Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 97-104).

How the linear protein chains fold into their three-dimensional active conformation is one of the remaining puzzles of modern science. Other than molecular chaperones, ribosome - the cellular protein synthesis machinery, has also been implicated in protein folding. The active site of protein folding activity of the ribosome (PFAR) is in the domain V of the main RNA component of the large ribosomal subunit, which also constitutes the peptidyl transferase center. We have characterized the mechanism of PFAR using ribosomes or ribosome-borne folding modulators (RFMs) and human carbonic anhydrase I (HCA) as a model system. RFMs from all three kingdoms of life showed PFAR.  By multiple addition of the denatured protein in the refolding assay we demonstrate that the RFMs can recycle efficiently to assist refolding of a new batch of denatured protein. The turnover of the RFMs, which includes release of the protein substrate, takes milliseconds. Furthermore, fast kinetics of HCA refolding suggests that an early folding intermediate is the substrate for PFAR. Our results demonstrate for the first time that PFAR is catalytic. It was shown that two anti-prion drugs 6AP and GA specifically inhibit PFAR by binding to the domain V of the 23S / 25S rRNA. Using UV-crosslinking followed by primer extension we have identified the interaction sites of 6AP on domain V of 23S rRNA, which overlap with the protein binding sites, and are sensitive to mutagenesis. We find that 6AP and GA inhibit PFAR by direct competition with the substrate protein for the binding sites. Also, 6AP derivatives inhibit PFAR in the same order as their antiprion activity, 6AP8CF3 > 6AP8Cl > 6AP > 6APi. These results suggest involvement of PFAR in prion processes. To clarify the role of PFAR in prion processes, we studied HET-s prion aggregation in the presence of domain V/ IV/II of rRNA. The rRNAs, especially domain V rRNA not only reduced HET-s aggregation, but also changed the morphology of the HET-s fibrils, which became shorter and less compact. These results show that PFAR actively prevents large amyloid aggregation and thus, possibly influence prion propagation.

Submitted by Antonio Bento de Oliveira Junior null (junioreif@hotmail.com) on 2018-01-23T13:42:06Z No. of bitstreams: 1 Tese-final.pdf: 43113195 bytes, checksum: 7cc85051e3a1420a2983ce716e0ae144 (MD5) / Rejected by Elza Mitiko Sato null (elzasato@ibilce.unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: Problema 01 : A data na capa deve conter somente o ano; Problema 02: A data na folha de aprovação deve ser a data da defesa; Problema 03: Se você teve financiamento da FAPESP é obrigatório constar também na folha de rosto e o numero do processo; Problema 04: As páginas viii, xvi, xviii, 10, 34, 38, 46 e 60 estão em branco; Problema 05: A numeração das páginas deve ser contínua. Caso ainda tenha dúvida consulte, por gentileza o modelo que consta na página da seção de pós-graduação, link Instruções para Qualificação e Defesas :http://www.ibilce.unesp.br/#!/pos-graduacao/instrucoes-para-aluno-que-vai-defender/ Agradecemos a compreensão. on 2018-01-23T17:41:25Z (GMT) / Submitted by Antonio Bento de Oliveira Junior null (junioreif@hotmail.com) on 2018-01-23T18:20:41Z No. of bitstreams: 1 Tese-final.pdf: 42848208 bytes, checksum: 26d4aab1e2a66d06ba87e4533f1cdd40 (MD5) / Approved for entry into archive by Elza Mitiko Sato null (elzasato@ibilce.unesp.br) on 2018-01-24T12:12:56Z (GMT) No. of bitstreams: 1 oliveirajunior_ab_dr_sjrp.pdf: 42589488 bytes, checksum: 6433ad3adeeb7e56b159e54ad745abe2 (MD5) / Made available in DSpace on 2018-01-24T12:12:56Z (GMT). No. of bitstreams: 1 oliveirajunior_ab_dr_sjrp.pdf: 42589488 bytes, checksum: 6433ad3adeeb7e56b159e54ad745abe2 (MD5) Previous issue date: 2017-12-05 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O enovelamento de proteínas acontece em um espaço de fase multidimensional, onde o número conformações possíveis é exponencialmente alta. Uma forma comum de representar essas conformações é utilizar uma coordenada de reação efetiva (por exemplo, fração de contatos nativos). Porém, como a informação de cada conformação não é representada neste tipo de aproximação estatistifica, alguns mecanismos do enovelamento de proteínas não são possíveis de ser descritos ou analisados. Neste trabalho, usou-se uma métrica para descrever a distancia entre quaisquer duas conformações, essa métrica é calculada levando em conta as distâncias internas dos aminoácidos presentes em cada estrutura. Utilizando-se um método de projeção efetiva é possível ir além da representação em uma dimensão e visualizar a superfície de enovelamento da proteína em duas ou três dimensões. Para aplicar essa metodologia realizou-se simulações computacionais do enovelamento de proteínas utilizando o modelo baseado em estrutura, com aproximação para Cα. Três proteínas foram analisadas: CI-2, o Domínio SH3 e a Proteína A. Dos resultados, foi possível observar que para cada tipo de "motifs"estrutural (folha-β e/ou α-hélice) projetou funis de enovelamento distintos. A partir da visualização foi possível analisar o processo de enovelamento em detalhes, sendo possível identificar