated morphology that gives these materials their useful characteristics. Polyurethanes in which a single asymmetric diisocyanate comprising the whole of the hard segment were found to display poor microphase separation. Conversely, polyurethanes in which a single symmetric diisocyanate composed the hard segment were found to display good microphase separation. The more efficient packing of the symmetric hard segments also led to an increase in hard segment connectivity and hence higher values of storage moduli in these systems. When hydroxyl-terminated diisocyanates were replaced with amine-terminated diisocyanates, polyureas were formed. Here too, diisocyanate symmetry was found to play a key role with symmetric diisocyanates leading to better microphase separation. In addition, the polyurea materials displayed broader service temperature windows than their polyurethane counterparts as the relatively stronger bidentate hydrogen bonding replaced monodentate hydrogen bonding in these materials. A thread-like, microphase separated morphology was visually confirmed using atomic force microscopy. Other techniques such as ambient temperature tensile testing, and wide and small angle x-ray scattering were employed to confirm the presence of the microphase separated structure. The investigation into the effects of diisocyanate chemistry and its symmetry was broadened to incorporate non-chain extended polyurethane materials with different soft segment molecular weights, as well as polyurethanes that did contain chain extenders. Once again the effect of using symmetric versus asymmetric diisocyanates was evident in the structure–property behavior of these systems, with symmetric diisocyanates forming materials that displayed better microphase separation and more connectivity of their hard domains. Lastly, in a departure from the segmented copolymer area, a study was conducted into the influence of casting variables on the solid-state structure of synthetic polypeptide films based on glutamate chemistry. The effect of solvent evaporation was determined to play a key role in the morphology of these polypeptide films. Measured small angle light scattering patterns were compared to computer calculated patterns to reveal information about the structure, shape, and length scale of the polypeptide structure. / Ph. D.

Aggregation of proteins into amyloid deposits is a common feature among dozens of diseases. Two such diseases that feature amyloid deposits are Alzheimer's disease (AD) and type 2 diabetes (T2D). AD toxicity has been associated with the aggregation and accumulation of the amyloid β-peptide (Aβ); Aβ exerts its toxic effects through interactions with neuronal cell membranes. A characteristic feature of T2D is the deposition of the islet amyloid polypeptide (IAPP) in the pancreatic islets of Langerhans. It is currently unknown if IAPP aggregation is a cause or consequence of T2D, but it does lead to β-cell dysfunction and death, exacerbating the effects of diabetes. Characterizing the fundamental interactions between both Aβ and IAPP with lipid membranes and in solution will give greater insight into mechanisms of toxicity exhibited by amyloid proteins. In this work, molecular dynamics (MD) simulations were used to study the secondary, tertiary, and quatnary structure of Aβ and IAPP, in addition to peptide-membrane interactions and membrane perturbation as independently caused by both peptides. Studies were conducted to address the following questions: (1) what influence do solution conditions and oxidation state have on monomeric Aβ] (2) how and in what way does monomeric Aβ interact with model lipid membranes and what role does sequence play on these peptide-membrane interactions; (3) can MD simulations be utilized to understand Aβ tetramer formation, rearrangement, and tetramer-membrane interactions; (4) how does IAP interact with model membranes and how does that vary from non-toxic (rat) IAPP peptide-membrane interactions. These studies led to conclusions that showed variance in lipid affinity and degree of perturbation as based on peptide sequence, in addition to insight into the type of perturbation caused to membranes by these amyloid peptides. Understanding the differences in peptide-membrane interactions of amyloidogenic and non-amyloidogenic (rat) peptides gave insight into the overall mechanism of amyloidogenicity, leading to the detection of specific amino acids essential in peptide-membrane perturbation. These residues can then be targeted for novel therapeutic design to attenuate the perturbation and potential cell death as caused by these peptides. / Ph. D.

