ATP-dependent chromatin remodellers represent a class of proteins that restructure chromatin through the action of a conserved helicase-like ATPase domain. Remodellers typically have several accessory binding domains alongside the ATPase. These confer target specificity and most commonly recognise histone post-translational modifications. SMARCAD1 is a ubiquitous chromatin remodeller involved with DNA replication and re- pair. It binds directly to PCNA at the site of DNA replication and recruits co-repressor KAP1 in order to silence newly produced chromatin. In contrast to most other chromatin remodellers, SMARCAD1 does not contain several different types of accessory domains. Only two CUE do- mains have been identified in addition to the SMARCAD1 core ATPase domain. CUE domains are a type of helical ubiquitin-binding domain. This thesis presents the findings of an investigation into the structure and function of the SMARCAD1 double CUE domain. The solution NMR structure is presented with results from NMR binding experiments mapped onto the structure. Each CUE domain was found to be an independent helix bundle connected by a dynamic flexible linker. The N-terminal CUE domain, CUE-1, binds ubiquitin and has an adjacent SUMO (a ubiquitin-like protein) binding motif on a protruding extended helix. The C-terminal CUE domain, CUE-2, has a very similar structure to several published CUE domains but does not bind ubiquitin due to a charged substitution at a highly conserved CUE consensus position. The SMARCAD1 double CUE domain binds KAP1 from nuclear extract and is likely to mediate the interaction between SMARCAD1 and KAP1. SMARCAD1 double CUE domain is not involved with PCNA binding.

This thesis describes the development of a novel approach for prediction of the three-dimensional structure of transmembrane regions of membrane proteins directly from amino acid sequence and basic transmembrane region topology. The development rationale employed involved a knowledge-based approach. Based on determined membrane protein structures, 20x20 association matrices were generated to summarise the distance associations between amino acid side chains on different alpha helical transmembrane regions of membrane proteins. Using these association matrices, combined with a knowledge-based scale for propensity for residue orientation in transmembrane segments (kPROT) (Pilpel et al., 1999), the software predicts the optimal orientations and associations of transmembrane regions and generates a 3D structural model of a gi ven membrane protein, based on the amino acid sequence composition of its transmembrane regions. During the development, several structural and biostatistical analyses of determined membrane protein structures were undertaken with the aim of ensuring a consistent and reliable association matrix upon which to base the predictions. Evaluation of the model structures obtained for the protein sequences of a dataset of 17 membrane proteins of detennined structure based on cross-validated leave-one-out testing revealed generally high accuracy of prediction, with over 80% of associations between transmembrane regions being correctly predicted. These results provide a promising basis for future development and refinement of the algorithm, and to this end, work is underway using evolutionary computing approaches. As it stands, the approach gives scope for significant immediate benefit to researchers as a valuable starting point in the prediction of structure for membrane proteins of hitherto unknown structure.

Doctor of Philosophy / Department of Biochemistry / Michal Zolkiewski / ClpB is a bacterial heat-shock protein that disaggregates and reactivates strongly aggregated proteins in cooperation with the DnaK chaperone system. ClpB contains two ATP-binding AAA+ modules, a linker coiled-coil domain, and a highly mobile N-terminal domain. It forms ring-shaped hexamers in a nucleotide-dependent manner. The unique aggregation reversing chaperone activity of ClpB involves ATP-dependent translocation of substrates through the central channel in the ClpB ring. The initial events of aggregate recognition and the events preceding the translocation step are poorly understood. In addition to the full-length ClpB95, a truncated isoform ClpB80, that is missing the whole N-terminal domain, is also produced in vivo. Various aspects of the structure and function of ClpB were addressed in this work. The thermodynamic stability of ClpB in its monomeric and oligomeric forms, as well as the nucleotide-induced conformational changes in ClpB were investigated by fluorescence spectroscopy. Equilibrium urea-induced unfolding showed that two structural domains-the small domain of the C-terminal AAA+ module and the coiled-coil domain-were destabilized in the oligomeric form of ClpB, which indicates that only those domains change their conformation or interactions during formation of the ClpB rings. Several locations of Trp-fluorescence probes were also found to respond to nucleotide binding. The biological role of the two naturally-occurring ClpB isoforms was also investigated. We discovered that ClpB achieves optimum chaperone activity by synergistic cooperation of the two isoforms that form hetero-oligomers. We found that ClpB95/ClpB80 hetero-oligomers form preferentially at low protein concentration with higher affinity than homo-oligomers of ClpB95. Moreover, hetero-oligomers bind to aggregated substrates with a similar efficiency as homo-oligomers of ClpB95, do not show enhanced ATPase activity over that of the homo-oligomers, but display a strongly stimulated chaperone activity during the reactivation of aggregated proteins. We propose that extraction of single polypeptides from aggregates and their delivery to the ClpB channel for translocation is the rate-limiting step in aggregate reactivation and that step is supported by the mobility of the N-terminal domain of ClpB. We conclude that the enhancement of the chaperone activity of the hetero-oligomers is linked to an enhancement of mobility of the N-terminal domains.

