Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.

Detalhes bibliográficos
Ano de defesa: 2018
Autor(a) principal: BORGES, Ueliton Galdino
Orientador(a): OLIVEIRA, Ronaldo Júnio de lattes
Banca de defesa: Não Informado pela instituição
Tipo de documento: Dissertação
Tipo de acesso: Acesso aberto
Idioma: por
Instituição de defesa: Universidade Federal do Triângulo Mineiro
Programa de Pós-Graduação: Programa de Pós-Graduação Multicêntrico em Química de Minas Gerais
Departamento: Instituto de Ciências Exatas, Naturais e Educação - ICENE
País: Brasil
Palavras-chave em Português:
Proteínas homologas.
Termoestabilidade.
Dinâmica Molecular.
Modelo baseado em estrutura.
Superfície de energia.
Palavras-chave em Inglês:
Cold Shock.
Homologous proteins.
Thermostability.
Molecular dynamics.
Structure-based model.
Energy Landscape.
Área do conhecimento CNPq:
Química Teórica
Link de acesso: http://bdtd.uftm.edu.br/handle/tede/620
Resumo: The functions that proteins perform are extremely important to living things, this function is directly linked to its thermostability, and may undergo temperature variations. As thermostability is the focus of this work, specifically addressing the different transition temperatures between the unfolding / unfolding of the homologous proteins, using as study object and starting point for these and other questions, Cold Shock homologous proteins of the psychophilic bacteria, Listeria monocytogenes (Cs-pLa), mesophilic, Bacillus caldolyticus (Bs-CspB), thermophilic, Bacillus subtilis (Bc-Csp) and hyperthermophilic, Thermotoga maritime (Tm-Csp), considering the variations in temperature and their interactions, taking into account the aspects of these proteins as well as their identity and similarity. It may be noted that there are several methods of determining protein structures in both in vitro and in silicon. In this work, we propose an in silico method, which discusses the simulation of protein structure and optimization, considering simultaneously the energetic and structural aspects of proteins. For the Molecular Dynamics simulations the GROMACS software was used. To better understand these thermodynamic differences and the thermostability that occurs due to the variations of the chains in Cold Shock proteins proteins. We performed computational simulations taking into account only the alpha carbon (CĮ) that considerably reduces the simulation time. The theoretical results found corroborated with experimental data showing that the Cold Shock protein Hyperthermophilic Thermotoga marine bacteria present the highest value of folding temperature and the largest difference of RMSD among all four Cold Shock proteins currently studied. Due to the finding that the Cold Shock proteins presented favorable thermostability to the residue changes that can be carried out in order to be used in processes that require a change in temperature.
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spelling OLIVEIRA, Ronaldo Júnio dehttp://lattes.cnpq.br/9945821072452088BORGES, Ueliton Galdino2019-03-26T18:13:48Z2018-12-18BORGES, Ueliton Galdino. Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.. 2018. 66f. Dissertação (Mestrado em Química) - Programa de Pós-Graduação Multicêntrico em Química de Minas Gerais, Universidade Federal do Triângulo Mineiro, Uberaba, 2018http://bdtd.uftm.edu.br/handle/tede/620The functions that proteins perform are extremely important to living things, this function is directly linked to its thermostability, and may undergo temperature variations. As thermostability is the focus of this work, specifically addressing the different transition temperatures between the unfolding / unfolding of the homologous proteins, using as study object and starting point for these and other questions, Cold Shock homologous proteins of the psychophilic bacteria, Listeria monocytogenes (Cs-pLa), mesophilic, Bacillus caldolyticus (Bs-CspB), thermophilic, Bacillus subtilis (Bc-Csp) and hyperthermophilic, Thermotoga maritime (Tm-Csp), considering the variations in temperature and their interactions, taking into account the aspects of these proteins as well as their identity and similarity. It may be noted that there are several methods of determining protein structures in both in vitro and in silicon. In this work, we propose an in silico method, which discusses the simulation of protein structure and optimization, considering simultaneously the energetic and structural aspects of proteins. For the Molecular Dynamics simulations the GROMACS software was used. To better understand these thermodynamic differences and the thermostability that occurs due to the variations of the chains in Cold Shock proteins proteins. We performed computational simulations taking into account only the alpha carbon (CĮ) that considerably reduces the simulation time. The theoretical results found corroborated with experimental data showing that the Cold Shock protein Hyperthermophilic Thermotoga marine bacteria present the highest value of folding temperature and the largest difference of RMSD among all four Cold Shock proteins currently studied. Due to the finding that the Cold Shock proteins presented