Lectins are ubiquitous proteins that has domain(s) for recognition and binding to carbohydrates and that can decipher the glicocode in the structures of the glycans linked to soluble glycoproteins and membrane. Molecular interactions based on protein-carbohydrate recognition play key roles in numbers biological processes, such as: cellular communication, gametes recognition, embryonic development, and immune response, among others. Lectins from algae are poorly studied compared to plant lectins and this fact is due to the difficulty of obtaining material for study. The isolectins isolated from red marine alga Solieria filiformis have purification protocols well established. Furthermore, these isolectins have a bacteriostatic effect over gram-negative bacteria and antinociceptive and anti- inflammatory activities. The aim of this study was to determine the primary structure of the isolectins isolated from marine red alga Solieria filiformis. The primary structure of two isoforms (SfL1 and SFL2) were determined by combination of mass spectrometry and molecular biology. The sequences of the two isolectinas were compared to databases (NCBI) and showed similarity to lectins belonging to the family OAAH. The structural similarity of these proteins suggests that bacteria, cyanobacteria and macroalgae are evolutionarily related. Others bioinformatic analysis showed that the SfLs have four internal repeated domains in its sequences as well as presence of an N-glycosylation site and a conserved carbohydrate-binding site with high identity to the CRD from OAAHs. This family of lectins is related to the anti-HIV activity due to its characteristics of binding the high‐mannose‐type N‐glycans. What makes these two isoforms molecules potential for the study of anti-HIV activity. / Lectinas sÃo proteÃnas ubÃquas que possuem domÃnio(s) de reconhecimento e ligaÃÃo a carboidratos e podem decifrar o glicocÃdigo das estruturas dos glicanos associados à glicoproteÃnas solÃveis e de membrana. As interaÃÃes moleculares baseadas no reconhecimento proteÃna-carboidrato desempenham papÃis chave em nÃmeros processos biolÃgicos, tais como: comunicaÃÃo celular, reconhecimento de gametas, desenvolvimento embrionÃrio, reposta imune, entre outras. As lectinas de algas marinhas sÃo pouco estudadas em comparaÃÃo Ãs lectinas de plantas e isso se deve, em parte, à dificuldade de obtenÃÃo de material para estudo. As isolectinas da alga vermelha Solieria filiformis jà possuem protocolo de purificaÃÃo estabelecido. AlÃm disso, jà fora observado efeito bacteriostÃtico contra bactÃrias gram-negativas, atividade antinociceptiva e anti-inflamatÃria para estas lectinas. O objetivo desse trabalho foi determinar a estrutura primÃria das isolectinas da alga marinha vermelha Solieria filiformis. A estrutura primÃria de duas isoformas (SfL1 e SfL2) foi determinada por combinaÃÃo de espectrometria de massas e biologia molecular. As sequÃncias das duas isolectinas foram comparados a sequÃncias depositadas em bancos de dados (NCBI) e houve similaridade com as lectinas pertencentes à famÃlia OAAH. A semelhanÃa estrutural dessas proteÃnas sugere que as bactÃrias, cianobactÃrias e as macroalgas sÃo evolutivamente relacionadas. Outras anÃlises de bioinformÃtica demostraram que as SfLs possuem quatro domÃnios internos repetidos em suas sequÃncias, a existÃncia de um sÃtio de N-glicosilaÃÃo, e um sÃtio de ligaÃÃo a carboidrato conservado e com alta identidade com os sÃtios das OAAHs. Essa famÃlia de lectinas està relacionada à atividade anti-HIV devido a suas caracterÃsticas de ligaÃÃo a N-glicanos ricos em manose. O que torna estas duas isoformas molÃculas potenciais para o estudo de atividade anti-HIV.

