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CLIC1 is an intracellular membrane protein that is unusual in that it can exist in both a soluble and an integral membrane form. The manner in which this protein inserts into membranes is unknown although it is proposed to undergo a change in structure whereby it initially experiences a degree of unfolding and then refolds into its new membrane-bound conformation. This study focuses on the characterisation of CLIC1 in terms of its secondary, tertiary and quaternary structure, the determination of its conformational stability at equilibrium and the establishment of its unfolding kinetics, all under conditions of varying pH, polarity, redox conditions, temperature and ionic strength. CLIC1 was found to be most stable at pH 7.0 / 20oC. The unfolding process is two-state and cooperative, producing a DG(H2O) of ~10 kcal/mol and a m-value of ~2 kcal/mol per molar urea. A decrease in pH to 5.5 or an increase in temperature to 37oC resulted in the stabilisation of an equilibrium intermediate species under mild denaturing conditions and a destabilisation of the native state. This was further evidenced by an increase in the rate of unfolding of CLIC1 from the native state to the denatured state under these conditions. A state with similar properties to the intermediate species was detected in the absence of urea at pH 5.5 / 37oC and under non-reducing conditions at both pH 7.0 / 20oC and pH 5.5 / 20oC. The intermediate species is more hydrophobic than either the native or denatured state; it is stabilised by salts, has a reduced secondary structure, increased flexibility and a buried Trp35 relative to the native state. The rate of formation of the intermediate species is a slow process which may involve an oligomerisation step. The results from this study provide an interpretation for the structure and mechanism of CLIC1 pore formation in vivo by comparing the effects of the environment on the structure and stability of the protein.

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In this study we have focused on the codon usage bias in E. coli. In chapter 3, we use the population genetics model and the data available on the protein and mRNA levels of the E. coli genes to understand the pattern of codon usage in different genes with different expression levels and see which measure best explains the codon usage pattern. Besides codon bias, by testing for the over-parametrization of the model, we are able to test for the existence of context dependent mutation. We have also fitted the model for the codon usage patter in the Yeast and also tested for the context dependent mutation in this organism. In chapter 4, we focus on the first 10-15 codons in the genes of E. coli. Motivated by the fact that in this region we observe two phenomena, reduction in translation efficiency and suppression of mRNA secondary structures, we investigate whether the former is a side effect of selection for the latter. For this matter we have generated a set of synonymous randomized sequences, and then by selecting the ones which show weak secondary structures in the mentioned region, we would be able to test the theory. We will also look at the frequencies of the amino acids in E. coli genes and see whether the selection for weak secondary structures in the translation initiation region could be strong enough to not only affect the codon usage, but also the choice of amino acids. We would also provide information on the correlation between the strength of the mRNA secondary structure in the first 13 codons and the overall translation efficiency of the genes. / Thesis / Master of Science (MSc)

