Uma das espécies que atualmente vem despertando interesse econômico por seu elevado valor de mercado é o maracuzajeiro doce (Passiflora alata Curtis). Entretanto, a cultura é afetada por diferentes doenças que prejudicam a produtividade e a qualidade dos frutos, sendo a doença causada pelo Cowpea aphid-borne mosaic virus (CABMV) a que mais afeta a cultura do maracujazeiro no Brasil. O presente trabalho teve como objetivo a obtenção de plantas transgênicas de P. alata visando resistência ao CABMV. O processo de transformação genética utilizado foi via Agrobacterium tumefaciens, estirpe EHA105, contendo o cassete de expressão com um fragmento do gene da proteína capsidial do CABMV, numa construção tipo hairpin e o gene de seleção nptII que confere resistência ao antibiótico canamicina. Para os experimentos de transformação genética foram utilizados como explantes segmentos de hipocótilo e segmentos internodais. Após 2 a 3 dias de co-cultivo em meio de cultura MS (MURASHIGE; SKOOG, 1962) contendo acetosseringona (100 mM), os explantes foram transferidos para meio de cultura de seleção e regeneração constituído de sais minerais e vitaminas de MS, suplementado com benzilaminopurina (BAP - 1mg/L) + thidiazuron (TDZ - 0,5 mg/L) + canamicina (100 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L), pH 5,8. Após 4 a 6 semanas de incubação, determinou-se o número de explantes responsivos e as gemas adventícias desenvolvidas foram transferidas para meio de cultura de alongamento MSM + GA3 (1,0 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L). As plantas desenvolvidas foram aclimatizadas e analisadas por PCR, utilizando primers específicos para a detecção do fragmento do gene da proteína capsidial do CABMV e do gene de seleção (nptII). Foram identificadas 47 plantas transgênicas PCR positivas para do gene nptII. Até o momento, a integração do gene nptII foi confirmada por Southern blot em 9 plantas / One species that is currently attracting interest due to its high economic value is the sweet passionflower (Passiflora alata Curtis). However, the culture is affected by different diseases that harm the productivity and fruit quality. The disease caused by Cowpea aphid-borne mosaic virus (CABMV) is the one that more affect the culture of passionflower in Brazil. This work aimed to obtain transgenic plants of P. alata resistant to the CABMV. The genetic transformation process was via Agrobacterium tumefaciens, strain EHA105, containing the expression cassette with a fragment of the coat protein gene of CABMV, in a hairpin construct and the selection gene nptII, which confers resistance to the antibiotic kanamycin. In the experiments of genetic transformation hypocotyl segments and internodal segments were used as explants. After 2-3 days of co-cultivation in MS medium (MURASHIGE; SKOOG, 1962) containing acetosyringone (100 mM), the explants were transferred to the selection and regeneration culture medium consisting of mineral salts and vitamins of MS medium supplemented with benzylaminopurine (BAP - 1 mg/L) + thidiazuron (TDZ - 0.5 mg/L) + kanamycin (100 mg/L) + cefotaxime (500 mg/L) + silver nitrate (4.0 mg /L), pH 5.8. After 4-6 weeks of incubation, it was determined the number of responsive explants. Shoots developed were transferred to elongating culture medium MSM + GA3 (1.0 mg/L) + cefotaxime (500 mg/L) + nitrate silver (4.0 mg/L). The developed plants were acclimatized and analyzed by PCR using specific primers to detect the fragment of CABMV and the selection gene (nptII). It was identified 47 transgenic plants PCR positive for the gene nptII. Until this moment, the integration of the nptII gene was confirmed by Southern blot in 9 plants

This master's thesis is engage in suggestion of low noise 70 cm band amplifier with filter and diode attenuator. At first the thesis describes the basic parameters of amplifier, for example gain, noise figure and dynamic extent. Later in detail describes individual parts, which are the device consist of. At every part of system is mentioned the diagram of connection and values of components, which are ascertained from calculation, simulation and recommendation of producer. The characteristic parameters of amplifier were measured after construction.