a conectividade entre as conformações assim como, possíveis rotas de enovelamento (f olding pathsways). Analisou-se também as diferenças estruturais da rota dominante no domínio SH3 e a competitividade entre a estrutura do estado nativo e do estado espelhado que acontece em proteínas que possuem somente α-hélice, como é o caso da proteína A. / Protein folding occurs in a very high dimensional phase space, in which an exponentially large number of states is represented in terms of one effective reaction coordinate. Since the role of each local minimum is not considered in this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective onedimensional representation. In this work, we used a metric to describe the distance between any two conformations, which is based on internal distances between amino acids in each conformation. A effective projection method allows to go beyond the one-dimensional representation and visualizing a 2D folding funnel representation. Computer simulations of protein folding were performed using Cα structure-based model. Three proteins have been studied: CI2, SH3 Domain and Protein-A. Distinct funnels have been generated according to the major motifs in each proteins, (β-sheet or/and α-helix). The visualization allows assessing the folding process in detail, e.g. by identifying the connectivity between conformations and establishing the paths that lead to the native state and we analyzed structural differences in the dominant route of SH3 and the competitiveness between the native and mirror structures in protein A.

No description available.

The work presented in this thesis focusses primarily on the determination of protein structure at atomic resolution, with NMR spectroscopy as the principle investigative tool. The thesis is divided into four parts. Part I consists of Chapter 1 which provides an introduction to protein structure, folding and NMR spectroscopy. Part II, consisting of Chapters 2 and 3, describes the effects of aromatic interactions on nucleating structure in disordered regions of proteins, using variants of apo-cytochrome b5 as a model system. Part III consists of Chapter 4, which describes structural effects of introducing cross-strand disulfide bonds using variants of Thioredoxin. Part IV of this thesis consists of the Appendices A, B and C. Appendix A describes the purification and characterization of ilvM, the regulatory subunit of the E.coli enzyme AHAS II. Appendices B and C contain chemical shift information corresponding to Chapter 3 and Chapter 4 respectively. Part I : Introduction to protein structure, folding and solution structure studies Chapter 1 first gives a brief overview of protein structure followed by an introduction to protein folding, focussing on the forces involved in determining the final three-dimensional shape of the protein as well as the experimental and computational techniques involved in studying or predicting the fold of a given protein. The second section of this chapter details the methodology followed to obtain solution structures of proteins using NMR spectroscopy. Part II : Engineering aromatic interactions to nucleate folding in intrinsically disordered regions of proteins Chapter 2 describes site-specific mutagenesis, recombinant over-expression, purifica-tion and preliminary biophysical characterization of two aromatic mutants of the molten globule apo-cytochrome b5 (apocytb5) : H43F H67F cytochrome b5 (FFcytb5) and H43W H67F cytochrome b5 (WFcytb5). Analysis of the structure of wild-type apo - cytochrome b5 was done to introduce surface mutations and avoid perturbation of the interior pack-ing of the protein. The bacterial host E.coli BL21(DE3) was used for recombinant over-expression, and both mutant proteins were purified by anion-exchange chromatography followed by size-exclusion chromatography. Biophysical studies show a decrease in the hydrodynamic radii and surface hydropho-bicity of FFcytb5 and WFcytb5 compared to wt -apo cytb5. An increase in protein stability was also seen from the wt apocytb5 to WFcytb5 and FFcytb5 in the presence of the chemical denaturant Urea. Proton 1D NMR spectra exhibited sharp lines and good spectral dispersion in the amide region, indicating that both mutant proteins are well folded. In addition, conservation of two distinctive up field and downfield shifted resonances present in apocytb5 indicated that structural changes upon mutation accrued on the upon the scaffold of apocytb5. Chapter 3 describes solution structure studies to determine secondary and tertiary structure of FFcytb5 and WFcytb5. Structural studies were carried out using homonu-clear and heteronuclear NMR methods, for which isotopically enriched 15N- and 13C, 15N samples were prepared for each protein. Additionally a 2H, 13C, 15N ILV methyl labeled sample was prepared for FFcytb5 to obtain unambiguous NOE correlation data. The hydrogen bond network for WFcytb5 was determined using hydrogen/deuterium exchange data. The restraints required to define the orientations and interactions of the aromatic groups were obtained from 15N-edited NOESY HSQC, 13C -edited NOESY HSQC and 2D 1H - 1H NOE spectra. These correlations were crucial in determining the aromatic interactions