Self-folding polymer films were only recently proposed as an alternative method for the design of three-dimensional constructs. Due to the relative novelty of the approach, insufficient amount of data on the behavior of such systems is available in the literature. This study is bound to fill the gaps and give a deeper insight into the understanding of how and why different types of folding occur. In this study, four different types of folding of polymer bilayers are presented. Rectangles are one of the simplest geometrical forms and were therefore adopted as a convenient initial system for the investigation of the folding behavior of polymer bilayers. We chose PNIPAM for the active polymer, as it is a well-studied polymer with sharp Lower Critical Transition Temperature at around 33 C. For the passive layer, poly(methyl methacrylate) and poly(caprolactone) were chosen. The influence of different parameters of the system, such as polymer thickness and temperature was thoroughly investigated in order to be accounted for in later experiments. It was demonstrated that bilayers placed on a substrate start to roll from the corners due to quicker diffusion of water. Rolling from the long-side starts later but dominates at high aspect ratio. We showed that the main reasons causing a variety of rolling scenarios are (i) non-homogenous swelling due to slow diffusion of water in hydrogels and (ii) adhesion of polymer to a substrate until a certain threshold. Moreover, non-homogenous swelling determines folding in the first moments, while adhesion plays a decisive role at later stages of folding. After having understood the abovementioned basics, we decided to explore how those applied to more complex shapes. For the purpose, four- and six-arm stars were chosen, the main idea behind this being the creation of self-folding polymer capsules capable of encapsulation of microparticles and cells. Adjusting the polymer thickness and thus the radius of folding allowed creating structures, capable of reversible self-folding and unfolding. The possibility to reversibly encapsulate and release objects in the micro-range was demonstrated on the example of yeast cells. Noteworthy, the capsules were produced by means of the same process we used for the design of tubes – when compared to the folding of rectangles, it was the shape of the initial pattern and the folding radius that were changed; the mechanism was the same – simple one-step folding towards the center of the bilayer. Clearly the number of structures that can be generated by this method is fairly limited. The search for means to overcome this constraint led to the idea of hierarchical multi-step folding. Due to the edge-activation of the bilayers, the observed deformed shapes differ from the classical ones obtained by homogeneous activation. It was found that films could demonstrate several kinds of actuation behavior such as wrinkling, bending and folding that result in a variety of shapes. It was demonstrated that one can introduce hinges into the folded structure by proper design of the bilayer's external shape through diffusion without having to use site selective deposition of active polymers. Experimental observations led us to derive four empirical rules: 1) “Bilayer polymer films placed on a substrate start to fold from their periphery and the number of formed wrinkles/tubes decreases until the angle between adjacent wrinkles/tubes approaches 130°”; 2) “After the wrinkles along the perimeter of the film form tubes, further folding proceeds along the lines connecting the vertexes of the folded film”; 3) “The folding goes along the lines which are closer to the periphery of the films”; 4) „Folding of the rays may result in blocking of the neighboring rays if the angle between the base of the folded ray and the shoulders of the neighboring rays is close to 180°”. These rules were then applied to direct the folding of edge-activated polymer bilayers through a concrete example - the design of a 3D pyramid. One consequence of the second and third rules is that generally triangles are formed during the multi-step folding process. In order to create a cube, or any other 3D structure with non-triangular sides, an effective way to stop the folding along the lines, connecting neighboring vertexes had to be thought of. A possible solution would be the insertion of a rigid element inside the bilayer, perpendicular to the direction of folding. The solution of this problem was to design structures with pores. A pore would normally decrease the rigidity of a structure but in our case, a pore basically comprised an edge inside the structure and could thus form tubes which, as was already shown, exhibit much higher rigidity than a film. On the other hand, a pore, or many pores, would expose different parts of the active layer to the solvent and would strongly influence its swelling and, as a consequence, folding behavior. Hence, the influence of a pore on the swelling and the folding behavior of polymer bilayers had to be investigated. It was shown that pores of the right form and dimensions did indeed hinder the folding as intended. Instead, the polymer films took other ways to fold. As a result, despite the correctness of our reasoning, we failed to produce a cube by hierarchical folding of polymer bilayers. However, other sophisticated 3D objects were obtained, further increasing the arsenal of available structures, as well as giving an in-depth insight on the folding process.

Cancer has been a pervasive and deadly problem for many years. No treatments have been developed that effectively destroy cancer cells while also keeping healthy cells safe. In this work, the knob-socket construct is used to analyze two systems involved in cancer pathways, the PDZ domain and the Bcl-BH3 complex. Application of the knob-socket model in mapping the packing surface topology (PST) allows a direct analysis of the residue groups important for peptide specificity and affinity in both of these systems. PDZ domains are regulatory proteins that bind the C-terminus of peptides involved in the signaling pathway of cancer progression. The domain includes five -strands, two -helices, and six coils/turns. In this study, the PST of all eight solved crystal structures of T-cell lymphoma invasion and metastasis 1 (Tiam1) PDZ domains are mapped to reveal details of ligand-domain binding pockets and packing interactions. Four main interactions were identified in the comparison of the PST maps and a consensus sequence was calculated using knob-socket interaction data. In the case of the Bcl-BH3 complex, binding of these two proteins prevents an unhealthy cell from undergoing apoptosis. In the knob-socket mapped protein-ligand interactions, the helical ligand consists of 8 to 10 residues that specifically interact with four helices on the binding protein: the N-terminus of Helix2, the main bodies of Helix3 and Helix4 and the C-terminus of Helix5. Among all of the interactions that were analyzed, there were three amino acids from the ligand, glycine, leucine, and isoleucine, that always packed into the hydrophobic groove that is key for ligand recognition. By using knob-socket analysis to map quaternary packing structure, it was possible to identify the quaternary-level protein interactions that define ligand specificity and binding strength. From this analysis, possible protein mimetics can be developed that could be used as cancer treatments.

