Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-01-13T11:27:01Z No. of bitstreams: 1 KatyannaSalesBezerra_DISSERT.pdf: 4450152 bytes, checksum: af5649a1fafdfce841b2477524a3e184 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-01-23T11:32:53Z (GMT) No. of bitstreams: 1 KatyannaSalesBezerra_DISSERT.pdf: 4450152 bytes, checksum: af5649a1fafdfce841b2477524a3e184 (MD5) / Made available in DSpace on 2017-01-23T11:32:53Z (GMT). No. of bitstreams: 1 KatyannaSalesBezerra_DISSERT.pdf: 4450152 bytes, checksum: af5649a1fafdfce841b2477524a3e184 (MD5) Previous issue date: 2016-03-18 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / A matriz extracelular (MEC) dos tecidos conjuntivos representa um complexo de numerosos membros de v?rias fam?lias de prote?nas que delineiam sua integridade estrutural e v?rias fun??es fisiol?gicas. As intera??es que ocorrem entre a c?lula e a matriz desempenham um papel preponderante na fixa??o celular e migra??o, assim como tamb?m regulam e promovem a diferencia??o celular e a express?o de genes. O controle dessas intera??es celulares ? crucial para grande parte dos processos biol?gicos. As integrinas s?o uma fam?lia de glicoprote?nas transmembranares, que funcionam como os principais receptores metazo?rios para a ades?o celular, desempenhando um papel central em fun??es de suporte f?sico para a transdu??o de sinais, montagem do citoesqueleto de actina, express?o g?nica e fun??es celulares. Estas glicoprote?nas podem se ligar a glicoprote?nas da matriz extracelular, tal como o col?geno, esta liga??o permite a regula??o e integridade da ades?o celular, migra??o celular e resposta imune. Neste sentido, este trabalho tem como objetivo realizar uma an?lise ab initio da intera??o entre o dom?nio-I da integrina ?2?1 e o col?geno com sequ?ncia GFOGER. A an?lise foi desenvolvida utilizando-se c?lculos de mec?nica qu?ntica, no ?mbito da Teoria do Funcional da Densidade (DFT), com aproxima??es do Gradiente Generalizado (GGA) para descri??o dos efeitos de correla??o e troca. As energias de intera??o entre os res?duos do dom?nio-I ?2 da integrina e os res?duos do col?geno foram calculadas utilizando-se o m?todo de fragmenta??o molecular com capas conjugadas (MFCC). Os resultados encontrados comprovam a import?ncia do ?on met?lico presente na regi?o MIDAS da integrina para a intera??o com a mol?cula do col?geno. A an?lise das energias de intera??o apresentaram os res?duos Glu11, Glu33, Glu55, Arg12, Arg34 e Arg56 da sequ?ncia GFOGER do col?geno, como cruciais para a intera??o com a integrina. J? os res?duos da integrina que demonstraram ser de grande relev?ncia para a intera??o foram a Thr221, Asp219, Asp254 e Glu256. Al?m disso, os resultados tamb?m destacam a import?ncia da altera??o da conforma??o destes res?duos durante a intera??o entre as prote?nas. Logo, o conhecimento das peculiaridades que envolvem a intera??o entre a integrina ?2?1 podem auxiliar a compreens?o de eventos ainda n?o totalmente esclarecidos, bem como fornecer dados relevantes sobre os aspectos particulares apresentados em modelos de muta??es. / The extracellular matrix (ECM) of connective tissues is a complex of many members of several families of proteins that delineate its structural integrity and various physiological functions. The interactions occurring between the matrix cell and play a key role in cell attachment and migration, as well as regulate and promote cell differentiation and gene expression. The control of these cellular interactions is determinative for most biological processes. Integrins are a family of transmembrane glycoproteins that function as the main metazoan receptors for cell adhesion plays a central role in a physical support functions for signal transduction, cytoskeletal actin assembly, gene expression and cell functions. These glycoproteins may bind to the extracellular matrix glycoproteins such as collagen, this connection allows adjustment and integrity of cell adhesion, cell migration and immune response. Thus, this study aims to perform an ab initio analysis of the interaction between the domain-I integrin ?2?1 and collagen with GFOGER sequence. The analysis was carried out using quantum mechanical calculations within Density Functional Theory (DFT) with the Generalized Gradient Approximation (GGA) for describing the exchange and correlation effects. The energies of interaction between domain-I ?2 integrin residues and collagen residues were calculated using the Molecular Fragmentation with Conjugated Caps (MFCC). The results demonstrate the importance of metal ion present in the MIDAS region of the integrin for interaction with the collagen molecule. The analysis showed the interaction energies residues Arg12, Glu33, Arg34, Glu55, and Arg56 GFOGER sequence of collagen, as important to the interaction with the integrin. In the residues of integrin shown to be of great relevance to the interaction were Thr221, Asp219, Asp254 and Glu256. Moreover, the results also highlight the importance of changing the conformation of these residues during the interaction between the proteins. These results can aid understanding of events involving the interaction between integrin ?2?1 and collagen as well as provide relevant data on special aspects presented in mutations models.