Proteínas desempenham uma grande variedade de funções biológicas. O conhecimento da estrutura tridimensional proteica pode ajudar no entendimento da função desempenhada. De acordo com a hipótese de Anfisen, a estrutura terciária nativa de uma proteína pode ser determinada a partir da informação contida na sequência primária, o que permitiria que métodos computacionais poderiam ser usados para predizer estruturas terciárias quando a primária estiver disponível. No entanto, ainda não existe uma ferramenta computacional capaz de predizer a estrutura tridimensional para uma grande variedade de proteínas. Desse modo, o problema de Predição de Estruturas de Proteínas (PEP) permanece como um desafio para a Biologia Molecular. A conformação nativa de uma proteína é frequentemente a configuração termodinamicamente mais estável, ou seja, que possui menor energia livre. Assim, PEP pode ser vista como um problema de otimização, onde a estrutura com menor energia livre deve ser encontrada dentre todas as possíveis. Entretanto, este é um problema NP-completo, no qual métodos tradicionais de otimização, em geral, não apresentam um bom desempenho. Algoritmos Genéticos (AGs), devido às suas características, são interessantes para essa classe de problemas. O principal objetivo desse trabalho é verificar se a adição de informação pode ser útil aos AGs aplicados em PEP, valendo-se dede modelos moleculares simplificados. Cada indivíduo do AG representa uma solução que, neste caso, é uma possível conformação que será avaliada por um campo de força. Dessa forma, o indivíduo é codificado por um conjunto de ângulos de torção de cada aminoácido. Para auxiliar no processo de busca, bases de dados compostas de ângulos determinados por cristalografia e RNM são utilizadas. Com o objetivo de guiar o processo de busca e manter a diversidade nos AGs, duas estratégias são aqui testadas: Imigrantes Aleatórios e Imigrantes por Similaridade. A última delas foi criada baseando-se na similaridade da sequência primária. Além disso, é investigado neste trabalho o uso de um campo de força coarse grained, que utiliza os átomos de carbono- para representar a cadeia proteica, para avaliar os indivíduos do AG. / Proteins exhibit an enormous variety of biology functions. The knowledge of tertiary structures can help the understanding of the proteins function. According to Anfisen, the native tertiary structure of a protein can be determined by its primary structure information, what could allow that computational methods could be used to predict the tertiary structure when the primary structure is available. However, there is still not a computational tool to solve the structure prediction problem for a large range of proteins. In this way, Protein Structure Prediction (PSP) has been a challenge to Molecular Biology. The conformation of native protein is usually the thermodynamically most stable configuration, i.e., the one having the lowest free energy. Hence, PSP can be viewed as a problem of optimization, where the structure with the lowest free energy should be found among all possible structures. However, this is an NP-problem, where traditional optimization methods, in general, do not have good performance. Genetic algorithms (GAs), due to their characteristics, are interesting for this class of problems. In recent years, there is a growing interest in using GAs for the protein structure prediction problem. The main objective of this work is to verify the addition of useful information to GAs employed in PSP. Each individual of the GA represents a solution for the optimization problem which is, in this case, a possible conformation that will be evaluated by a force field function. Thus, an individual is encoded by a set of torsion angles of each amino acid. In order to reduce the search space, a database composed of angles, determined by crystallography and NMR, is used. With the aim to guide the final search process and maintain diversity in GAs, two strategies were employed here: Random Immigrants and Similarity-based Immigrants. The last strategy was based on similarity of primary amino acid sequence. Furthermore, in this work, a coarse-grained force field, which uses -carbon to represent the protein backbone was employed to evaluate the individuals of GA.