The study of synthetic peptides aid in improving our current understanding of the fundamental principles for the de novo design of functional proteins. The investigation of designed peptides has been instrumental in providing answers to many questions ranging from the conformational preferences of amino acids to the compact folded structures and also in developing tools for understanding the growth and formation of the protein secondary structures (helices, sheets and turns). In addition, the self-assembly of peptides through non-covalent interactions is also an emerging area of growing interest. The design of peptides which can mimic the protein secondary structures relies on the use of stereochemically constrained amino acid residues at select positions in the linear peptide sequences, leading to the construction of protein secondary structural modules like helices, hairpins and turns. The use of non-coded amino acid residues with strict preferences for adopting particular conformations in the conformational space becomes the most crucial step in peptide design strategies. In addition the crystallographic characterization and analysis of the sequences provides the necessary optimization of the design strategies. The crystallographic characterization of designed peptides provides a definitive and conclusive proof of the success of a design strategy. Furthermore, the X-ray structures provide an atomic view of the interactions, both strong and weak, which govern the growth of the crystal. The information on the geometric parameters and stereochemical properties of a series of peptides, through a systematic study, provides the necessary basis for further scientific investigation, like the molecular dynamics and can also aid in improving the force field parameters meant for carrying out molecular simulations. This can be further complemented by constructing biologically active peptide sequences. The focus of this thesis is to characterize crystallographically the conformational and structural aspects of peptide nanotubes and encapsulated water wires and the β-hairpin peptide models of β-sheets. The systematic study of a series of pentapeptide and octapeptide sequences, containing Aib and D-amino acid residues incorporated at strategic positions, establish the conformation and structural properties of designed peptides as mimics of protein secondary structures and hydrophobic tubular peptide channels and close-packed forms. The structures reported in this thesis are given below: 1 Boc-DPro-Aib-Leu-Aib-Val-OMe (DPUL5) C30H53N5O8 2 Boc-DPro-Aib-Val-Aib-Val-OMe (DPUV5a) C29H51N5O8 .(0.5) H2O 3 Boc-DPro-Aib-Val-Aib-Val-OMe (DPUV5b) C27H51N5O8 .(0.17) H2O 4 Boc-DPro-Aib-Ala-Aib-Val-OMe (DPUA5) C27H47N5O8 5 Boc-DPro-Aib-Phe-Aib-Val-OMe (DPUF5) C33H48N5O8 6 Boc-Pro-Aib-DLeu-Aib-DVal-OMe (PUDL5) C30H53N5O8 7 Boc-Pro-Aib-DVal-Aib-DVal-OMe (PUDV5a) C27H51N5O8 .(0.17) H2O 8 Boc-Pro-Aib-DVal-Aib-DVal-OMe (PUDV5b) C27H51N5O8 . 2H2O 9 Boc-Pro-Aib-DAla-Aib-DVal-OMe (PUDA5) C27H47N5O8 10 Boc-Pro-Aib-DPhe-Aib-DVal-OMe (PUDF5) C33H48N5O8 11 Ac-Phe-Pro-Trp-OMe (FPW) C28H32N4O5.(0.33)H2O 12 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPLP8) C56H84N8O1 1 .(0.5) H2O 13 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (YDPP8) C56H83N8O12 .(1.5) H2O 14 Boc-Leu-Val-Val-DPro-ψPro-Leu-Val-Val-OMe (PSIP8) C56H84N8O11S1 .(1.5) H2O 15 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPPV8) C48H84N8O11 16 Boc-Leu-Phe-Val-DPro-Aib-Leu-Phe-Val-OMe (DPUF8) C57H88N8O11.(1.5) H2O 17 Piv-Pro-ψH,CH3Pro-NHMe (PSPL3) C22H37N3O5S1 18 Boc-Leu-Val-Val-Aib-DPro-Leu-Val-Val-OMe (UDPV8) C47H84N8O11.2(C3H7NO) 19 Boc-Leu-Phe-Val-DPro-Ala-Leu-Phe-Val-OMe (BH1P8) C54H78N8O11.H2O 20 Boc-Leu-Phe-Val-DPro-Aib-Leu-Phe-Val-OMe (DPUFP8) C55H84N8O11. (0.5) H2O 21 Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (YDPPP8) C56H83N8O12. (1.5) H2O The crystal structure determination of the peptides presented in this thesis provides a wealth of information on the folding patterns of the sequences, in addition to the characterization of many structural and geometric properties. In particular, the study sheds light on the growth and formation of peptide nanotubes and the structure of