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-10-04T22:23:59Z No. of bitstreams: 1 DalilaNascimentoManso_DISSERT.pdf: 1914411 bytes, checksum: 966fc442e252d656c3946bff697a75f5 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-10-13T21:33:08Z (GMT) No. of bitstreams: 1 DalilaNascimentoManso_DISSERT.pdf: 1914411 bytes, checksum: 966fc442e252d656c3946bff697a75f5 (MD5) / Made available in DSpace on 2017-10-13T21:33:08Z (GMT). No. of bitstreams: 1 DalilaNascimentoManso_DISSERT.pdf: 1914411 bytes, checksum: 966fc442e252d656c3946bff697a75f5 (MD5) Previous issue date: 2017-04-19 / A mais recente pandemia do v?rus influenza ocorreu no ano de 2009, causada pela cepa do influenza A (H1N1), e popularmente conhecida como gripe A ou gripe su?na, gerou preocupa??o aos ?rg?os mundiais de sa?de. Com um quadro sintom?tico que inclui febre, tosse, inflama??o na garganta na maioria dos casos, alguns pacientes, principalmente imunossuprimidos que podem apresentar complica??es que evoluem ao ?bito. A transmiss?o do v?rus ocorre atrav?s do contato entre pessoa a pessoa e seu mecanismo de infec??o se d? a partir das duas glicoprote?nas de superf?cie, a hemaglutinina e a neuraminidase. A hemaglutinina atua se ligando aos receptores do ?cido si?lico favorecendo a entrada do v?rus nas c?lulas-alvo e a neuraminidase cliva as c?lulas do receptor de res?duos do ?cido si?lico, onde as novas part?culas virais est?o se ligando. Atrav?s dessa quebra haver? libera??o das novas part?culas virais, que atrav?s da hemaglutinina invadir?o novas c?lulas. Baseado nisso, f?rmacos foram desenvolvidos com intuito de inibir a a??o da neuraminidase, os chamados inibidores da neuraminidase que interferem na libera??o dessas novas part?culas virais evitando a dissemina??o da infec??o no trato respirat?rio. Dentre estes inibidores o oseltamivir ? o f?rmaco de escolha para profilaxia e tratamento da gripe A; por?m, relatos de resist?ncia a esse f?rmaco foram descritos, o que causou preocupa??o nos profissionais da sa?de e governantes. A muta??o mais encontrada ? a HIS275TIR, onde a histidina ? substitu?da por uma tirosina, promovendo uma s?rie de altera??es conformacionais que diminuem a afinidade do f?rmaco pelo v?rus originando a resist?ncia. A partir da obten??o de dados cristalogr?ficos e simula??o computacional, calculamos a energia de intera??o da neuraminidase selvagem e com a presen?a da muta??o HIS275TIR ligadas ao oseltamivir utilizando a Teoria Funcional da Densidade (DFT) e do M?todo de Fracionamento Molecular com Capas Conjugadas (MFCC). Obtivemos 115 res?duos de intera??o para a neuraminidase selvagem (cristal 4B7R) e 109 res?duos de intera??o para o cristal com a neuraminidase mutante (3CL0). Os resultados foram avaliados de acordo com a relev?ncia dos valores energ?ticos para energias repulsivas e energias atrativas. Os c?lculos energ?ticos realizados confirmaram a redu??o da afinidade da cepa contendo a muta??o HIS275TIR e destacaram a import?ncia energ?tica do s?tio ativo da neuraminidase mostrando que os principais res?duos energ?ticos s?o encontrados nele tornando um alvo para obten??o de novos f?rmacos devido a sua conserva??o. As altera??es causadas pela substitui??o do amino?cido histidina por uma tirosina levaram a uma s?rie de mudan?as conformacionais nos amino?cidos vizinhos que provocaram altera??es eletrost?ticas resultando na resist?ncia ao f?rmaco. A partir desse estudo ser? poss?vel conhecer melhor as intera??es moleculares da neuraminidase mutante e posteriormente projetar novos designs de f?rmacos para serem elaborados e se tornarem mais eficientes na intera??o com as cepas mutantes desse v?rus. / The latest influenza pandemic occurred in the year 2009, caused by the strain of influenza A (H1N1), and popularly known as influenza A or swine flu, generated concern to the global health agencies. With a symptomatic picture that includes fever, cough, throat inflammation in most cases, some patients, mainly immunosuppressed, that can to present complications that evolve to death. Transmission of the virus takes place through contact between person to person and its mechanism of infection occurs from the two surface glycoproteins, hemagglutinin and neuraminidase. The hemagglutinin acts by binding to the sialic acid receptors favoring the entry of the virus into the target cells and the neuraminidase cleaves the receptor cells of sialic acid residues, where the new viral particles are binding. Through this breakdown there will be release of the new particles that through hemagglutinin will attack new cells. Based on these, drugs were developed in an attempt to inhibit the action of neuraminidase, so called neuraminidase inhibitors that interfere in the release of these new viral particles avoiding the spread of infection in the respiratory tract. Among the inhibitors, oseltamivir is the drug of choice for prophylaxis and treatment of influenza A, but reports of resistance to this drug have been described, which has caused concern in health professionals and rulers. The HIS275TIR mutation is most commonly found, where histidine is replaced by a tyrosine, promoting a series of conformational changes that decrease the affinity of the drug for the virus causing resistance. Based on crystallographic data and computational simulation, we calculated the interaction energy of the wild neuraminidase and the presence of the HIS275TIR mutation bonded to oseltamivir using the Functional Density Theory (DFT) and the Molecular Fractionation with Conjugated Caps (MFCC). We obtained 115 interaction residues for the wild neuraminidase (4B7R crystal) and 109 interaction residues for the crystal with the mutant neuraminidase (3CL0). The results were evaluated according to the relevance of the energy values for repulsive energies and attractive energies. The energetic calculations confirmed the reduction of the affinity of the strain containing the HIS275TIR mutation and highlighted the energy importance of the active site of the neuraminidase, showing that the main energy residues are found in it becoming a target for obtaining new drugs due to its conservation. The changes caused by the substitution of the amino acid histidine for a tyrosine led to a series of conformational changes in the neighboring amino acids that provoked electrostatic changes resulting in the resistance to the drug. From this study, it will be possible to know better the molecular interactions of the mutant neuraminidase and subsequently to project new drugs designs to be elaborated and become more efficient in the interaction with the mutant strains of this virus.