A produção de soro no Brasil, único tratamento eficaz nos casos de acidentes ofídicos, utiliza equinos que apesar do grande porte, apresentam diminuição da longevidade quando comparado com os cavalos não imunizados. A radiação ionizante tem se mostrado como excelente ferramenta na diminuição da toxicidade de venenos e toxinas isoladas, além de promover a obtenção de melhores imunógenos para a produção de soro. Sabe-se, contudo, que os efeitos da radiação ionizante em materiais protéicos caracterizam-se por diversas alterações químicas, como fragmentação, cross-linking, agregação e oxidação devido aos produtos gerados pela radiólise da água. Porém, a ação da radiação gama em toxinas ainda não está totalmente esclarecida do ponto de vista estrutural e farmacológico, fato que impede a aplicação de tal metodologia no processo de produção do soro. Assim, foi proposto nesse trabalho a caracterização da crotamina, uma das principais proteínas do veneno da espécie Crotalus durissus terrificus, irradiada com raios gama de 60Co. Após o isolamento da toxina por técnicas cromatográficas e a realização de testes para comprovar a obtenção da crotamina pura, a toxina, nos estados nativo e irradiado, foi submetida às análises estruturais de Fluorescência e Dicroísmo Circular. Testes utilizando altas pressões hidrostáticas também foram realizados com o intuito de verificar se as alterações conformacionais causadas pela radiação sofreriam modificações sob altas pressões. Do ponto de vista farmacológico, testes de contração muscular foram realizados com o objetivo de delimitar a ação da crotamina em musculatura lisa, bem como a mudança na ação da toxina frente às alterações estruturais ocasionadas. As análises de Fluorescência e Dicroísmo Circular mostraram que há mudanças na conformação da crotamina quando submetida à radiação gama e que tais alterações possivelmente ocorrem na estrutura terciária e secundária da proteína. O observado nos testes farmacológicos mostraram que a crotamina irradiada foi menos eficaz na diminuição da contração muscular do ducto deferente de ratos em comparação com a crotamina nativa. Além disso, o comportamento da toxina irradiada na contração tônica, modulada por noradrenalina, foi distinto daquele observado para a toxina nativa. / The serum production in Brazil, the only effective treatment in cases of snakebites, uses horses that although large size, have reduced llifespan compared with horses not immunized. Ionizing radiation has been shown as an excellent tool in reducing the toxicity of venoms and toxins isolated, and promote the achievement of better immunogens for serum production, and contributing to the welfare of serum-producing animals. It is known, however, that the effects of ionizing radiation on protein are characterized by various chemical modifications, such as fragmentation, cross-linking due to aggregation and oxidation products generated by water radiolysis. However, the action of gamma radiation on toxins is not yet fully understood structurally and pharmacologically, a fact that prevents the application of this methodology in the serum production process. So we proposed in this paper the characterization of crotamine, an important protein from the venom of Crotalus durissus terrificus species, irradiated with 60Co gamma rays. After isolating the toxin by chromatographic techniques and testing to prove the obtaining of pure crotamine, it was irradiated with gamma rays and subjected to structural analysis, Fluorescence and Circular Dichroism. Using high hydrostatic pressure tests were also conducted in order to verify that the conformational changes caused by radiation suffer modifications under high pressures. From the pharmacological point of view, muscle contraction tests were conducted with the objective of limiting the action of crotamine in smooth muscle as well as the change in the action of toxin caused structural changes to the front. Analysis of Circular Dichroism and Fluorescence showed changes in structural conformation of crotamine when subjected to gamma radiation and that such changes possibly occurring in the secondary and tertiary structure of the protein. The observed in pharmacological tests showed that the irradiated crotamine was less effective in lowering the vas deferens twitch in rats in comparison to native crotamine. In addition, the behavior of irradiated toxin in tonic contraction, modulated by noradrenaline, was different from that observed for the native toxin.