encapsulated water wires, and also the structural details of Type I′ and Type II′β-turn nucleated hairpins. The study provides the backbone and side chain conformational parameters of the sequences, highlighting the varied conformational excursions possible in the peptide molecules. The thesis is divided into 6 chapters and one appendix. Chapter 1 gives a general introduction to the stereochemistry of the polypeptide chain, description of backbone torsion angles of α-amino acid residues and the major secondary structures of α-peptides, namely α-helix, β-sheet and β-turns. The basic structural features of helices and sheets are given. A brief introduction to polymorphism and weak interactions is also presented, followed by a discussion on X-ray diffraction and solution to the phase problem. Chapter 2 is divided into two parts. PART 1 describes the crystal structures of a series of eight related enantiomeric peptide sequences (Raghavender et al., 2009; Raghavender et al., 2010). The crystal structures of four sequences with the general formula Boc-DPro-Aib-Xxx-Aib-Val-OMe (Xxx = Ala/Val/Leu/Phe) and the enantiomeric sequences provided a set of crystal structures withdifferent packing arrangements. The structure of the peptide with Xxx = Leu revealed a nanotube formation with the Leu lining the inner walls of channel. The channels were found to be empty. The sequence with Xxx = Val revealed a solvent-filled water channel.Investigation of the water wire structures on the diffraction data collected on the same crystal over a period of time revealed the existence of two different kinds of water wires in thechannels. Comparison with the peptide tubular structures available in the literature and the water structure inside the aquaporin channels are contrasted. Close-packed structures are observed in the case of Xxx=Ala and Phe. The backbone conformations are essentially identical. Enantiomeric sequences also revealed similar structures. Polymorphic forms were observed in the case of DVal(3) containing sequence. One form is observed to have water-filled channels forming a nanotube, as opposed to the close-packed structure in the polymorphic form. Crystal parameters DPUL5: C30H53N5O8; P65; a = b = 24.3673 (9) Å, c = 10.6844 (13) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0671, wR2 = 0.1446. DPUV5a: C29H51N5O8 .(0.5) H2O; P65; a = b = 24.2920 (13) Å, c = 10.4838 (11) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0554, wR2 = 0.1546. DPUV5b: C29H51N5O8 .(0.17) H2O; P65; a = b = 24.3161 (3) Å, c = 10.1805 (1) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0617, wR2 = 0.1844. DPUA5: C27H47N5O8; P212121; a = 12.2403 (8), b = 15.7531 (11) Å, c = 16.6894 (11) Å; Z =4; R = 0.0439, wR2 = 0.1249. DPUF5: C33H48N5O8; P212121; a = 10.3268 (8), b = 18.7549 (15) Å, c = 18.9682 (16) Å; Z = 4; R = 0.0472, wR2 = 0.1325. PUDL5: C30H53N5O8; P61; a = b = 24.4102 (8) Å, c = 10.6627 (7) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0543, wR2 = 0.1495. PUDV5a: C29H51N5O8 .(0.17)H2O; P61; a = b = 24.3645 (14) Å, c = 10.4875 (14) Å; α = β = 90°, γ = 120°; Z = 6; R = 0.0745, wR2 = 0.1810. PUDV5b: C29H51N5O8. 2H2O; C2; a = 20.7278 (35), b = 9.1079 (15) Å, c = 19.5728 (33) Å; α = γ = 90°, β = 94.207°; Z = 6; R = 0.0659, wR2 = 0.1755. PUDA5: C27H47N5O8; P212121; a = 12.2528 (12), b = 15.7498 (16) Å, c = 16.6866 (16) Å; Z = 4; R = 0.0473, wR2 = 0.1278. PUDF5: C33H48N5O8; P212121; a = 10.3354 (8), b = 18.7733 (10) Å, c = 18.9820 (10) Å; Z = 4; R = 0.0510, wR2 = 0.1526. PART 2 describes the crystallographic characterization of the tubular structure in a tripeptide Ac-Phe-Pro-Trp-OMe (FPW) sequence. The arrangement of the single-file water moleculesin the peptide nanotubes of FPW could be established by X-ray diffraction. In addition, the energetically favoured arrangement of the water wire inside the peptide channels could be modeled by understanding the construction of the peptide nanotube. In particular, the helicalmacrodipole of the peptide nanotube and the water wire dipoles prefer an antiparallel arrangement inside the peptide channels as opposed to parallel arrangements, is established by the classical dipole-dipole interaction energy calculation. In addition, the growth of thenanotubes and the arrangement of the water wires inside the channels could be correlated to the macroscopic dimensions of the crystal by the indexing of the crystal faces and contrasted with the structure of DPUV5. Crystal parameters FPW: C28H32N4O5.