Made available in DSpace on 2014-12-17T14:10:28Z (GMT). No. of bitstreams: 1 DiegoSD_DISSERT.pdf: 4467915 bytes, checksum: 1bb0defec90e5ed329ebefbf24ac108a (MD5) Previous issue date: 2013-02-28 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Currently, computational methods have been increasingly used to aid in the characterization of molecular biological systems, especially when they relevant to human health. Ibuprofen is a nonsteroidal antiinflammatory or broadband use in the clinic. Once in the bloodstream, most of ibuprofen is linked to human serum albumin, the major protein of blood plasma, decreasing its bioavailability and requiring larger doses to produce its antiinflamatory action. This study aimes to characterize, through the interaction energy, how is the binding of ibuprofen to albumin and to establish what are the main amino acids and molecular interactions involved in the process. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant ε = 40 was used. The findings corroborate the literature in which the Sudlow site I (I-FA3) is the primary binding site and the site I-FA6 as secondary site. However, it differs in identifying the most important amino acids, which by interaction energy, in order of decreasing energy, are: Arg410, Lys414, Ser 489, Leu453 and Tyr411 to the I-Site FA3 and Leu481, Ser480, Lys351, Val482 and Arg209 to the site I-FA6. The quantification of interaction energy and description of the most important amino acids opens new avenues for studies aiming at manipulating the structure of ibuprofen, in order to decrease its interaction with albumin, and consequently increase its distribution / Na atualidade, os m?todos computacionais v?m sendo cada vez mais utilizados para auxiliar a biologia molecular na caracteriza??o de sistemas biol?gicos, principalmente quando esses possuem relev?ncia para a sa?de humana. O ibuprofeno ? um antiinflamat?rio n?o-esteroidal de larga utiliza??o na cl?nica. Uma vez na corrente sangu?nea, boa parte do ibuprofeno fica ligada a albumina de soro humano, a principal prote?na do plasma sangu?neo, diminuindo a sua biodisponibilidade e necessitando de maiores doses para a produ??o de seu efeito antiinflamat?rio. Este estudo teve por objetivo caracterizar, atrav?s da energia de intera??o, como ocorre a liga??o do ibuprofeno ? albumina e estabelecer quais os principais amino?cidos e intera??es moleculares envolvidas no processo. Para tal desenvolveu-se um estudo in silico, com utiliza??o de c?lculos de mec?nica qu?ntica, baseada na Teoria do Funcional da Densidade (DFT), com aproxima??es do Gradiente Generalizado (GGA) para descri??o dos efeitos de correla??o e troca. A energia de intera??o de cada amino?cido do s?tio de liga??o, com o ligante foi calculada com base no m?todo de fragmenta??o molecular com capas conjugadas (MFCC). Al?m da energia, foram calculadas as dist?ncias, tipos de intera??es moleculares e grupos at?micos envolvidos. Os modelos te?ricos utilizados foram satisfat?rios e demonstraram uma descri??o mais precisa com a utiliza??o da constante diel?trica ε=40. Os achados corroboram com a literatura colocando o s?tio Sudlow I (I-FA3) como o principal s?tio de liga??o e o s?tio I-FA6 como s?tio secund?rio. Contudo, difere quanto ? identifica??o dos amino?cidos mais importantes, que por meio da energia de intera??o, em ordem decrescente de energia, s?o: Arg410, Lys414, Ser 489, Leu453 e Tyr411 para o S?tio I-FA3 e Leu481, Ser480, Lys351, Val482 e Arg209 para o s?tio I-FA6. A quantifica??o da energia de intera??o e a descri??o dos amino?cidos mais importantes abre caminhos para novos estudos que visem a manipula??o da estrutura do ibuprofeno, no sentido de diminuir a intera??o desse com a albumina, e consequentemente aumentar a sua distribui??o