L’auto-assemblage de copolymères à blocs amphiphiles est un outil puissant de la chimie supramoléculaire pour la conception de nano-objets complexes et fonctionnels. Dans ces travaux de thèse, l’étude approfondie d’un copolymère à blocs « hybride » synthétique-b-peptidique poly(triméthylène carbonate)-b-poly(acide glutamique) pour des applications de vectorisation a été menée. Des morphologies vésiculaires, obtenues par auto-assemblage en voie « co-solvant » et présentant une grande stabilité ainsi qu’un caractère stimulable ont été mises en évidence. Une transition inédite en température, par des phénomènes de fusion et de fission, a pu être observée. L’encapsulation dans ces vésicules polymères d’un principe actif anti-tumoral et de nanoparticules magnétiques, à des taux très élevés, permet d’améliorer le contraste en IRM ainsi que de moduler la libération de la molécule par une variation des paramètres environnementaux (pH, T) ou par un effet d’hyperthermie magnétique. / Block copolymer self-assembly is a powerful tool within supramolecular chemistry to design smart and functional nano-objects. In this thesis work, comprehensive study of hybrid poly(trimethylene carbonate)-b-poly(glutamic acid) block copolymers for drug delivery applications has been conducted. Highly stable vesicular morphologies presenting stimuli-responsive behaviour were prepared using a solvent-injection method. In particular, original temperature responsiveness mediated by fusion and fission events has been evidenced. Dual loading of an anticancer drug and superparamagnetic nanoparticles in these vesicles, at very high loading contents, allows enhancing MRI contrast and controlling drug release kinetics by varying environmental conditions (pH, T) or by using a magnetic hyperthermia effect.

Die vorliegende Arbeit beschreibt das Verhalten von Polypeptid-Blockcopolymeren in der festen Phase und in selektiven Lösungsmitteln. Blockcopolymere auf Basis von Poly(L-glutaminsäure-5-benzylester) (PBLGlu) oder Poly(Nε-benzoyloxycarbonyl-L-lysin) (PZLLys), die in dieser Arbeit eingesetzt wurden, besitzen wegen ihrer helikalen Sekundärstruktur eine sog. Stäbchen-Knäuel-Geometrie, wobei die Knäuelkomponente Polystyrol oder Polybutadien ist. Die Phasenbildung dieser Blockcopolymere ist durch die Packungseigenschaften des rigiden Blocks beeinflusst. Es wurden bevorzugt lamellare Strukturen gebildet, in denen die Stäbchen parallel angeordnet sind. Das Vorhandensein eines permanenten Dipolmomentes führt zur Wechselwirkung zwischen den Helices und zur Erhöhung des Ordnungsgrades in der Phase. Ein zusätzlicher Parameter, der die Morphologie der Phase beeinflußt, ist die Chiralität der Peptidhelix, durch die chirale Überstrukturen induziert werden. In dünnen Filmen (40 nm), wo die Geometrie begrenzt ist, führt es zu Frustrationen in der Phase. Die dadurch entstandene Spannung wurde durch einen zick-zack-artigen Lamellenverlauf abgebaut. In selektiven Lösungsmitteln für die synthetische Komponente (PS) bilden die Polypeptid-Blockcopolymere vesikuläre Strukturen, deren kugel- oder wurmförmige Geometrie von der Elastizität der Membran abhängig ist. Durch Entfernung der Z-Schutzgruppe kann PZLLys in eine wasserlösliche Form überführt werden, so dass die PB-PLLys Blockcopolymere unter Bildung von Vesikeln in Wasser löslich sind. Dabei ist die Konformation des Peptids vom pH-Wert des Mediums abhängig und kann von einem Knäuel zu einer Helix reversibel geschaltet werden. Beim Modifizieren der Sekundärstruktur wurde eine Änderung der Aggregationszahl beobachtet. Somit können diese Blockcopolymere für die Herstellung von schaltbaren Aggregaten eingesetzt werden. / The presented work describes the behaviour of polypeptide-blockcopolymers in the solid-state and well as in selective solvents. Blockcopolymers consisting of PBLGlu or PZLLys / which have been utilized in this work, possess, because of their helical structure, a so-called Rod-Coil Geometry, where the coil component consists of polystyrene or polybutadiene. The phase morphology of these block copolymers is dominated by the packing properties of the rigid blocks. Most commonly, lamellar structures were formed, where the rods were ordered in a parallel fashion. The presence of a permanent dipole moment leads to an interaction between the helices and to an increase in the degree of order within the phase. An additional parameter that influences the phase morphology is the chirality of the peptide helix, which induces the formation of chiral superstructures. In thin films (40 nm), where the geometry is limited, a disordering within the phase is observed. The resulting tension leads to the formation of a zig-zag lamellar pattern. In selective solvents of the synthetic component (PS) of the blockcopolymer, formation of vesicular structures are observed, with spherical or worm-like geometry, depending on the elasticity of the membrane. Through removal of the z-protective groups, PZLLys becomes soluble in water, through the formation of PB-PLLys blockcopolymer vesicles. The conformation of the peptide is dependent on the pH value of the medium and can be reversibly changed from a coil to a helix structure. Through modification of the secondary structure, a change in the aggregation number is observed. Thereby, these blockcopolymers may find application in the fabrication of switchable aggregates.