Phosducin-like protein (PhLP), a G protein beta gamma subunit dimer binder and G protein signaling regulator, was suggested to regulate the activity of cytosolic chaperonin CCT by their high affinity interaction. In the present study, the three-dimensional structure of PhLP:CCT complex has been solved by cryoelectron microscopy. PhLP was found to bind only one of the chaperonin rings with both N- and C-terminal domains. It spans the central folding cavity of CCT and interacts with two opposite sides of the top apical region, inducing the constraining of the entry of the folding cavity. These findings support a putative role of PhLP as a co-chaperone similar to prefoldin. Docking studies with the atomic model of PhLP generated from several known structures of the homologous phosducin (Pdc) together with the immuno-EM studies have provided more details of the complex structure and predicted some regions of PhLP and the subunits of CCT involved in the interaction. Taking advantage of the fact that Pdc is highly homologous to PhLP but lack of binding to CCT, the regions of PhLP involved in the interaction with CCT were determined by testing various PhLP/Pdc chimeric proteins in the CCT binding assay. In the other part of this dissertation, the physiological role of PhLP in G protein signaling was investigated. Cellular expression of PhLP was blocked using RNA interference targeting PhLP. Together with overexpression of PhLP variants and kinetic studies of G protein beta gamma dimer formation, PhLP was determined to be a positive mediator of G protein signaling and essential for G protein beta gamma dimer expression and dimer formation. Phosphorylation of PhLP at serines 18—20 by protein kinase CK2 was required for G protein beta gamma dimer formation, while a high-affinity interaction of PhLP with CCT appeared unnecessary. Interestingly, G protein beta subunit was found to interact with CCT by co-immunoprecipitation and PhLP over-expression increased the binding of G protein beta subunit to CCT. These results suggest that PhLP and CCT act as co-chaperones in the folding and assembly of the G protein beta gamma subunit dimer by forming a ternary PhLP-Gbeta-CCT complex that is a necessary intermediate in the assembly process.

This master thesis deals with automatic summarization of text and how semantic folding can be used as a similarity measure between sentences in the TextRank algorithm. The method was implemented and compared with two common similarity measures. These two similarity measures were cosine similarity of tf-idf vectors and the number of overlapping terms in two sentences. The three methods were implemented and the linguistic features used in the construction were stop words, part-of-speech filtering and stemming. Five different part-of-speech filters were used, with different mixtures of nouns, verbs, and adjectives. The three methods were evaluated by summarizing documents from the Document Understanding Conference and comparing them to gold-standard summarization created by human judges. Comparison between the system summaries and gold-standard summaries was made with the ROUGE-1 measure. The algorithm with semantic folding performed worst of the three methods, but only 0.0096 worse in F-score than cosine similarity of tf-idf vectors that performed best. For semantic folding, the average precision was 46.2% and recall 45.7% for the best-performing part-of-speech filter. / Det här examensarbetet behandlar automatisk textsammanfattning och hur semantisk vikning kan användas som likhetsmått mellan meningar i algoritmen TextRank. Metoden implementerades och jämfördes med två vanliga likhetsmått. Dessa två likhetsmått var cosinus-likhet mellan tf-idf-vektorer samt antal överlappande termer i två meningar. De tre metoderna implementerades och de lingvistiska särdragen som användes vid konstruktionen var stoppord, filtrering av ordklasser samt en avstämmare. Fem olika filter för ordklasser användes, med olika blandningar av substantiv, verb och adjektiv. De tre metoderna utvärderades genom att sammanfatta dokument från DUC och jämföra dessa mot guldsammanfattningar skapade av mänskliga domare. Jämförelse mellan systemsammanfattningar och guldsammanfattningar gjordes med måttet ROUGE-1. Algoritmen med semantisk vikning presterade sämst av de tre jämförda metoderna, dock bara 0.0096 sämre i F-score än cosinus-likhet mellan tf-idf-vektorer som presterade bäst. För semantisk vikning var den genomsnittliga precisionen 46.2% och recall 45.7% för det ordklassfiltret som presterade bäst.