A large body of literature exists regarding linear and nonlinear dynamic absorbers, but the vast majority of it deals with linear primary structures. However, nonlinearity is a frequency occurrence in engineering applications. Therefore, the present thesis focuses on the mitigation of vibrations of nonlinear primary systems using nonlinear dynamic absorbers. Because most existing contributions about their design rely on optimization and sensitivity analysis procedures, which are computationally demanding, or on analytic methods, which may be limited to small-amplitude motions, this thesis sets the emphasis on a tuning procedure of nonlinear vibration absorbers that can be computationally tractable and treat strongly nonlinear regimes of motion. The proposed methodology is a two-step procedure relying on a frequency-energy based approach followed by a bifurcation analysis. The first step, carried out in the free vibration case, imposes the absorber to possess a qualitatively similar dependence on energy as the primary system. This gives rise to an optimal nonlinear functional form and an initial set of absorber parameters. Based upon these initial results, the second step, carried out in the forced vibration case, exploits the relevant information contained within the nonlinear frequency response functions, namely, the bifurcation points. Their tracking in parameter space enables the adjustment of the design parameter values to reach a suitable tuning of the absorber. The use of the resulting integrated tuning methodology on nonlinear vibration absorbers coupled to systems with nonlinear damping is then investigated. The objective lies in determining an appropriate functional form for the absorber so that the limit cycle oscillation suppression is maximized. Finally, the proposed tuning methodology of nonlinear vibration absorbers may impose the use of complicated nonlinear functional forms whose practical realization, using mechanical elements, may be difficult. In this context, an electro-mechanical nonlinear vibration absorber relying on piezoelectric shunting possesses attractive features as various functional forms for the absorber nonlinearity can be achieved through proper circuit design. The foundation of this new approach are laid down and the perspectives are discussed.

Recently, there has been growing interest on the behaviour of unbound granular material in road base layers. Researchers have studied that the design of a new pavement and prediction of service life need proper characterization of unbound granular materials, which is one of the requirements for a new mechanistic design method in flexible pavement. Adequate knowledge of the strength and deformation characteristics of unbound layer in pavements is a prerequisite for proper thickness design, residual life determination, and overall economic optimization of the pavement structure. The current knowledge concerning the granular materials employed in pavement structures is limited. In addition, to date, no general framework has been established to explain satisfactorily the behaviour of unbound granular materials under the complex repeated loading which they experience. In this study, a conceptual method, packing theory-based model is introduced; this framework evaluates the stability and performance of granular materials based on their packing arrangement. In the framework two basic aggregate structures named as Primary Structure (PS), and Secondary Structure (SS). The Primary Structure (PS) is a range of interactive grain sizes that forms the network of unbound granular materials. The Secondary Structure (SS) includes granular materials smaller than the primary structure. The Secondary Structures fill the gaps between the particles in the Primary Structure and larger particles essentially float in the skeleton. In this particular packing theory-based model; the Primary Structure porosity, the average contact points (coordination number) of Primary Structure, and a new parameter named Disruption Potential are the key parameters that determine whether or not a particular gradation results in a suitable aggregate structure. Parameters mentioned above play major role in the aggregate skeleton to perform well in terms of resistance to permanent deformation as well as load carrying capacity (resilient modulus). The skeleton of the materials must be composed of both coarse enough and a limited amount of fine granular materials to effectively resist deformation and carry traffic loads. / QC 20120601