favorable thermostability to the residue changes that can be carried out in order to be used in processes that require a change in temperature.As funções que as proteínas desempenham são de extrema importância para os seres vivos. Essas funções estão ligadas diretamente a sua termoestabilidade, podendo sofrer variações de temperatura. Sendo a termoestabilidade o foco deste trabalho, mais especificamente abordando as diferentes temperaturas de transição entre o enovelamento/desnovelamento das proteínas homologas. Serão utilizadas como objeto de estudo e ponto de partida para essas e outras questões, proteínas Cold Shock homologas das bactérias psicrofílica, Listeria monocytogenes (Cs-pLa), mesofílica, Bacillus caldolyticus (Bs-CspB), termofílica, Bacillus subtilis (Bc-Csp) e hipertermofílica, Thermotoga marítima (Tm-Csp), frente as variações de temperatura e de suas interações, levando em conta os aspectos estruturais dessas proteínas bem com a sua identidade e similaridade. Pode-se salientar que existem vários métodos de determinação das estruturas das proteínas tanto em in vitro quanto in silício. Neste trabalho propõe-se um método in silício, no qual aborda a simulação da estrutura da proteína e da otimização, considerando, simultaneamente, os aspectos energéticos e estruturais das proteínas. Para as simulações Dinâmica Molecular utilizou-se o software GROMACS. Para melhor compreender essas diferenças termodinâmicas e a termoestabilidade que ocorre devido as variações das cadeias nas proteínas Cold Shock realizamos simulações computacionais levando apenas em consideração o carbono alfa (CĮ) que diminui consideravelmente o tempo de simulação. Os resultados teóricos encontrados corroboraram com os dados experimentais que mostram que a proteína Cold Shock bactéria Hipertermofílica Thermotoga marítima apresenta o maior valor de temperatura de enovelamento e a maior diferença de RMSD entre todas as quatro proteínas Cold Shock estudas. Devido a constatação de que as proteínas Cold Shock apresentarem termoestabilidade favorável as alterações de resíduos podem ser realizadas no intuito de serem utilizadas em processos que necessitem alteração na temperatura.application/pdfhttp://bdtd.uftm.edu.br/retrieve/3834/Dissert%20Uelitom%20G%20Borges.pdf.jpgporUniversidade Federal do Triângulo MineiroPrograma de Pós-Graduação Multicêntrico em Química de Minas GeraisUFTMBrasilInstituto de Ciências Exatas, Naturais e Educação - ICENEALBER, Tom. Stabilization energies of protein conformation. In: Prediction of protein structure and the principles of protein conformation. Springer, Boston, MA, 1989. p. 161-192. ALMEIDA, A. B. Predição de estrutura terciária de proteínas com técnicas multiobjetivo no algoritmo de Monte Carlo. 2016. 129 f. Dissertação (Mestrado em Ciência da Computação) - Universidade Federal de Goiás, Goiânia, 2016. ANFINSEN, Christian B. Principles that govern the folding of protein chains. Science, v. 181, n. 4096, p. 223-230, 1973. ASTUTI, A. D.; MUTIARA, A. B. Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS. arXiv preprint arXiv: 0912.0893, 2009. BAYNES, Helton Godwin. Mythology of the Soul (Psychology Revivals): A Research Into the Unconscious from Schizophrenic Dreams and Drawings. Routledge, 2015. BENSON, D. A., CAVANAUGH, M., CLARK, K., KARSCH-MIZRACHI, I., LIPMAN, D. J., OSTELL, J., SAYERS, E. W. GenBank. Nucleic acids research, v. 41, n. D1, p. D36-D42, 2012. BERMAN, H. M., WESTBROOK, J., FENG, Z., GILLILAND, G., Bhat, T. N., WEISSIG, H., BOURNE, P. E. The protein data bank. Nucleic acids research, v. 28, n. 1, p. 235-242, 2000. CAMARGO, S. R. Identificação de genes e uso de promotores modulados por etanol em cana-de-açucar. 2007. 84p. Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia, Campinas, SP. CHANG, RAYMOND. Physical chemistry for the chemical and biological sciences. University Science Books, 2000. CHAVEZ, L. L.; ONUCHIC, J. N.; CLEMENTI, C. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. Journal of the American Chemical Society, v. 126, p. 8426-8432, 2004.58 CLEMENTI, C.; NYMEYER, H.; ONUCHIC, J. N. Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins. Journal of molecular biology, v. 298, p. 937-953, 2000. CONTESSOTO, V. G., OLIVEIRA, V. M., CARVALHO, S. J., OLIVEIRA, L. C., LEITE, V. B. NTL9 folding at constant pH: the importance of electrostatic interaction and pH dependence. Journal of chemical theory and computation, v. 12, n. 7, p. 3270-3277, 2016. CONTESSOTO, V. G., OLIVEIRA, V. M., FERNANDES, B. R., SLADE, G. G., LEITE, V. B. TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions. bioRxiv, p. 22156, 2017. CORNELL, W. D., CIEPLAK, P., BAYLY, C. I., GOULD, I. R., MERZ, K. M., FERGUSON, D. M., KOLLMAN, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, v. 117, n. 19, p. 5179-5197, 1995. D’ALFONSO, G.; TRAMONTANO, A.; LAHM, A. Structural conservation in single-domain proteins: implications for homology modeling. Journal of Structural Biology. v. 134, p. 246- 256, 2001. DA SILVA, VINICIUS B. Modelagem molecular de proteínas-alvo por homologia estrutural. Revista eletrônica de Farmácia, v. 4, n. 1, 2007. DE GODOI CONTESSOTO, V., DE OLIVEIRA