present within each protein. The structure of FFcytb5 was calculated using 1163 NOE distance restraints, 179 φ and ψ dihedral angle restraints, along with 40 hydrogen bond restraints. Similarly the structure of WFcytb5 was calculated using 1282 NOE distance restraints, 177 φ and ψ dihedral angle restraints and 40 hydrogen bond restraints. The ensemble of structures obtained for FFcytb5 showed a root mean square deviation of 1.01±0.21 Å . The ensemble of structures obtained for WFcytb5 showed a root mean square deviation of 0.58±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were found to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The final tertiary structure of both FFcytb5 and WFcytb5 consisted of a mixed four strand β -sheet with a four helix bundle resting on top and were seen to align well, with an RMSD of 0.6 Å. A comparison of the solution structures of apocytb5 with FFcytb5 and WFcytb5 convincingly showed the nucleation secondary and tertiary structure well beyond the site of mutation. The presence of aromatic trimers, non-canonical in context of the wt apoc-ytb5, was confirmed upon analysis of the structures of FFcytb5 and WFcytb5, with NOE correlations assigned to verify these interactions. The reduction in the hydrodynamic radii of FFcytb5 and WFcytb5 in relation to apocytb5 was also verified from tsuperscript15N-NMR relaxometry studies. The nucleation of long-range structure using aromatic interactions has been demonstrated in proteins for the first time, and can in principle be used to incorporate aromatic residues and interactions in protein design. Structural data, chemical shift data and restraints lists used for structure calculation of WFcytb5 and FFcytb5 were deposited with the PDB (accession numbers 5XE4 and 5XEE) and BMRB(accession numbers 36070, 36071) respectively1. Part III : Structural consequences of introducing disulfide bonds into β - sheets Chapter 3 describes the solution structure studies on two mutants of E.coli Thiore-doxin which were designed to incorporate a disulfide bond between two anti-parallel β-strands at the edge of the β-sheet. One mutant was designed with a disulfide bond at the hydrogen bonding position (HB, 78c90cTrx) and the other with the disulfide bond at the non-hydrogen bonding position (NHB, 77c91cTrx). Here we study the structural changes that accompany the introduction of a cross-strand disulfide and whether such structural changes could be correlated with the previously seen thermodynamic and catalytic changes. Solution structure studies were conducted using a suite of multidimensional heteronu-clear NMR experiments, for which isotopically enriched 15N and 13C, 15N labelled samples were used. The solution structure for 77c91cTrx was calculated using 1190 NOE distance restraints, 199 φ and ψ dihedral angle restraints and 48 hydrogen bond restraints. The solution structure for 78c90cTrx was calculated using 1123 NOE distance restraints, 197 φ and ψ dihedral angle restraints and 50 hydrogen bond restraints. The ensemble of structures for 77c91cTrx showed an RMSD of 0.78± 0.13 Å while the RMSD for the ensemble of structures of 78c90cTrx was seen to be 0.76±0.09 Å . In both cases, ≈ 80% of backbone dihedral angles were seen to be in the allowed regions and ≈ 20% in the additionally allowed regions of the Ramachandran map. The tertiary structures of both proteins were seen to have a 5-strand mixed β-sheet and 4 helices surrounding it. . A comparison of the solution structures of mutant and wt -Trx showed significant changes in secondary and tertiary structure. For example, an α helix was reduced from 3 turns to a single turn, and of the β-strands containing the mutation was elongated by 3 residues. A ≈ 50% loss of hydrogen bonds, primarily from the β -sheet, was seen for both mutants. The secondary and tertiary structure for both 77c91cTrx and 78c90cTrx was seen to be near identical, despite the greater strain of the disulfide bond at the hydrogen bonding position. In addition to this, the Ile75-Pro76 peptide bond is now seen to be in the trans conformation in 78c90cTrx, while in wt -Trx the Ile75-Pro76 peptide bond is in the cis conformation. This cis peptide bond is known to play a role in both folding and catalysis, and the solution structures were analyzed in the context of observed changes in folding and catalysis. The study shows that introducing disulfide bonds even at the edge of β sheets have long-range structural effects, and the structural effects cannot be directly correlated with the changes in stability. Part III: Appendix Appendix A describes the expression, purification and preliminary characterization of ilvM, the regulatory subunit of E.coliAHAS II, one of three enzyme isomers that catal-yse the first step in the synthesis of all branched chain amino acids. AHAS II is known to be insensitive to feedback regulation, but our studies showed that the presence of Ile, Leu and Val causes structural changes and increases the stability of ilvM. However we were not able to purify ilvM in sufficient quantities to proceed with solution structure studies. Appendices B and C contain chemical shift information for the structural studies carried out on FFcytb5, WFcytb5, 77c91cTrx and 78c90cTrx.