(0.33)H2O; P65; a = b = 21.5674 (3) Å, c = 10.1035 (2) Å; α = β = 90°, γ = 120 °; Z = 6; R = 0.0786, wR2 = 0.1771 Chapter 3 provides the crystal structures of five octapeptide β-hairpin forming sequences and a tripeptide containing a modified amino acid, with modification in the side chain (pseudo-proline, ψH,CH3Pro). The parent peptide, Boc-Leu-Phe-Val-DPro-Pro-Leu-Phe-Val-OMe (DPLP8), was observed to form a strong Type II′β-turn at the DPro-Pro segment, and the strand segments adopting a β-sheet conformation. Two molecules were observed in the asymmetric unit, inclined to each other at approximately 70°. Modification in the strand sequence Phe(2) to Tyr(2) also resulted in a hairpin with identical conformation and similar packing arrangement. The difference was in the solvent content. In both the cases the molecules were packed orthogonal with respect to each other, resulting in the formation of ribbon-like structures in three dimensions. The replacement of Phe(2) and Phe(7) with Valine residues, with the retention of DPro-Pro β-turn segment, results in an entiely different packing arrangement (parallel). Modification of Pro(5) residue of the turn segment to Aib(5) and ψPro, also results in the molecules packing orthogonally to each other. The tripeptide with a modified form of ψPro, namely ψH,CH3Pro, resulted in a folded structure with a Type VIa β-turn, with the amide bond between the Pro-ψH,CH3Pro segment adopting a cis configuration (Kantharaju et al., 2009). Crystal parameters DPLP8: C56H84N8O11 .(0.5) H2O; P21; a = 14.4028 (8), b = 18.9623 (11) Å, c = 25.4903 (17) Å, β = 105.674 ° (4); Z = 4; R = 0.0959, wR2 = 0.2251. YDPP8: C56H84N8O12 .(1.5) H2O; P212121; a = 14.4028 (8), b = 18.9623 (11) Å, c = 25.4903 (17) Å, Z = 8; R = 0.0989, wR2 = 0.2064. PSIP8: C57H86N8O11S1.(1.5) H2O; C2; a = 34.6080 (2), b = 15.3179 (10) Å, c = 25.6025 (15) Å, β = 103.593 ° (3); Z = 4; R = 0.0931, wR2 = 0.2259. DPPV8: C48H84N8O11; P1; a = 9.922 (3), b = 11.229 (4) Å, c = 26.423 (9) Å, α = 87.146 (6), β = 89.440° (6), γ = 73.282 (7); Z = 2; R = 0.1058, wR2 = 0.2354. DPUF8: C57H88N8O11 .(1.5) H2O; P21; a = 18.410 (2), b = 23.220 (3) Å, c = 19.240 (3) Å, β = 118.036 ° (4); Z = 4; R = 0.1012, wR2 = 0.2061. PSPL3: C22H37N3O5S1; P31; a = b = 14.6323 (22), c = 10.4359 (22) Å, α = β = 90°, γ = 120°; Z = 3; R = 0.0597, wR2 = 0.1590. Chapter 4 describes the crystal structure and molecular conformation of Type I′β-turn nucleated hairpin. The incorporation of Aib-DPro segment in the middle of Leu-Val-Val strands in the peptide sequence Boc-Leu-Val-Val-Aib-DPro-Leu-Val-Val-OMe results in an obligatory Type I′ turn containing hairpin. The molecular conformation and the packing arrangement of the molecules in the crystal are contrasted with the only Type I′β-hairpin reported in the literature and with a sequence where the turn residues are flipped and strand residues replaced with Phe(2) and Phe(7). Crystal parameters UDPV8: C47H84N8O11.2(C3H7NO); P21; a = 11.0623 (53), b = 18.7635 (89) Å, c = 16.6426 (80) Å, β = 102.369 (8); Z = 2; R = 0.0947, wR2 = 0.1730. Chapter 5 provides the crystal structures of three polymorphic forms of β-hairpins. The structure of BH1P8 provides new insights into the packing of hairpins inclined orthogonally to each other. The two polymorphic forms differ not only in their modes of packing in crystals but also in the strong and weak interactions stabilizing the packing arrangements. The polymorphic forms of DPUFP8 differ only in the content of the solvent in the asymmetric unit and the role it plays in bridging the symmetry related pairs of molecules. The polymorphic form YDPPP8 crystallized in a completely different space group, revealing a completely different mode of packing and also the cocrystallized solvent participating in a different set of interactions. Crystal parameters BH1P8: C54H78N8O11.H2O; P212121; a = 18.7511 (9), b = 23.3396 (11) Å, c = 28.1926 (13)Å; Z = 8; R = 