JUNIOR, A. B., CHAHINE, J., DE OLIVEIRA, R. J., LEITE, V. B. P. (2018) Introdução ao problema de enovelamento de proteínas: uma abordagem utilizando modelos computacionais simplificados. Revista Brasileira de Ensino de Física, v. 40, n. 4, p. e4307, 2018. DILL, K.; BROMBERG, S. Molecular driving forces: statistical thermodynamics in biology, chemistry, physics, and nanoscience. [S.l.]: Garland Science, 2012. DOBSON, C. M. Protein folding and misfolding. Nature, v. 426, p. 884, 2003. DOYE, J. P. K.; MILLER, M. A.; WALES, D. J. Evolution of the potential energy surface with size for Lennard-Jones clusters. The Journal of chemical physics, v. 111, p. 8417-8428, 1999 - a.59 DOYE, J. P. K.; MILLER, M. A.; WALES, D. J. The double-funnel energy landscape of the 38-atom Lennard-Jones cluster. The Journal of Chemical Physics, v. 110, p. 6896-6906, 1999 - b. DURHAM, E. H. A. B. Bioinformática estrutural de proteínas modificadas por eventos de splicing alternativo. 2007. 131 f. Tese de Doutorado. Universidade de São Paulo, São Paulo, 2007. EVANS, DAVID A.; WALES, DAVID J. The free energy landscape and dynamics of metenkephalin. The Journal of chemical physics, v. 119, n. 18, p. 9947-9955, 2003. FERRENBERG, ALAN M.; SWENDSEN, ROBERT H. New Monte Carlo technique for studying phase transitions. Physical review letters, v. 61, n. 23, p. 2635, 1988. FERRENBERG, A. M.; SWENDSEN, R. H. Optimized monte carlo data analysis. Computers in Physics, v. 3, p. 101-104, 1989. FISCHER, DANIEL. Servers for protein structure prediction. Current opinion in structural biology, v. 16, n. 2, p. 178-182, 2006. GONZALEZ, FELIX H. DIAZ; DA SILVA, SERGIO CERONI. Introdução à bioquímica clínica veterinária. 2017. GOSAVI, S., CHAVEZ, L. L., JENNINGS, P. A., ONUCHIC, J. N. Topological frustration and the folding of interleukin-1ȕ. Journal of molecular biology, v. 357, n. 3, p. 986-996, 2006. HARVEY, R. A.; FERRIER, D. R. Bioquıғmica ilustrada. [S.l.]: Artmed Editora, 2015. HESS B, KUTZNER C, VAN DER SPOEL D, LINDAHL E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation. 2008;4(3):435-47. HÖLTJE, H. D.; SIPPL, W.; ROGNAN, D.; FOLKERS, G. Introduction to comparative protein modeling. In Molecular Modeling: Basic Principles and Applications. Weinheim: WileyVCH, 2003. HUMPHREY, WILLIAM; DALKE, ANDREW; SCHULTEN, KLAUS. VMD: visual molecular dynamics. Journal of molecular graphics, v. 14, n. 1, p. 33-38, 1996.60 ITZHAKI, L. S.; OTZEN, D. E.; FERSHT, A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. Journal of molecular biology, v. 254, p. 260-288, 1995. KENDREW, J. C., BODO, G., DINTZIS, H. M., PARRISH, R. G., WYCKOFF, H., PHILLIPS, D. C. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, v. 181, n. 4610, p. 662-666, 1958. KOGA, N.; TAKADA, S. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences, 2012. Journal of molecular biology, v. 313, p. 171-180, 2001. KREMER, W., SCHULER, B., HARRIEDER, S., GEYER, M., GRONWALD, W., WELKER, C., KALBITZER, H. R. Solution NMR structure of the coldǦshock protein from the hyperthermophilic bacterium Thermotoga maritima. European journal of biochemistry, v. 268, n. 9, p. 2527-2539, 2001. KRIVOV, S. V.; KARPLUS, M. Free energy disconnectivity graphs: Application to peptide models. The Journal of chemical physics, v. 117, p. 10894-10903, 2002. KUMAR, S., ROSENBERG, J. M., BOUZIDA, D., SWENDSEN, R. H., KOLLMAN, P. A. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. Journal of Computational Chemistry. 1992;13(8):1011-21. LEE, J.; FREDDOLINO, P. L.; ZHANG, Y. Ab initio protein structure prediction. From protein structure to function with bioinformatics. Springer, 2017. p. 3-35. LI, HAO; TANG, CHAO; WINGREEN, NED S. Nature of driving force for protein folding: a result from analyzing the statistical potential. Physical review letters, v. 79, n. 4, p. 765, 1997. LESK, V. I.; STERNBERG, M. J. E. 3D-Garden: a system for modelling protein--protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics, v. 24, p. 1137-1144, 2008. LEVINTHAL, C. Are there pathways for protein folding? Journal de chimie physique, v. 65, p. 44-45, 1968.61 LUCAS, TÂNIA GOMES. Estudos de folding e efeito de chaperões químicos e moleculares em proteínas envolvidas na ȕ-oxidação de ácidos gordos. 2011. Tese de Doutorado. Faculdade de Ciências e Tecnologia. MILLER, M. A.; DOYE, J. P. K.; WALES, D. J. Structural relaxation in atomic clusters: Master equation dynamics. Physical Review E, v. 60, p. 3701, 1999. MILLER, STANLEY L. A production of amino acids under possible primitive earth conditions. Science, v. 117, n. 3046, p. 528-529, 1953. MOREIRA, L. M., MORAES, P. C. G. D., MENDONÇA, J. P. R. F. D., GUIMARÃES, L., LYON, J. P., AIMBIRE, F., IMASATO, H. Hemoglobina extracelular gigante de Glossoscolex paulistus: um extraordinário sistema supramolecular hemoproteico. Química Nova, v. 34, n. 1, p. 119-130, 2011. MUELLER, U., PERL, D., SCHMID, F. X., HEINEMANN, U. Thermal stability and atomicresolution crystal structure of the Bacillus caldolyticus cold shock protein1. Journal of molecular biology, v. 297, n. 4, p. 975-988, 2000. MUNIZ, J. R. C. Aplicação da bioinformática nos estudos dos genes e enzimas envolvidos na síntese da goma fastidiana produzida pela Xylela fastidiosa. 