Made available in DSpace on 2014-08-27T14:36:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-07-25Bitstream added on 2014-08-27T15:57:14Z : No. of bitstreams: 1 000723022.pdf: 4573012 bytes, checksum: 3b0b87ba2cdde44c7203a2dc8e7fb5db (MD5) / O enovelamento de proteínas é um problema fundamental em Biofísica Molecular. A teoria aceita, conhecida como “energy landscape”, utiliza o funil de energia potencial como conceito fundamental para o entendimento do enovelamento de proteínas. Este funil ocorre em uma superfície multidimensional de difícil visualização. A investigação de métodos para analisar quantitativamente a estrutura desse funil é importante para o completo entendimento do problema. Neste trabalho são apresentados meios de fazer a visualização desses funis de enovelamento de proteínas para o modelo de rede cúbica 3×3×3. A partir de simulaões do enovelamento de proteínas são calculados as distâncias entre mínimos locais por meio de uma métrica efetiva, onde considera-se os contatos não covalentes feitos em cada conformação. Esta análise é restrita para conformações próximas ao estado nativo. Técnicas de visualização e minimização são usadas para mapear o processo do enovelamento em um espaço de fase de menor dimensionalidade. Por meio desta visualização é possível analisar o enovelamento com detalhes, como a conectividade entre conformações, os diferentes caminhos para se atingir o estado nativo e regiões onde a proteína pode ?car armadilhada. Para este trabalho, utilizou-se cinco proteínas distintas, sendo duas altamente estáveis, duas que possuem baixa estabilidade e uma quinta que tem o estado nativo degenerado. A visualização dos funis se mostraram bastantes distintas, sendo possível notar um padrão para cada proteí?na mesmo quando variado alguns parâmetros. Tais resultados são consistentes com as ideias associadas à teoria do funil de enovelamento de proteínas / The protein folding is a fundamental problem in molecular biophysics. The accepted theory, known as energy landscape, uses the funnel potential energy as a fundamental concept to understand the protein folding problem. The energy funnel occurs in a multidimensional surface, which is difficult to be visualized. The investigation of methods for a quantitative analysis of the funnel structure is important for complete understanding of the problem. In this work, ways for visualize the protein folding funnels in a 3×3×3 lattice models are presented. Protein folding simulations are carried out. Distances between conformations are determined by the non-covalent contact sand de?ned by effective metric of the structural con?guration. The analysis is restricted to conformations close to the native state, i.e., beyond the transition state. Computer minimization and visualization techniques were used to map the dynamics of the folding process into a lower dimensionality phase space, and then represent the folding funnel in two and three-dimensional surface. These techniques are applied to ?ve distinct sequences, which two are highly stable, two marginally stable and the last has a native degenerated state. Their folding funnels are very distinct, where each sequence has a signature even when some parameters varied. These results are consistent with the ideas of the theory of protein folding funnel

Orientador: Vitor B. Pereira Leite / Banca: Laurent Emmanuel Dardenne / Banca: Sidney Jurado de Carvalho / Resumo: O enovelamento de proteínas é um problema fundamental em Biofísica Molecular. A teoria aceita, conhecida como "energy landscape", utiliza o funil de energia potencial como conceito fundamental para o entendimento do enovelamento de proteínas. Este funil ocorre em uma superfície multidimensional de difícil visualização. A investigação de métodos para analisar quantitativamente a estrutura desse funil é importante para o completo entendimento do problema. Neste trabalho são apresentados meios de fazer a visualização desses funis de enovelamento de proteínas para o modelo de rede cúbica 3×3×3. A partir de simulaões do enovelamento de proteínas são calculados as distâncias entre mínimos locais por meio de uma métrica efetiva, onde considera-se os contatos não covalentes feitos em cada conformação. Esta análise é restrita para conformações próximas ao estado nativo. Técnicas de visualização e minimização são usadas para mapear o processo do enovelamento em um espaço de fase de menor dimensionalidade. Por meio desta visualização é possível analisar o enovelamento com detalhes, como a conectividade entre conformações, os diferentes caminhos para se atingir o estado nativo e regiões onde a proteína pode ficar armadilhada. Para este trabalho, utilizou-se cinco proteínas distintas, sendo duas