0.1208, wR2 = 0.2898. DPUFP8: C55H84N8O11. (0.5) H2O; P21; a = 18.0950 (4), b = 23.0316 (5) Å, c = 18.6368 (5) Å, β = 117.471 (2); Z = 4; R = 0.0915, wR2 = 0.2096. YDPPP8: C56H83N8O12. (1.5) H2O; P21; a = 14.3184 (8), b = 18.9924 (9) Å, c = 25.1569 (14) Å, β = 105.590 (4); Z = 4; R = 0.1249, wR2 = 0.2929. Chapter 6 provides a comprehensive overview of the β-hairpin peptide crystal structures published in the literature as well as those included in the thesis. The hairpins are classified based on the residues composing the β-strands and the mode of their packing in the crystals. In the crystal structures the hairpins are observed to adopt either a Type II′ or Type I′β-turns. The indexing of the crystal faces of a few representative hairpin peptides crystallographically characterized in this thesis, provides a rational explanation for the preferential growth of the crystals in certain directions, when correlated with the strong directional forces (hydrogen bonding) and weak interactions (van der Waals, aromatic-aromatic) observed in the crystal packing. The insights gained by these studies would be highly valuable in understanding the nucleation and growth of β-hairpin peptides and the formation of β-sheet structures. Appendix I describes the Cambridge Structural Database (CSD) analysis of the conformational preferences of the proline residues found in the peptide crystal structures. The frequency distributions of the backbone φ, ψ and ω and side chain χ1, χ2, χ3, χ4 and θ torsion angles of the proline residues are calculated, tabulated and represented as graphical plots. The correlation between the backbone and endocyclic torsion angles provides for a clear evidence of the role of a particular torsion variable χ2 in deciding the state of puckering. In addition, the endocyclic bond angles also appear to be correlated, relatively strongly, with the χ2 torsion. This provides a geometrical explanation of the factors governing the puckering of the proline ring.

CAG/CTG repeat instability is associated with at least 14 neurological disorders, including Huntington’s disease and Myotonic dystrophy type 1. In vitro and in vivo studies have showed that CAG/CTG repeats form a stable hairpin that is believed to be the intermediate for repeat expansion and contraction. Addition of extra DNA is essential for repeat expansion, so DNA synthesis is one of the keys for repeat expansion. In vivo studies reveal that 3’ CTG slippage with subsequent hairpin formation (henceforth called the 3’ CTG slippage hairpin) occurs during DNA synthesis. It is proposed that hairpin tolerance machinery is activated because prolonged stalling of DNA polymerase triggers severe DNA damage. As a means toward studying the hairpin-mediated expansion, we created a special hairpin substrate, mimicking the 3’ CTG slippage hairpin, to determine which polymerase promotes hairpin bypass. Our studies reveal polymerase β (pol β) is involved in the initial hairpin synthesis while polymerase δ (pol δ) is responsible for the resumption of DNA synthesis beyond the hairpin (extension step). Surprisingly, we also found that the pol δ can remove the short CTG hairpin by excision of the hairpin with its 3’ to 5’ exonuclease activity. Besides repairing the hairpin directly, resolving the hairpin is an alternative pathway to maintain CAG/CTG repeat stability. With limited understanding of which human helicase is responsible for resolving CAG/CTG hairpins, we conducted a screening approach to identify the human helicase involved. Werner Syndrome Protein (WRN) induces the hairpin repair activity when (CTG)35 hairpin is formed on the template strand. Primer extension assay reveals that WRN stimulates pol δ synthesis on (CAG)35/(CTG)35 template and such induction was still found in the presence of accessory factors. Helicase assay confirms that WRN unwinds CTG hairpin structures. Our studies provide a better understanding of how polymerases and helicases play a role in CAG/CTG repeat instability. Considering CAG/CTG repeat instability associated disorders are still incurable, our studies can provide several potential therapeutic targets for treating and/or preventing CAG/CTG repeat associated disorders.