2003. 124p. Dissertação (Mestrado) Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, 2003. NAKAMURA, H. Roles of electrostatic interaction in proteins. Quarterly reviews of biophysics, v. 29, p. 1-90, 1996. NELSON, DAVID LEE; COX, MICHAEL M. Princípios de bioquímica de Lehninger. Porto Alegre: Artmed, 2014. NELSON, D. L.; LEHNINGER, A. L.; COX, M. M. Lehninger principles of biochemistry. [S.l.]: Macmillan, 2008. NEUDERT, G.; KLEBE, G. DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes. Journal of Chemical Information and Modeling, v. 51, p. 2731-2745, out. 2011.62 NOEL, J. K., WHITFORD, P. C., SANBONMATSU, K. Y., ONUCHIC, J. SMOG@ ctbp: simplified deployment of structure-based models in GROMACS. Nucleic acids research, v. 38, p. W657--W661, 2010. NOEL, JEFFREY K.; WHITFORD, PAUL C.; ONUCHIC, JOSÉ N. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. The Journal of Physical Chemistry B, v. 116, n. 29, p. 8692-8702, 2012. NOEL, J. K., LEVI, M., RAGHUNATHAN, M., LAMMERT, H., HAYES, R. L., ONUCHIC, J. N., WHITFORD, SMOG 2: A versatile software package for generating structure-based models. PLoS computational biology, v. 12, n. 3, p. e1004794, 2016. NOTREDAME, CÉDRIC; HIGGINS, DESMOND G.; HERINGA, JAAP. T-coffee: a novel method for fast and accurate multiple sequence alignment1. Journal of molecular biology, v. 302, n. 1, p. 205-217, 2000. NYMEYER, H.; GARCıA, A. E.; ONUCHIC, J. N. Folding funnels and frustration in off-lattice ғ minimalist protein landscapes. Proceedings of the National Academy of Sciences, v. 95, p. 5921-5928, 1998. OLIVEIRA, R. J. Estudo do coeficiente de difusão no enovelamento de proteínas na rede. 2007. 78 f. Dissertação (mestrado) - Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, 2007 OLIVEIRA, R. J. Estudo do coeficiente de difusão no enovelamento de proteína. 2011. 115 f. Tese (doutorado) - Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio Preto, 2011. ONUCHIC, JOSÉ NELSON; LUTHEY-SCHULTEN, ZAIDA; WOLYNES, PETER G. Theory of protein folding: the energy landscape perspective. Annual review of physical chemistry, v. 48, n. 1, p. 545-600, 1997. PAVLOPOULOU, A.; MICHALOPOULOS, I. State-of-the-art bioinformatics protein structure prediction tools. International journal of molecular medicine, v. 28, p. 295-310, 2011. PERL, D., WELKER, C., SCHINDLER, T., SCHRÖDER, K., MARAHIEL, M. A., JAENICKE, R., & SCHMID, F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and63 hyperthermophilic cold shock proteins. Nature Structural and Molecular Biology, v. 5, n. 3, p. 229, 1998. PHADTARE, SANGITA; ALSINA, JANIVETTE; INOUYE, MASAYORI. Cold-shock response and cold-shock proteins. Current opinion in microbiology, v. 2, n. 2, p. 175-180, 1999. POTOYAN, D. A.; PAPOIAN, G. A. Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. Journal of the American Chemical Society, v. 133, p. 7405-7415, 2011. PRIVALOV, P. L.; KHECHINASHVILI, N. N. A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. Journal of molecular biology, v. 86, p. 665-684, 1974. RAZVI, A.; SCHOLTZ, J. M. Lessons in stability from thermophilic proteins. Protein Science, v. 15, p. 1569-1578, 2006. REDDY, A. S., WANG, L., SINGH, S., LING, Y. L., BUCHANAN, L., ZANNI, M. T., SKINNER, J. L., Pablo, J. J. Stable and metastable states of human amylin in solution. Biophysical journal, v. 99, p. 2208-2216, 2010. RUSSO, S.; SILVER, M. Essentials of Introductory Chemistry. [S.l.]: Addison-Wesley Longman, Limited, 2001. ISBN ISBN: 9780321046383. Disponivel em: <https://books.google.com.br/books?id=vwJqgwfx4H0C>. SABOURY, A. A.; MOOSAVIǦMOVAHEDI, A. A. Clarification of calorimetric and van't hoff enthalpies for evaluation of protein transition states. Biochemical Education, v. 22, n. 4, p. 210-211, 1994. SALGUEIRO, M. E. F. Simulações on-line para o ensino e aprendizagem de Quıғmica, 2003. SALI, A. 100,000 protein structures for the biologist. Nature Structural & Molecular Biology. v. 05, p. 1029-1032, 1998. SANTOS FILHO, OSVALDO ANDRADE; ALENCASTRO, RB de. Modelagem de proteínas por homologia. Química Nova, v. 26, n. 2, p. 253-259, 2003.64 SCHINDELIN, HERMANN; MARAHIEL, MOHAMED A.; HEINEMANN, UDO. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature, v. 364, n. 6433, p. 164, 1993. SHAN, Y., ARKHIPOV, A., KIM, E. T., PAN, A. C., SHAW, D. E. Transitions to catalytically inactive conformations in EGFR kinase. Proceedings of the National Academy of Sciences, p. 201220843, 2013. SILVA, R. I. Enovelamento proteico: fatores topológicos. 2005. 