altamente estáveis, duas que possuem baixa estabilidade e uma quinta que tem o estado nativo degenerado. A visualização dos funis se mostraram bastantes distintas, sendo possível notar um padrão para cada proteíına mesmo quando variado alguns parâmetros. Tais resultados são consistentes com as ideias associadas à teoria do funil de enovelamento de proteínas / Abstract: The protein folding is a fundamental problem in molecular biophysics. The accepted theory, known as energy landscape, uses the funnel potential energy as a fundamental concept to understand the protein folding problem. The energy funnel occurs in a multidimensional surface, which is difficult to be visualized. The investigation of methods for a quantitative analysis of the funnel structure is important for complete understanding of the problem. In this work, ways for visualize the protein folding funnels in a 3×3×3 lattice models are presented. Protein folding simulations are carried out. Distances between conformations are determined by the non-covalent contact sand defined by effective metric of the structural configuration. The analysis is restricted to conformations close to the native state, i.e., beyond the transition state. Computer minimization and visualization techniques were used to map the dynamics of the folding process into a lower dimensionality phase space, and then represent the folding funnel in two and three-dimensional surface. These techniques are applied to five distinct sequences, which two are highly stable, two marginally stable and the last has a native degenerated state. Their folding funnels are very distinct, where each sequence has a signature even when some parameters varied. These results are consistent with the ideas of the theory of protein folding funnel / Mestre

Orientador: Aguinaldo Robinson de Souza / Banca: Julio Ricardo Sambrano / Banca: Antonio Caliri / O Programa de Pós-Graduação em Ciência e Tecnologia de Materiais, PosMat, tem caráter institucional e integra as atividades de pesquisa em materiais de diversos campi da Unesp / Resumo: Compreender como a sequencia de aminoácidos de uma proteína determina a sua funcionalidade biológica é de grande importância conceitual e prática como, por exemplo, no projeto de novas drogas. As proteínas consistem em polipeptídios composta por 20 L- aminoácidos diferentes, (formados pelos átomos de hidrogênio, carbono, nitrogênio e oxigênio) ligados por ligações peptídicas. O que torna as proteínas diferentes não é o número de aminoácidos, mas a sequencia deles na cadeia polipeptídica. No presente trabalho, apresentamos uma simulação computacional, com modelo simples, para a enumeração exata de todas as conformações possíveis em uma rede de todas as conformações possíveis em uma rede quadrada para n = 1 a 17 monômeros. Resultados mostram que 2.155.667 conformações diferentes são possíveis. Neste trabalho, confirmamos estes resultados e atribuímos aos sítios da rede quadrada os monômetros no modelo que foram usados para computar o número de contatos entre os monômeros, distribuição da energia configuracional, distância em relação a frequencia relativa de todas as conformações, contato topológico de longo alcance, aplicamos e comparamos os resultados das simulações do modelo com sequencia de Epitopos. / Abstract: The understanding of how the amino acids sequence determine the protein biological funtionality is one of the most practical and conceptual challenge as, for example, in the development of new drugs. The protein molecule consist of a long chain of polupeptides composed of 20 different amino acids (essentially formed by carbon, oxygen, nitrogen, and hydrogen atoms) linked together by peptide chemical bonds. What makes proteins different is not the number of amino acids in the chain but the amino acid sequence along the chain. In the present a computer simulation of a simple protein model, using the techinique of exact enumeration over all the possible conformations in the square lallice to a sequence of n = 1 to 17 monomers. The results indicate that we can found 2.155.1667 different possible conformations. We present the results for the Cartesian coordinates of all the monomers along the chain and computed the monomer-monomer contacts, the configurational energy, the long-range topological contact and a possible application of the HP model for a variety of epitopes sequences. / Mestre