A produção de soro no Brasil, único tratamento eficaz nos casos de acidentes ofídicos, utiliza equinos que apesar do grande porte, apresentam diminuição da longevidade quando comparado com os cavalos não imunizados. A radiação ionizante tem se mostrado como excelente ferramenta na diminuição da toxicidade de venenos e toxinas isoladas, além de promover a obtenção de melhores imunógenos para a produção de soro. Sabe-se, contudo, que os efeitos da radiação ionizante em materiais protéicos caracterizam-se por diversas alterações químicas, como fragmentação, cross-linking, agregação e oxidação devido aos produtos gerados pela radiólise da água. Porém, a ação da radiação gama em toxinas ainda não está totalmente esclarecida do ponto de vista estrutural e farmacológico, fato que impede a aplicação de tal metodologia no processo de produção do soro. Assim, foi proposto nesse trabalho a caracterização da crotamina, uma das principais proteínas do veneno da espécie Crotalus durissus terrificus, irradiada com raios gama de 60Co. Após o isolamento da toxina por técnicas cromatográficas e a realização de testes para comprovar a obtenção da crotamina pura, a toxina, nos estados nativo e irradiado, foi submetida às análises estruturais de Fluorescência e Dicroísmo Circular. Testes utilizando altas pressões hidrostáticas também foram realizados com o intuito de verificar se as alterações conformacionais causadas pela radiação sofreriam modificações sob altas pressões. Do ponto de vista farmacológico, testes de contração muscular foram realizados com o objetivo de delimitar a ação da crotamina em musculatura lisa, bem como a mudança na ação da toxina frente às alterações estruturais ocasionadas. As análises de Fluorescência e Dicroísmo Circular mostraram que há mudanças na conformação da crotamina quando submetida à radiação gama e que tais alterações possivelmente ocorrem na estrutura terciária e secundária da proteína. O observado nos testes farmacológicos mostraram que a crotamina irradiada foi menos eficaz na diminuição da contração muscular do ducto deferente de ratos em comparação com a crotamina nativa. Além disso, o comportamento da toxina irradiada na contração tônica, modulada por noradrenalina, foi distinto daquele observado para a toxina nativa. / The serum production in Brazil, the only effective treatment in cases of snakebites, uses horses that although large size, have reduced llifespan compared with horses not immunized. Ionizing radiation has been shown as an excellent tool in reducing the toxicity of venoms and toxins isolated, and promote the achievement of better immunogens for serum production, and contributing to the welfare of serum-producing animals. It is known, however, that the effects of ionizing radiation on protein are characterized by various chemical modifications, such as fragmentation, cross-linking due to aggregation and oxidation products generated by water radiolysis. However, the action of gamma radiation on toxins is not yet fully understood structurally and pharmacologically, a fact that prevents the application of this methodology in the serum production process. So we proposed in this paper the characterization of crotamine, an important protein from the venom of Crotalus durissus terrificus species, irradiated with 60Co gamma rays. After isolating the toxin by chromatographic techniques and testing to prove the obtaining of pure crotamine, it was irradiated with gamma rays and subjected to structural analysis, Fluorescence and Circular Dichroism. Using high hydrostatic pressure tests were also conducted in order to verify that the conformational changes caused by radiation suffer modifications under high pressures. From the pharmacological point of view, muscle contraction tests were conducted with the objective of limiting the action of crotamine in smooth muscle as well as the change in the action of toxin caused structural changes to the front. Analysis of Circular Dichroism and Fluorescence showed changes in structural conformation of crotamine when subjected to gamma radiation and that such changes possibly occurring in the secondary and tertiary structure of the protein. The observed in pharmacological tests showed that the irradiated crotamine was less effective in lowering the vas deferens twitch in rats in comparison to native crotamine. In addition, the behavior of irradiated toxin in tonic contraction, modulated by noradrenaline, was different from that observed for the native toxin.