74 p. Dissertação (Doutorado em Ciências) - Faculdade de Filosofia Ciências e Letras, Universidade de São Paulo, Ribeirão Preto. STERPONE, FABIO; MELCHIONNA, SIMONE. Thermophilic proteins: insight and perspective from in silico experiments. Chemical Society Reviews, v. 41, n. 5, p. 1665- 1676, 2012. SWENDSEN, R. H. Modern methods of analyzing Monte Carlo computer simulations. Physica A: Statistical Mechanics and its Applications, v. 194, p. 53-62, 1993. TEIXEIRA, Viviane Gomes; COUTINHO, Fernanda MB; GOMES, Ailton S. Principais métodos de caracterização da porosidade de resinas à base de divinilbenzeno. Química nova, v. 24, n. 6, p. 808-818, 2001. ULUSU, N. NURAY; TEZCAN, E. FERHAN. Cold shock proteins. Turkish Journal of Medical Sciences, v. 31, n. 4, p. 283-290, 2001. VITKUP, D.; MELAMUD, E.; MOULT, J.; SANDER, C. Completeness in structural genomics. Nature Structural & Molecular Biology. v. 08, p. 559-566, 2001. WALES, D. Energy landscapes: Applications to clusters, biomolecules and glasses. [S.l.]: Cambridge University Press, 2003. WALES, D. J. Energy landscapes: some new horizons. Current opinion in structural biology, v. 20, p. 3-10, 2010. WALES, D. J. Decoding the energy landscape: extracting structure, dynamics and thermodynamics. Phil. Trans. R. Soc. A, v. 370, p. 2877-2899, 2012.65 WANG, J., OLIVEIRA, R. J., CHU, X., WHITFORD, P. C., CHAHINE, J., HAN, W., LEITE, V. B. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences, 2012. WELKER, C., PERL, D., SCHINDLER, T., SCHRÖDER, K., MARAHIEL, M. A., JAENICKE, R., SCHMID, F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nature Structural and Molecular Biology, v. 5, n. 3, p. 229, 1998. XIAO, L.; HONIG, B. Electrostatic contributions to the stability of hyperthermophilic proteins1. Journal of molecular biology, v. 289, p. 1435-1444, 1999. ZHURAVLEV, P. I.; PAPOIAN, G. A. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Quarterly reviews of biophysics, v. 43, p. 295-332, 2010. ZORDAN, A. B. Estudo sobre o efeito da pressão em pectinases do suco de frutas utilizando método de simulação. 2017. 102 f. Dissertação de Mestrado. 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dc.title.por.fl_str_mv Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
title Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
spellingShingle Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
BORGES, Ueliton Galdino
Proteínas homologas.
Termoestabilidade.
Dinâmica Molecular.
Modelo baseado em estrutura.
Superfície de energia.
Cold Shock.
Homologous proteins.
Thermostability.
Molecular dynamics.
Structure-based model.
Energy Landscape.
Química Teórica
title_short Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
title_full Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
title_fullStr Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
title_full_unstemmed Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
title_sort Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.
author BORGES, Ueliton Galdino
author_facet BORGES, Ueliton Galdino
author_role author
dc.contributor.advisor1.fl_str_mv OLIVEIRA, Ronaldo Júnio de
dc.contributor.advisor1Lattes.fl_str_mv http://lattes.cnpq.br/9945821072452088
dc.contributor.author.fl_str_mv BORGES, Ueliton Galdino
contributor_str_mv OLIVEIRA, Ronaldo Júnio de
dc.subject.por.fl_str_mv Proteínas homologas.
Termoestabilidade.
Dinâmica Molecular.
Modelo baseado em estrutura.
Superfície de energia.
topic Proteínas homologas.
Termoestabilidade.
Dinâmica Molecular.
Modelo baseado em estrutura.
Superfície de energia.
Cold Shock.
Homologous proteins.
Thermostability.
Molecular dynamics.
Structure-based model.
Energy Landscape.
Química Teórica
dc.subject.eng.fl_str_mv Cold Shock.
Homologous proteins.
Thermostability.
Molecular dynamics.
Structure-based model.
Energy Landscape.
dc.subject.cnpq.fl_str_mv Química Teórica
description The functions that proteins perform are extremely important to living things, this function is directly linked to its thermostability, and may undergo temperature variations. As thermostability is the focus of this work, specifically addressing the different transition temperatures between the unfolding / unfolding of the homologous proteins, using as study object and starting point for these and other questions, Cold Shock homologous proteins of the psychophilic bacteria, Listeria monocytogenes (Cs-pLa), mesophilic, Bacillus caldolyticus (Bs-CspB), thermophilic, Bacillus subtilis (Bc-Csp) and hyperthermophilic, Thermotoga maritime (Tm-Csp), considering the variations in temperature and their interactions, taking into account the aspects of these proteins as well as their identity and similarity. It may be noted that there are several methods of determining protein structures in both in vitro and in silicon. In this work, we propose an in silico method, which discusses the simulation of protein structure and optimization, considering simultaneously the energetic and structural aspects of proteins. For the Molecular Dynamics simulations the GROMACS software was used. To better understand these thermodynamic differences and the thermostability that occurs due to the variations of the chains in Cold Shock proteins proteins. We performed computational simulations taking into account only the alpha carbon (CĮ) that considerably reduces the simulation time. The theoretical results found corroborated with experimental data showing that the Cold Shock protein Hyperthermophilic Thermotoga marine bacteria present the highest value of folding temperature and the largest difference of RMSD among all four Cold Shock proteins currently studied. Due to the finding that the Cold Shock proteins presented favorable thermostability to the residue changes that can be carried out in order to be used in processes that require a change in temperature.