Synthetic construction of protein molecules has been widely pursued over the last two decades. A primary goal behind de novo protein design has been to build minimal systems by capturing the essential features of protein structures. Such minimal models can be used to understand underlying principles governing folding, structure, and function of proteins molecules. Several approaches envisioning successful construction of synthetic proteins have been described over the years, some of them being admirably successful (DeGrado et al, 1999; Richardson et al> 1992; Baltzer, 1998). Specific patterning of polar and apolar residues in synthetic sequences has been widely used to achieve designed polypeptide structures like helix bundles (DeGrado et ah, 1999) and (3-sheets (Smith and Regan, 1997; Lacroix et a/., 1998), with reliance on hydrophobic driving forces for folding. Our laboratory has been pursuing a distinctly alternative approach, that employs stereochemically constrained amino acids to generate specific secondary structures which can then be assembled into composite structures by appropriately chosen linking segments. This approach, which involves linking prefabricated modules of secondary structures can be termed as a "Meccano set" approach to protein design (Balaram, 1992). The studies embodied in the present thesis describe attempts at construction of synthetic polypeptide motifs using the stereochemically directing influence of conformationally constrained amino acid residues, such as DPro or Aib (α-aminoisobutyric acid). This thesis is subdivided into 8 chapters, with Chapter 1 providing a perspective of the field of protein design. Subsequent chapters (2-8) describe studies directed towards the specific goal of construction of polypeptide motifs. Chapter 2 describes synthesis and conformational characterization of two octapeptides Boc-Leu-Val-Val-DPro-LAla-Leu-Val-Val-OMe (1) and Boc-Leu-Val-Val-DPro-DAla-Leu-Val-Val-OMe (2), designed to investigate the effect of specific β-turn stereochemistry on β-hairpin structures. 500 MHz NMR studies establish that both peptides 1 and 2 adopt predominantly β-hairpin conformations in chloroform and methanol solutions, with interstrand registry established by observation of long-range nuclear Overhauser effects (NOEs). Specific NOEs provide evidence for a type II' β-turn conformation for the DPro-LAla segment in 1, while the NMR data suggest that a type I' DPro-DAla β-turn conformation predominates in the peptide 2. The crystal structure of 1 reveals two independent molecules in the crystallographic asymmetric unit, both of which adopt β-hairpin conformations nucleated by a type II’ β-turn across DPro-LAla and stabilized by 3 cross strand hydrogen bonds. These designed β-hairpins with defined tight turns produce characteristic vibrational circular dichroism (VCD) patterns, demonstrating the utility of VCD as a probe for conformational analysis of β-hairpins. In Chapter 3, we present conformational analysis on designed β-hairpin sequences incorporating a 'Phe-Phe' residue pair at a non-hydrogen bonding position. Two octapeptides Boc-Leu-Phe-Val-DPro-Gly-Leu-Phe-Val-OMe and Boc-Leu-Phe-Val-DPro-Ala-Leu-Phe-Val-OMe were synthesized and conformationally characterized by 500 MHz NMR spectroscopy. Specific NOEs observed in solution provide conclusive evidence favoring specific orientation effects pertaining to the 'Phe-Phe' pair. The peptides exhibited anomalous electronic CD, which has been explained in terms of aromatic contributions by the side chain chromophores. Interestingly, the VCD patterns obtained for these peptides were almost identical to those obtained for other β-hairpins, described in Chapter 2. Chapter 4 describes the synthesis and conformational analysis of designed decapeptide sequences with centrally located DPro-Xxx β-trun segments. Two sequences Boc-Met-Leu»Phe-Val'DPro-Ala-Leu-Val-Val-Phe-OMe (1) and Boc-Met-Leu-Val-Val-^ro-Gly-Leu-Val-Val-Phe-OMe (2) were designed to study the effect of chain length elongation, of β-strands, on designed β-hairpin structures. 