A contração muscular esquelética é regulada pelo complexo troponina/tropomiosina de maneira dependente de Ca2+. O complexo troponina consiste de três subunidades: a troponina C (TnC), a troponina I (TnI) e a troponina T (TnT). A troponina C é a subunidade que liga Ca2+, a TnI é a subunidade inibitória e a TnT liga-se fortemente à tropomiosina. A TnI e a TnT são altamente insolúveis a baixas forças iônicas, a não ser que estejam complexadas com a TnC. O complexo troponina pode ser reconstituído \"in vitro\" a partir das subunidades isoladas simplesmente misturando-se as subunidades em razões equimolares em uréia, que depois é removida através de diálise. Na primeira parte deste trabalho um vetor para a co-expressão da TnC, TnI e TnT em E.coli foi construído. Utilizando este vetor nós produzimos um complexo troponina funcional montado no citoplasma de E.coli. A presença da TnT é requerida para regulação dependente de Ca2+ da contração muscular esquelética. O papel da TnT em conferir sensibilidade ao Ca2+ à atividade ATPásica da acto-miosina foi analisado. Mutantes de deleção da TnT foram construídos através de mutação sítio-dirigida e expressos em E.coli. Complexos troponina contendo os mutantes de TnT e/ou mutantes de TnI foram reconstituídos e analisados em ensaios de ligação ao filamento fino e ensaios de atividade ATPásica. Baseado nestes resultados a TnT foi subdividida em três domínios: o domínio ativatório (aminoácidos 157-216), o domínio inibitório (aminoácidos 157-216) e o domínio de ancoragem do dímero TnC/TnI (aminoácidos 216-263). Nós demonstramos que o dímero TnC/TnI está ancorado ao filamento fino através da interação entre a região amino-terminal da TnI e da região carbóxi-terminal da TnT (aminoácidos 216-263). Um modelo para o papel da TnT na regulação da contração muscular dependente de Ca2+ é proposto. / The contraction of skeletal muscle is regulated by troponin and tropomyosin in a Ca2+ dependent manner. The troponin complex consists of three subunits: troponin C (TnC), troponin I (TnI) and troponin T (TnT). Troponin C is the Ca2+ binding subunit, TnI is the inhibitory subunit and TnT binds tightly to tropomyosin. TnI and TnT are highly insoluble proteins at low ionic strengths, unless they are complexed with TnC. The troponin complex can be reconstituted \"in vitro\" from the isolated subunits simply by mixing the subunits at equimolar ratios in urea, which is then removed by dialysis. In the first part of this work a vector for the co-expression of TnC, TnI and TnT in E.coli was constructed. Using this vector we were able to produce a functional troponin complex assembled \"in vivo\" in the E.coli cytoplasm The presence of TnT is required for the Ca2+ dependente regulation of the skeletal muscle contraction. The role of TnT in conferring full Ca2+ sensitivity to the ATPase activity of acto-myosin was analyzed. Deletion mutants of TnT were constructed by site-directed mutagenesis and expressed in E.coli. Troponin complexes containing the TnT deletion mutants and/or TnI deletion mutants, were reconstituted and analyzed in thin filament binding assays and in ATPase activity assays. Based on these studies, TnT was subdivided into three domains: the activation domain (comprised of aminoacids 1-157), the inhibitory domain (comprised of amino acids 157-216) and the TnC/TnI dimer anchoring domain (aminoacids 216-263). We demonstrated that the TnC/TnI is anchored to the thin filament through interaction between the amino-terminal domain of TnI and the region comprised of aminoacids 216-263 of TnT. A model for the role of TnT in the Ca2+ dependent regulation of muscle contraction is proposed.

The paralogous multi-functional adaptor proteins YAP and TAZ are nuclear effectors of the Hippo pathway, a central regulator of developmental organ size control, tissue homeostasis and tumour suppression. YAP/TAZ target the TEAD transcription factor family to promote cell survival and inhibit apoptosis. TEAD proteins contain a DNAbinding domain and a YAP/TAZ interaction domain. PCR analysis of medaka fish TEAD cDNA revealed the presence of alternative TEAD splice-forms with variations at the C-terminus of the DNA-binding domain. Structural analysis indicated the YAPbinding domain of TEAD proteins is folded and globular. NMR spectroscopy showed that the TEAD binding domain of YAP does not contain secondary structure. YAP and TAZ both contain WW domains, which are small protein-protein interaction modules. Two YAP isoforms are known, YAP1 and YAP2 that contain one and two WW domains, respectively. To date, only a single WW isoform of TAZ has been described. PCR analysis of medaka TAZ cDNA identified both single WW and tandem WW isoforms of TAZ. NMR spectroscopy was used to characterise structural, conformational, and peptide binding features of the tandem WW domains from YAP and TAZ. The YAP WW2 solution structure confirms that the domain has the canonical anti-parallel β-sheet WW fold. WW1 of YAP and both WW domains of TAZ undergo conformational exchange. The region linking the two WW domains is flexible and allows interaction of both WW domains with peptides containing single and dual PPxY binding motifs. In addition to YAP and TAZ, tandem WW domains are also present in the core and upstream Hippo pathway proteins Salvador and Kibra. Both proteins contain one atypical WW domain; the tandem WW domains of these two proteins are unstable. Understanding structure and function of Hippo pathway components could contribute to drug development and will also contribute to knowledge of protein folding and interactions.