publishDate 2018
dc.date.issued.fl_str_mv 2018-12-18
dc.date.accessioned.fl_str_mv 2019-03-26T18:13:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.citation.fl_str_mv BORGES, Ueliton Galdino. Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.. 2018. 66f. Dissertação (Mestrado em Química) - Programa de Pós-Graduação Multicêntrico em Química de Minas Gerais, Universidade Federal do Triângulo Mineiro, Uberaba, 2018
dc.identifier.uri.fl_str_mv http://bdtd.uftm.edu.br/handle/tede/620
identifier_str_mv BORGES, Ueliton Galdino. Estudo da termoestabilidade de proteínas cold shock homólogas por modelos teóricos simplificados.. 2018. 66f. Dissertação (Mestrado em Química) - Programa de Pós-Graduação Multicêntrico em Química de Minas Gerais, Universidade Federal do Triângulo Mineiro, Uberaba, 2018
url http://bdtd.uftm.edu.br/handle/tede/620
dc.language.iso.fl_str_mv por
language por
dc.relation.references.por.fl_str_mv ALBER, Tom. Stabilization energies of protein conformation. In: Prediction of protein structure and the principles of protein conformation. Springer, Boston, MA, 1989. p. 161-192. ALMEIDA, A. B. Predição de estrutura terciária de proteínas com técnicas multiobjetivo no algoritmo de Monte Carlo. 2016. 129 f. Dissertação (Mestrado em Ciência da Computação) - Universidade Federal de Goiás, Goiânia, 2016. ANFINSEN, Christian B. Principles that govern the folding of protein chains. Science, v. 181, n. 4096, p. 223-230, 1973. ASTUTI, A. D.; MUTIARA, A. B. Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS. arXiv preprint arXiv: 0912.0893, 2009. BAYNES, Helton Godwin. Mythology of the Soul (Psychology Revivals): A Research Into the Unconscious from Schizophrenic Dreams and Drawings. Routledge, 2015. BENSON, D. A., CAVANAUGH, M., CLARK, K., KARSCH-MIZRACHI, I., LIPMAN, D. J., OSTELL, J., SAYERS, E. W. GenBank. Nucleic acids research, v. 41, n. D1, p. D36-D42, 2012. BERMAN, H. M., WESTBROOK, J., FENG, Z., GILLILAND, G., Bhat, T. N., WEISSIG, H., BOURNE, P. E. The protein data bank. Nucleic acids research, v. 28, n. 1, p. 235-242, 2000. CAMARGO, S. R. Identificação de genes e uso de promotores modulados por etanol em cana-de-açucar. 2007. 84p. Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia, Campinas, SP. CHANG, RAYMOND. Physical chemistry for the chemical and biological sciences. University Science Books, 2000. CHAVEZ, L. L.; ONUCHIC, J. N.; CLEMENTI, C. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. Journal of the American Chemical Society, v. 126, p. 8426-8432, 2004.58 CLEMENTI, C.; NYMEYER, H.; ONUCHIC, J. N. Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins. Journal of molecular biology, v. 298, p. 937-953, 2000. CONTESSOTO, V. G., OLIVEIRA, V. M., CARVALHO, S. J., OLIVEIRA, L. C., LEITE, V. B. NTL9 folding at constant pH: the importance of electrostatic interaction and pH dependence. Journal of chemical theory and computation, v. 12, n. 7, p. 3270-3277, 2016. CONTESSOTO, V. G., OLIVEIRA, V. M., FERNANDES, B. R., SLADE, G. G., LEITE, V. B. TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions. bioRxiv, p. 22156, 2017. CORNELL, W. D., CIEPLAK, P., BAYLY, C. I., GOULD, I. R., MERZ, K. M., FERGUSON, D. M., KOLLMAN, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, v. 117, n. 19, p. 5179-5197, 1995. D’ALFONSO, G.; TRAMONTANO, A.; LAHM, A. Structural conservation in single-domain proteins: implications for homology modeling. Journal of Structural Biology. v. 134, p. 246- 256, 2001. DA SILVA, VINICIUS B. Modelagem molecular de proteínas-alvo por homologia estrutural. Revista eletrônica de Farmácia, v. 4, n. 1, 2007. DE GODOI CONTESSOTO, V., DE OLIVEIRA JUNIOR, A. B., CHAHINE, J., DE OLIVEIRA, R. J., LEITE, V. B. P. (2018) Introdução ao problema de enovelamento de proteínas: uma abordagem utilizando modelos computacionais simplificados. Revista Brasileira de Ensino de Física, v. 40, n. 4, p. e4307, 2018. DILL, K.; BROMBERG, S. Molecular driving forces: statistical thermodynamics in biology, chemistry, physics, and nanoscience. [S.l.]: Garland Science, 2012. DOBSON, C. M. Protein folding and misfolding. Nature, v. 426, p. 884, 2003. DOYE, J. P. K.; MILLER, M. A.; WALES, D. J. Evolution of the potential energy surface with size for Lennard-Jones clusters. The Journal of chemical physics, v. 111, p. 8417-8428, 1999 - a.59 DOYE, J. P. K.; MILLER, M. A.; WALES, D. J. The double-funnel energy landscape of the 38-atom Lennard-Jones cluster. The Journal of Chemical Physics, v. 110, p. 6896-6906, 1999 - b. DURHAM, E. H. A. B. Bioinformática estrutural de proteínas modificadas por eventos de splicing alternativo. 2007. 131 f. Tese de Doutorado. Universidade de São Paulo, São Paulo, 2007. EVANS, DAVID A.; WALES, DAVID J. The free energy landscape and dynamics of metenkephalin. The Journal of chemical physics, v. 119, n. 18, p. 9947-9955, 2003. FERRENBERG, ALAN M.; SWENDSEN, ROBERT H. New Monte Carlo technique for studying phase transitions. Physical review letters, v. 61, n. 23, p. 2635, 1988. FERRENBERG, A. M.; SWENDSEN, R. H. Optimized monte carlo data analysis. Computers in Physics, v. 3, p. 101-104, 1989. FISCHER, DANIEL. Servers for protein structure prediction. Current opinion in structural biology, v. 16, n. 2, p. 178-182, 2006. GONZALEZ, FELIX H. DIAZ; DA SILVA, SERGIO CERONI. Introdução à bioquímica clínica veterinária. 