500 MHz NMR studies establish β-hairpin folds in both these sequences, with strand segments aligned even at the termini of the structures. Multi-stranded, antiparallel β-sheet structures can be generated by successive placement of β-hairpin sequences in a single polypeptide chain. The successful construction of three stranded β-sheet structures is described in Chapter 5 of this dissertation. A 14-residue peptide Boc-Leu-Phe-Val-DPro-Gly-Leu-Val-Leu-Ala-DPro-Gly-Phe-Val-Leu-OMe (LFV14) was designed such that it is composed of three strand segments linked by two DPro-Gly turn segments. The peptide showed excellent solubility in apolar media, permitting detailed conformational analysis by 500 MHz NMR spectroscopy in organic solvents. Observation of long-range, interstrand NOEs, diagnostic of multiple hairpin structures, provides conclusive evidence for a predominantly populated three stranded β-sheet structure in solution. Extension of this strategy has been described in which an 18-residue peptide, Arg-Gly-Thr-Ile-Lys-DPro-Gly-Val-Thr-Phe-Ala-DPro-Ala-Thr-Lys-Tyr-Gly-Arg, was designed with enhanced solutility in water to probe (β-sheet structure formation in aqueous and mixed aqueous-methanol systems. NMR data provided conclusive evidence in favor of the desired structure being significantly populated in methanol and methanol-water mixtures (50 %, v/v). In water, spectroscopic evidence suggests that the long-range order expected of a three-stranded structure is lost, possibly due to water invading the interstrand hydrogen bonds. Successful construction of a four-stranded antiparallel β-sheet structure has been demonstrated in Chapter 6. A 26-residue peptide Arg-Gly-Thr-Ile-Lys»DPro-Gly-Ile-Thr- Phe-Ala-DPro-Ala-Thr-Val-Leu-Phe-Ala-Val-DPro-Gly-Lys-Thr-Leu-Tyr-Arg was designed to have four strand segments linked by three DPro-Xxx turn segments. The peptide exhibited excellent NMR properties permitting structure determination by analysis of NOE data, which revealed that a four stranded β-sheet structure is indeed populated in methanol. Structural studies on this peptide in mixed methanol-water established that the four stranded β-sheet is appreciably populated at a composition of 50 % (v/v) methanol-water mixture, with the β-sheet structure still detectable even at a composition of 70 % water-30 % methanol. In a completely aqueous environment, the β-sheet structures is significantly disrupted, presumably due to solvent invasion. The nucleating β-turns, however, appear to have retained their structural integrity even in this competitive environment. Chapter 7 describes the insertion of L-Lactic acid (Lac), a hydroxy acid, into polypeptide helices stabilized by a-aminoisobutyricacid (Aib). This study was undertaken to investigate the effect of hydrogen bond deletion on peptide helices. Crystal structure determination of three oligopeptides containing Lac residues has been performed. Peptide 1, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe, and peptide 2, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Leu-OMe adopt completely helical conformations in the crystalline state, with the Lac(6) residue comfortably accommodated in the center of a helix. NMR studies of peptide 1 and its all amide analog 4, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe, provide firm evidence for a continuous helical segment in both the cases. In a 14-residue peptide 3, Boc-Val-Ala-Leu-Aib- Val- Ala-Leu- Val- Ala-Leu- Aib-Val-Lac-Leu-OMe, residues Val( 1 )-Leu( 10) adopt a helical conformation, which is terminated