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / A glycosylated lectin (CTL) with specificity for mannose and glucose has been detected and purified from seeds of Centrolobium tomentosum, a legume plant from the Dalbergieae tribe. CTL was isolated by mannose-Sepharose affinity chromatography. The primary structure was determined by tandem mass spectrometry and consists of 245 amino acids and one N-glycosylation site, possessing high similarity with the lectin Platypodium elegans (PELa) and Pterocarpus angolensis (PAL) derived from the same tribe. Two crystal structures of CTL, with monoclinic and tetragonal forms, both complexed with methyl dimanosÃdeo has been solved at 2.25 and 1.9 Ã, respectively, with high similarity. The lectin adopts a typical canonical dimeric organization of legume lectins. The carbohydrate recognition domain (CRD), metal binding site, and glycosylation site have been characterized and the structural basis for interaction with carbohydrate been elucidated. CTL showed acute inflammatory effect in a paw edema model. The protein structure was subjected to ligand screening (dimannosides and trimannoside) by molecular docking, revealing a higher affinity for trimannosides and their interactions were compared with similar lectins, which have the same binding specificity. This is the first report of a crystal structure of a native mannose lectin / specific glucose Dalbergieae tribe with pro-inflammatory activity / Uma lectina glicosilada (CTL) com especificidade a manose e glucose foi detectada e purificada a partir de sementes de Centrolobium Tomentosum, uma leguminosa pertencente à tribo Dalbergieae. CTL foi isolada por cromatografia de afinidade de Sepharose-Manose. A estrutura primÃria foi determinada por espectrometria de massas e consiste em 245 aminoÃcidos e um sitio de ÂNÂ-glicosilaÃÃo, demonstrando similaridade com a lectina de Platypodium elegans (PELa), Pterocarpus angolensis (PAL), dentre outras, oriundas da mesma tribo. Duas estruturas cristalinas de CTL, de formas monoclÃnica e tetragonal, ambas complexadas com metil-dimanosÃdeo, foram resolvidas a 2,25 e 1,9 Ã, respectivamente, apresentando alta similaridade entre si. A lectina mostrou adotar uma organizaÃÃo dimÃrica canÃnica tÃpica de lectinas de leguminosas. O domÃnio de reconhecimento de carboidratos (CRD), local de ligaÃÃo do metal e local de glicosilaÃÃo foram caracterizados e a base estrutural para a interaÃÃo com carboidratos foi elucidado. CTL mostrou efeito inflamatÃrio agudo em um modelo de edema de pata. A estrutura da proteÃna foi submetida a uma anÃlise de interaÃÃes com dimanosÃdeos e trimanosÃdeos por Docking Molecular, revelando sua maior afinidade por trimanosÃdeos e suas interaÃÃes foram comparadas com lectinas similares que possuam a mesma especificidade de ligaÃÃo. Esse à o primeiro relato de estrutura cristalina de uma lectina nativa manose/glucose especÃfica da tribo Dalbergieae com atividade prÃ-inflamatÃria

Dans ce travail, des méthodes itératives ont été étudiées afin de préparer des oligomères à séquences bien définies en utilisant des supports solides ou solubles. Trois stratégies de couplage de monomères ont été exploitées (i) AB + AB, (ii) AB + CD et (iii) AA + BB. La première méthode a permis la synthèse d’oligopeptides en utilisant les protocoles classiques de la synthèse peptidique à partir notamment d’amino-acides protégés par des groupements Fmoc. Les deux autres stratégies ont permis de préparer des oligo(alcoxyamine amide)s et des oligoamides, en l’absence de groupements protecteurs. Dans ces cas, le contrôle de la structure primaire de l’oligomère a été rendu possible soit par l’utilisation de réactions chimio-sélectives (AB + CD) soit en introduisant un large excès de monomères bifonctionnels (AA + BB). Ainsi, les oligo(alkoxyamine amide)s ont été préparés en utilisant des couplages successifs de bromo-anhydride et d’amino-nitroxide ; et les oligoamides ont été obtenus par couplages de diacides et de diamines.L'approche pratique permettant la formation de ces oligomères à séquence contrôlée ainsi que leur caractérisation seront décrites dans cette thèse. / In this work, iterative methods have been studied to prepare sequence-defined oligomers on solid and soluble supports. Three model monomer coupling strategies have been exploited, (i) AB + AB, (ii) AB + CD and (iii) AA + BB, for the synthesis of oligopeptides, oligo(alkoxyamine amide)s and oligoamides, respectively. In the first strategy (AB + AB), oligopeptides have been synthesized using classical peptide synthesis protocols, in which Fmoc-protected amino acids were used. The other two strategies (AB + CD and AA + BB) are protecting-group free methods. In this case, the control over the oligomer primary structure has been achieved using chemoselective reactions (AB + CD) or a large excess of bifunctional monomers (AA + BB). The oligo(alkoxyamine amide)s have been prepared using successive coupling of bromo-anhydride and amino-nitroxide building blocks. The oligoamides have been obtained by sequential coupling of diacid and diamine building blocks. The practical approach to these primary structures using solid- and liquid-phase methodologies followed by the characterization of formed oligomers is the scope of this thesis.

This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.