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express <em>&alpha;</em>-helix and <em>&beta;</em>-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a <em>&beta;</em>-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both <em>&alpha;</em>-helix and <em>&beta;</em>-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of <em>&beta;</em>-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between <em>&alpha;</em>-helix and <em>&beta;</em>-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined.

The secondary structure of peptides is of pivotal importance for their biological function. The introduction of photoswitchable moieties into the backbones of peptides provides a unique way of regulating their conformation using an external stimulus, i.e., light. This thesis addresses the design, synthesis, and conformational analysis of photoswitchable peptidomimetics (PSPM). Examples of photomodulation of their functional properties are given. PSPM were prepared by incorporation of stilbene and thioaurone chromophores (switches) into dipeptides. Synthetic schemes for preparing these chromophores have been developed. Their suitability for incorporation into peptidomimetics has been demonstrated, and the resulting PSPM have been subjected to photoisomerization as well as computational and spectroscopic conformational analysis. The chromophore’s potential as a β-hairpin inducer was particularly interesting. To investigate the factors that govern the formation of β-hairpins, a series of decapeptides were prepared. Turn regions consisting of amino acids or chromophores were combined with antiparallel peptide strands with hydrophobic side chains. Linear tryptophan zipper peptidomimetics and cyclic peptidomimetics with a second, hairpin-inducing turn region were particularly promising. Comparison between switches revealed that the more flexible stilbene is a better choice for upholding the β-hairpin conformation than the thioaurone. The catalytic properties of an artificial hydrolase with a helix-loop-helix structure can be improved by introducing a stilbene photoswitch into the loop region. Photoisomerization regulates the catalytic activity of this peptidomimetic, and provides a means to control its aggregation state. The activity of the enzyme Mycobacterium tuberculosis ribonucleotide reductase was realized by incorporating a stilbene moiety into a linear peptide. Here, one photoisomer proved to be an inhibitor at nM concentrations. A significantly lower effect was observed for the other isomer. Finally, the decomposition of thioaurones, mainly to thioflavonols and thiaindenes, under conditions used for solid-phase peptide synthesis has been mapped. These findings are expected to have implications for future use of this chromophore.

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express <em>&alpha;</em>-helix and <em>&beta;</em>-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a <em>&beta;</em>-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both <em>&alpha;</em>-helix and <em>&beta;</em>-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of <em>&beta;</em>-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between <em>&alpha;</em>-helix and <em>&beta;</em>-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined.