Antibodies are soluble proteins produced by the adaptive immune system to bind and counteract invading pathogens. The binding properties of a typical human antibody are determined by the structure of its variable domain, composed of two chains – heavy and light and by the conformation of six loops located on the surface of the variable domain, known as Complementarity Determining Regions (CDRs). In the first chapter, we describe our analysis of the conformational space occupied by five out of six antibody CDRs (L1, L2, L3, H1 and H2) and the development of a novel, length-independent method for grouping these CDRs into structural clusters (canonical forms). We show that using our method we can increase coverage and precision of assigning CDR sequences into clusters. In the next chapter, we describe a method for ranking structural decoys of the CDR-H3 loop. We show that by computationally perturbing CDR-H3 decoys we can improve the performance of existing ranking methods. In the same chapter, we discuss the development of a method for high-throughput assignment of heavy-light chain orientation. The power of the method was demonstrated by assigning orientation to billions of potential Fv sequences. The third Chapter describes the analysis of a large dataset of CDR sequences with the aim of identifying sequence patterns responsible for the loops' structure. Using a neural network methodology, we found several groups of CDR sequences which might be indicative of previously-unseen conformations. In the final results Chapter, we describe how we used the structural knowledge developed throughout the rest of the thesis to create a novel pipeline for computational antibody design. We show that the binders developed using our methodology had similar features to available antibody therapeutics and low predicted propensity to cause an immunogenic response. These results demonstrate the potential for using computational methods for designing high affinity therapeutics with human properties.

O problema de predição de estruturas tridimensionais de proteínas pode ser visto computacionalmente como um problema de otimização, tal que dada a sequência de aminoácidos, deve-se encontrar a estrutura tridimensional da proteína dentre as muitas possíveis através da obtenção de mínimos de funções de energia. Vários pesquisadores têm proposto estratégias de Computação Evolutiva para a determinação de estruturas tridimensionais das proteínas, entretanto nem sempre resultados animadores têm sido alcançados visto que entre outros fatores, há um grande número de ótimos locais no espaço de busca. Geralmente as funções de fitness empregadas pelos algoritmos de otimização são baseadas em campos de força com diferentes termos de energia, sendo que os parâmetros destes termos são ajustados a priori e são mantidos estáticos ao longo do processo de otimização. Alguns pesquisadores sugerem que o uso de funções de fitness dinâmicas, ou seja, que mudam durante um processo de otimização evolutivo, pode aumentar a capacidade das populações fugirem de ótimos locais em problemas altamente multimodais. Neste trabalho, propõe-se que os parâmetros dos termos do campo de força utilizado sejam modificados durante o processo de otimização realizado por Algoritmos Genéticos (AGs) no problema de predição de estruturas de proteínas, sendo aumentados ou diminuídos, por exemplo, de acordo com a sua influência na formação de estruturas secundárias e no seu ajuste fino. Como a função de avaliação será modificada durante o processo de otimização, a predição de estruturas tridimensionais de proteínas torna-se um problema de otimização dinâmica, sendo que o uso de Algoritmos Genéticos específicos para tais problemas, como o AG com hipermutação e os AGs com imigrantes aleatórios são investigados aqui. É proposta uma nova métrica relacionada ao alinhamento da estrutura secundária da proteína, para auxiliar a análise dos dados obtidos e os resultados dos experimentos indicam que os algoritmos com função de avaliação dinâmica obtiveram resultados melhores que os algoritmos estáticos, o que é explicado pelo fato de as mudanças na função de fitness possibilitarem eventuais fugas de ótimos locais, bem como um aumento da diversidade da população. / The protein structure prediction can be seen as an optimization problem where given an amino acid sequence, the tertiary protein structure must be found amongst many possible by obtaining energy functions minima. Many researchers have been proposing Evolutionary Computation strategies to find tridimensional structures of proteins; however results are not always satisfactory since among other factors, there are always a great number of local optima in the search space. Usually, the fitness functions used by optimization algorithms are based on force fields with different energy terms with parameters from those terms being adjusted a priori, kept static through the optimization process. Some researchers suggest that the use of dynamic functions, i.e., that can be changed during the evolutionary process, can help the population to escape from local optima in highly multimodal problems. In this work we propose that the force field parameters can be changed during the optimization process of Genetic Algorithms (GAs) in the protein structure prediction problem, being increased or decreased, for instance, according with its influence on formation of secondary structures and its fine tuning. Since the cost function will be changed during the optimization process, the protein tridimensional structure prediction becomes a dynamic optimization problem and specific Genetic Algorithms for this kind of problem, like the hypermutation GA and random immigrants GA are investigated. We also propose a new metric related to the proteins secondary structure alignment to help the analysis of obtained data. Results indicate that the dynamic function algorithms obtained better results than static algorithms since changes on the fitness function allow the population to escape local optima, as well as an increase on the population diversity.