by formation of a Schellman motif, with Aib(ll) as the site of chiral reversal. The loss of the hydrogen bond at the C-terminus appears to facilitate the chiral reversal at Aib(l 1). In the final section of this thesis, Chapter 8, successful construction of a synthetic motif containing two distinct elements of secondary structure, a (β-hairpin and a helix, has been described. The design of a 17-residue peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-DPro-Gly-Leu-Phe-Val-OMe, BH17, is based on a modular approach, in which previously characterized β-hairpin (Leu-Phe-Val-DPro-Gly-Leu-Phe-Val) and helix (Val-Ala-Leu-Aib-Val-Ala-Leu) modules are linked by a Gly-Gly linker. The positioning of the achiral Gly residue at position 8 facilitates termination of the potential helical segment (residues 1-7) by formation of a Schellman motif. Gly(9) is anticipated to be the sole conformationally flexible residue. NMR studies on BH17 indicated the presence of both the helix (residues 1-7) and the β-hairpin (residues 10-17) structures in the sequence, with four major conformational possibilities at the linking segment. Crystal structure determination of BH17 revealed that the two elements of structure are approximately arranged in an orthogonal fashion. The crystal structure validates the original premise that a modular assembly strategy may be viable for the construction of larger synthetic structures. Chapter 9 summarises the major results of this thesis. (For formulae, please refer "pdf" format)

<p>This thesis examines the effect of surgical weight loss on gut and adipose tissue peptides involved in appetite regulation and energy homeostasis in morbidly obese humans. Roux-en-Y gastric bypass (RYGBP) is the gold standard operation used for effective long-term weight loss and improved health. The exact mechanisms for this outcome are under investigation.</p><p>We measured ghrelin, a recently discovered hunger hormone, insulin, adiponectin and leptin along with anthropometry measures in 66 morbidly obese patients prior to and 6 and 12 months after RYGBP. Impressive weight loss occurred postoperatively as did alterations in the peptides. Consistent correlations were found between weight, leptin, ghrelin and insulin. The main findings were low ghrelin concentrations in obesity and an increase after RYGBP.</p><p>We explored inflammatory proteins C-reactive protein (CRP), serum amyloid A and interleukin-6 before and during massive weight loss 6 and 12 months after RYGBP in morbidly obese subjects. The studied proteins declined after surgery and a correlation between CRP and homeostatic model of assessment for insulin resistance, independent of BMI, strongly linked insulin resistance and inflammation. CRP declined most in insulin-sensitive subjects.</p><p>We examined the excluded stomach mucosa and vagus nerve by measuring gastrin, pepsinogen I (PGI), pancreatic polypeptide (PP) and ghrelin levels during week 1 and year after RYGBP. Ghrelin levels rose with weight loss but declined 24-hours after surgery, like PP, indicating transient vagal nerve damage. Low levels of gastrin and PGI suggest a resting mucosa.</p><p>We evaluated gut peptides: peptide YY (PYY), glucaogon like peptide-1 (GLP-1), pro-neurotensin (pro-NT) and PP, in lean (young and middle-aged), obese and postoperative RYGBP subjects pre- and postprandially. RYGBP subjects had exaggerated levels of PYY and GLP-1 postprandially and higher basal proNT levels, implying a ‘satiety peptide tone’ that may contribute to the maintenance of weight loss.</p><p>In summary, RYGBP results in marked weight loss and alterations in gut and adipose tissue peptides involved in appetite regulation and energy homeostasis. These postoperative peptide changes may contribute to impressive weight loss observed after RYGBP.</p>