Predicting protein structure using its primary sequence has always been a challenging topic in biochemistry. Although it seems as simple as finding the minimal energy conformation, it has been quite difficult to provide an accurate yet reliable solution for the problem. On the one hand, the lack of understanding of the hydrophobic effect as well as the relationship between different stabilizing forces, such as hydrophobic interaction, hydrogen bonding and electronic static interaction prevent the scientist from developing potential functions to estimate free energy. On the other hand, structure databases are limited with redundant structures, which represent a noncontinuous, sparsely-sampled conformational space, and preventing the development of a method suitable for high-resolution, high-accuracy structure prediction that can be applied for functional annotation of an unknown protein sequence. Thus, in this study, we use molecular dynamics simulation as a tool to sample conformational space. Structures were generated with physically realistic conformations that represented the properties of ensembles of native structures. First, we focused our study on the relationship among different factors that stabilize protein structure. Using a wellcharacterized mutation system of the B-hairpin, a fundamental building block of protein, we were able to identify the effect of terminal ion-pairs (salt-bridges) on the stability of the beta-hairpin, and its relationship with hydrophobic interactions and hydrogen bonds. In the same study, we also correlated our theoretical simulations qualitatively with experimental results. Such analysis provides us a better understanding of beta-hairpin stability and helps us to improve the protein engineering method to design more stable hairpins. Second, with large-scale simulations of different representative protein folds, we were able to conduct a fine-grained analysis by sampling the continuous conformational space to characterize the relationship among backbone conformation, side-chain conformation and side-chain packing. Such information is valuable for improving high-resolution structure prediction. Last, with this information, we developed a new prediction algorithm using packing information derived from the conserved relative packing groups. Based on its performance in CASP7, we were able to draw the conclusion that our simulated dataset as well as our packing-oriented prediction method are useful for template based structure prediction.

Les plasmas radio-fréquences à couplage inductif en gaz halogénés simples (cl2/hbr/o2) sont fortement utilisés dans l'industrie des semi-conducteurs. Cependant, notre connaissance des processus réactionnels de ces plasmas est encore très partielle. De nombreux travaux de simulations (fluides, particulaires...), visant à améliorer celle-ci, ont été produits ces dernières décennies. Toutefois, trop peu de résultats expérimentaux sont disponibles dans la littérature afin de valider ou améliorer ces simulations. L'objectif de cette thèse est alors de produire un ensemble complet de résultats experimentaux. Nous nous focalisons essentiellement sur le cas des plasmas de cl2 et de o2 purs. Dans cette thèse, nous étendons les résultats expérimentaux déjà présents dans la littérature : densités de charges et de neutres, températures translationnelles. En particulier, les tendances en fonction de la pression, essentielles pour la simulation, sont soigneusement étudiées. Les vibrations moléculaires sont également étudiées à l'aide d'un montage innovant de spectroscopie d'absorption. Nous montrons que les simulations sont encore loin de représenter fidèlement les processus réactionnels des plasmas étudiés. Nous tentons de fournir à cet effet quelques pistes d'améliorations. Ce travail est la base nécessaire à l'amélioration continue des plasmas industriels utilisés pour la gravure de semi-conducteurs. / Radio-frequency inductively-coupled plasmas in simple halogen gases (cl2/hbr/o2) are widely used in the semi-conductor industry. However, our knowledge of these plasmas is still incomplete. To improve it, numerous simulation studies have been performed in the last decades. Unfortunately, experimental results to compare these studies are still scarce. The objectives of this thesis is to provide a comprehensive set of experimental results. We focused on the plasmas of pure o2 and cl2. In this thesis, we extend the already available experimental results : neutral nd charges densities, translational temperatures. In particular, the tendancies of these parameters as a function of the pressure are carefully studied. Molecular vibrations are studied as well using a new kind of absorption spectroscopy setup. We show that the recent simulations are still far from representing the reactional processes in the studied plasmas. We then try to provide some ideas of improvement. This work is the needed start to improve etching plasma industrial processes.

The secondary structure of DNA is variable and depends on the sequence of nu- cleotides in a strand. While DNA can form duplexes, formations of three, four, or even a single strand have been observed in vivo and in vitro as well. In this thesis, we study the effect of small changes of oligonucleotide sequences on the stability of hairpins formed by DNA heptamers by 1 H nuclear magnetic resonance (NMR) spectroscopy. Suitable DNA sequences were selected based on symmetry rules and stability prediction by near- est neighbor model. Two-dimensional 1 H -1 H NOESY spectra were used to assign the 1 H resonances of aromatic hydrogens. Variable-temperature 1D spectra served for ob- taining melting curves, from which the thermodynamic properties of the hairpins were determined. The presence of hairpins in the solutions was confirmed by the character of the NOESY spectra, independence of melting temperature on oligonucleotide concen- tration, and comparison of competing melting-curve models of duplex and hairpin. Our results point out the importance of the order of the stem base pairs and contribute to the description of the extraordinary stability of DNA mini-hairpins. 1