Orientador: Vitor Barbanti Pereira Leite / Banca: Leandro Cristante de Oliveira / Banca: Sidney Jurado de Carvalho / Resumo: No processo de enovelamento as proteínas seguem o principio de "mínima frustração", garantindo ao estado nativo o seu mínimo global de energia e a sua estabilidade termodinâmica. Apesar de, a proteína estar no seu estado nativo, esta condição não impede o surgimento de algumas interações energeticamente desfavoráveis, caracterizando a frustração no estado nativo. Há evidências indicando que um pequeno grau de frustração pode favorecer o processo de enovelamento. Neste estudo são investigadas as condições em que a presença de frustração, é ou não, favorável ao processo de enovelamento. São realizadas simulações computacionais de dinâmica molecular utilizando o modelo Cα (um modelo baseado em estrutura e sem frustração). É adicionado um termo ao potencial do modelo associado à presença de frustração. As simulações do modelo Cα são realizadas para um grupo de proteína com características distintas. É introduzido um critério determinando os casos em que a frustração auxilia o processo de enovelamento. São observados os efeitos da presença de frustração ao longo do processo de enovelamento e sua influência na alteração da temperatura e do tempo de enovelamento. De acordo com o critério introduzido é possível separar as proteínas estudadas em dois grupos distintos, um grupo em que a adição de frustração auxilia o processo de enovelamento e outro grupo em que a presença de frustração não é favorável. A separação das proteínas em dois grupos distintos está relacionada com a ordem de contato absoluta e com a barreira de energia livre de cada proteína / Abstract: In the folding process the proteins follow the "minimal frustration" principle, which guarantees to the native state the minimum global energy and the thermodynamic stability. However, not even the native state can prevent the occurrence of some unfavorable interactions, characterizing the frustration in the native state. There are evidences that a low degree of frustration can favorable to the folding process. In this work it was investigated the conditions under which some frustration helps the protein folding process. Through computer simulations of molecular dynamics, using a structure-based model (non-frustrated model) and adding a parameterized nonspecific energetic frustration to the potential, were studied the kinetics and the thermodynamics properties of a large group of proteins. It is introduced a criterion to determine when the presence of frustration assists the folding process. The effects of the frustration addition are observed and its influence produces changes in the folding temperature and in the folding time. In agree with the adopted criterion, it was observed two well separated groups: one in which some frustration helps the folding process, and another in which frustration hinders it, determining when the presence of frustration is favorable. These results are correlated with the proteins absolute contact order parameter and free energy barrier / Mestre

Orientador: Vitor Barbanti Pereira Leite / Banca: Elso Drigo Filho / Banca: Leandro Cristante de Oliveira / Resumo: Por meio de simulações computacionais, acompanhamos o processo de enovelamento de um conjunto de proteínas. Neste estudo utilizamos a abordagem conhecida como teoria de Superfície de Energia (Energy Landscape), que trata o enovelamento por uma descrição estatística. O modelo utilizado foi um modelo baseado em estrutura. Para investigarmos os efeitos das interações não nativas no enovelamento de um grupo de proteínas, acrescentamos um termo de frustração ao potencial de energia. Os resultados obtidos a partir dos estudos das propriedades termodinâmicas e cinéticas das proteínas, mostraram que para um grupo de proteínas a frustração ajudou o enovelamento e para outro grupo a frustração atrapalhou. Analizando propriedades como ordem de contato absoluta, tamanho da proteína e barreira de energia livre, foi possível obter um limiar em que a frustração auxilia no enovelamento. Para encontrarmos um limiar, foi necessário uma quantidade grande de proteínas de diferentes tamanhos e diferentes motifs / Abstract: Through computational simulations, the folding process of a set of proteins was monitored. The framework used to describe protein folding was the energy landscape theory, which is a statistical description of folding. The model used was the structural based model. A frustration term was added to the potential to investigate the non-native interactions effect. The results obtained from studies of thermodynamics and kinetics properties, showed for a one group of proteins the frustration helps the folding and for another group the frustrations hinders the folding. The properties as absolute contact order, size of protein and free energy barrier was analyzed and it was possible to obtain a threshold that the frustration helps the folding. It was necessary a large set of proteins of different sizes and motifs to find a threshold / Mestre