2017. GOSAVI, S., CHAVEZ, L. L., JENNINGS, P. A., ONUCHIC, J. N. Topological frustration and the folding of interleukin-1ȕ. Journal of molecular biology, v. 357, n. 3, p. 986-996, 2006. HARVEY, R. A.; FERRIER, D. R. Bioquıғmica ilustrada. [S.l.]: Artmed Editora, 2015. HESS B, KUTZNER C, VAN DER SPOEL D, LINDAHL E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation. 2008;4(3):435-47. HÖLTJE, H. D.; SIPPL, W.; ROGNAN, D.; FOLKERS, G. Introduction to comparative protein modeling. In Molecular Modeling: Basic Principles and Applications. Weinheim: WileyVCH, 2003. HUMPHREY, WILLIAM; DALKE, ANDREW; SCHULTEN, KLAUS. VMD: visual molecular dynamics. Journal of molecular graphics, v. 14, n. 1, p. 33-38, 1996.60 ITZHAKI, L. S.; OTZEN, D. E.; FERSHT, A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. Journal of molecular biology, v. 254, p. 260-288, 1995. KENDREW, J. C., BODO, G., DINTZIS, H. M., PARRISH, R. G., WYCKOFF, H., PHILLIPS, D. C. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, v. 181, n. 4610, p. 662-666, 1958. KOGA, N.; TAKADA, S. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences, 2012. Journal of molecular biology, v. 313, p. 171-180, 2001. KREMER, W., SCHULER, B., HARRIEDER, S., GEYER, M., GRONWALD, W., WELKER, C., KALBITZER, H. R. Solution NMR structure of the coldǦshock protein from the hyperthermophilic bacterium Thermotoga maritima. European journal of biochemistry, v. 268, n. 9, p. 2527-2539, 2001. KRIVOV, S. V.; KARPLUS, M. Free energy disconnectivity graphs: Application to peptide models. The Journal of chemical physics, v. 117, p. 10894-10903, 2002. KUMAR, S., ROSENBERG, J. M., BOUZIDA, D., SWENDSEN, R. H., KOLLMAN, P. A. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. Journal of Computational Chemistry. 1992;13(8):1011-21. LEE, J.; FREDDOLINO, P. L.; ZHANG, Y. Ab initio protein structure prediction. From protein structure to function with bioinformatics. Springer, 2017. p. 3-35. LI, HAO; TANG, CHAO; WINGREEN, NED S. Nature of driving force for protein folding: a result from analyzing the statistical potential. Physical review letters, v. 79, n. 4, p. 765, 1997. LESK, V. I.; STERNBERG, M. J. E. 3D-Garden: a system for modelling protein--protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics, v. 24, p. 1137-1144, 2008. LEVINTHAL, C. Are there pathways for protein folding? Journal de chimie physique, v. 65, p. 44-45, 1968.61 LUCAS, TÂNIA GOMES. Estudos de folding e efeito de chaperões químicos e moleculares em proteínas envolvidas na ȕ-oxidação de ácidos gordos. 2011. Tese de Doutorado. Faculdade de Ciências e Tecnologia. MILLER, M. A.; DOYE, J. P. K.; WALES, D. J. Structural relaxation in atomic clusters: Master equation dynamics. Physical Review E, v. 60, p. 3701, 1999. MILLER, STANLEY L. A production of amino acids under possible primitive earth conditions. Science, v. 117, n. 3046, p. 528-529, 1953. MOREIRA, L. M., MORAES, P. C. G. D., MENDONÇA, J. P. R. F. D., GUIMARÃES, L., LYON, J. P., AIMBIRE, F., IMASATO, H. Hemoglobina extracelular gigante de Glossoscolex paulistus: um extraordinário sistema supramolecular hemoproteico. Química Nova, v. 34, n. 1, p. 119-130, 2011. MUELLER, U., PERL, D., SCHMID, F. X., HEINEMANN, U. Thermal stability and atomicresolution crystal structure of the Bacillus caldolyticus cold shock protein1. Journal of molecular biology, v. 297, n. 4, p. 975-988, 2000. MUNIZ, J. R. C. Aplicação da bioinformática nos estudos dos genes e enzimas envolvidos na síntese da goma fastidiana produzida pela Xylela fastidiosa. 2003. 124p. Dissertação (Mestrado) Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, 2003. NAKAMURA, H. Roles of electrostatic interaction in proteins. Quarterly reviews of biophysics, v. 29, p. 1-90, 1996. NELSON, DAVID LEE; COX, MICHAEL M. Princípios de bioquímica de Lehninger. Porto Alegre: Artmed, 2014. NELSON, D. L.; LEHNINGER, A. L.; COX, M. M. Lehninger principles of biochemistry. [S.l.]: Macmillan, 2008. NEUDERT, G.; KLEBE, G. DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes. Journal of Chemical Information and Modeling, v. 51, p. 2731-2745, out. 2011.62 NOEL, J. K., WHITFORD, P. C., SANBONMATSU, K. Y., ONUCHIC, J. SMOG@ ctbp: simplified deployment of structure-based models in GROMACS. Nucleic acids research, v. 38, p. W657--W661, 2010. NOEL, JEFFREY K.; WHITFORD, PAUL C.; ONUCHIC, JOSÉ N. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. The Journal of Physical Chemistry B, v. 116, n. 29, p. 8692-8702, 2012. NOEL, J. K., LEVI, M., RAGHUNATHAN, M., LAMMERT, H., HAYES, R. L., ONUCHIC, J. N., WHITFORD, SMOG 2: A versatile software package for generating structure-based models. PLoS computational biology, v. 12, n. 3, p. e1004794, 2016. NOTREDAME, CÉDRIC; HIGGINS, DESMOND G.; HERINGA, JAAP. T-coffee: a novel method for fast and accurate multiple sequence alignment1. Journal of molecular biology, v. 302, n. 1, p. 205-217, 2000. NYMEYER, H.; GARCıA, A. E.; ONUCHIC, J. N. Folding funnels and frustration in off-lattice ғ minimalist protein landscapes. Proceedings of the National Academy of Sciences, v. 95, p. 5921-5928, 1998. OLIVEIRA, R. J. Estudo do coeficiente de difusão no enovelamento de proteínas na rede. 2007. 78 f. Dissertação (mestrado) - Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, 2007 OLIVEIRA, R. J. Estudo do coeficiente de difusão no enovelamento de proteína. 2011. 115 f. Tese (doutorado) - Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio Preto, 2011. ONUCHIC, JOSÉ NELSON; LUTHEY-SCHULTEN, ZAIDA; WOLYNES, PETER G. Theory of protein folding: the energy landscape perspective. Annual review of physical chemistry, v. 48, n. 1, p. 545-600, 1997. PAVLOPOULOU, A.; MICHALOPOULOS, I. State-of-the-art bioinformatics protein structure prediction tools. International journal of molecular medicine, v. 28, p. 295-310, 2011. PERL, D., WELKER, C., SCHINDLER, T., SCHRÖDER, K., MARAHIEL, M. A., JAENICKE, R., & SCHMID, F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and63 hyperthermophilic cold shock proteins. Nature Structural and Molecular Biology, v. 5, n. 3, p. 229, 1998. PHADTARE, SANGITA; ALSINA, JANIVETTE; INOUYE, MASAYORI. Cold-shock response and cold-shock proteins. Current opinion in microbiology, v. 2, n. 2, p. 175-180, 1999. POTOYAN, D. A.; PAPOIAN, G. A. Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. Journal of the American Chemical Society, v. 133, p. 7405-7415, 2011. PRIVALOV, P. L.; KHECHINASHVILI, N. N. A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. Journal of molecular biology, v. 86, p. 665-684, 1974. RAZVI, A.; SCHOLTZ, J. M. Lessons in stability from thermophilic proteins. Protein Science, v. 15, p. 1569-1578, 2006. REDDY, A. S., WANG, L., SINGH, S., LING, Y. L., BUCHANAN, L., ZANNI, M. T., SKINNER, J. L., Pablo, J. J. Stable and metastable states of human amylin in solution. Biophysical journal, v. 99, p. 2208-2216, 2010. RUSSO, S.; SILVER, M. Essentials of Introductory Chemistry. [S.l.]: Addison-Wesley Longman, Limited, 2001. ISBN ISBN: 9780321046383. Disponivel em: <https://books.google.com.br/books?id=vwJqgwfx4H0C>. SABOURY, A. A.; MOOSAVIǦMOVAHEDI, A. A. Clarification of calorimetric and van't hoff enthalpies for evaluation of protein transition states. Biochemical Education, v. 22, n. 4, p. 210-211, 1994. SALGUEIRO, M. E. F. Simulações on-line para o ensino e aprendizagem de Quıғmica, 2003. SALI, A. 100,000 protein structures for the biologist. Nature Structural & Molecular Biology. v. 05, p. 1029-1032, 1998. SANTOS FILHO, OSVALDO ANDRADE; ALENCASTRO, RB de. Modelagem de proteínas por homologia. Química Nova, v. 26, n. 2, p. 253-259, 2003.64 SCHINDELIN, HERMANN; MARAHIEL, MOHAMED A.; HEINEMANN, UDO. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature, v. 364, n. 6433, p. 164, 1993. SHAN, Y., ARKHIPOV, A., KIM, E. T., PAN, A. C., SHAW, D. E. Transitions to catalytically inactive conformations in EGFR kinase. Proceedings of the National Academy of Sciences, p. 201220843, 2013. SILVA, R. I. Enovelamento proteico: fatores topológicos. 2005. 74 p. Dissertação (Doutorado em Ciências) - Faculdade de Filosofia Ciências e Letras, Universidade de São Paulo, Ribeirão Preto. STERPONE, FABIO; MELCHIONNA, SIMONE. Thermophilic proteins: insight and perspective from in silico experiments. Chemical Society Reviews, v. 41, n. 5, p. 1665- 1676, 2012. SWENDSEN, R. H. Modern methods of analyzing Monte Carlo computer simulations. Physica A: Statistical Mechanics and its Applications, v. 194, p. 53-62, 1993. TEIXEIRA, Viviane Gomes; COUTINHO, Fernanda MB; GOMES, Ailton S. Principais métodos de caracterização da porosidade de resinas à base de divinilbenzeno. Química nova, v. 24, n. 6, p. 808-818, 2001. ULUSU, N. NURAY; TEZCAN, E. FERHAN. Cold shock proteins. Turkish Journal of Medical Sciences, v. 31, n. 4, p. 283-290, 2001. VITKUP, D.; MELAMUD, E.; MOULT, J.; SANDER, C. Completeness in structural genomics. Nature Structural & Molecular Biology. v. 08, p. 559-566, 2001. WALES, D. Energy landscapes: Applications to clusters, biomolecules and glasses. [S.l.]: Cambridge University Press, 2003. WALES, D. J. Energy landscapes: some new horizons. Current opinion in structural biology, v. 20, p. 3-10, 2010. WALES, D. J. Decoding the energy landscape: extracting structure, dynamics and thermodynamics. Phil. Trans. R. Soc. A, v. 370, p. 2877-2899, 2012.65 WANG, J., OLIVEIRA, R. J., CHU, X., WHITFORD, P. C., CHAHINE, J., HAN, W., LEITE, V. B. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences, 2012. WELKER, C., PERL, D., SCHINDLER, T., SCHRÖDER, K., MARAHIEL, M. A., JAENICKE, R., SCHMID, F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nature Structural and Molecular Biology, v. 5, n. 3, p. 229, 1998. XIAO, L.; HONIG, B. Electrostatic contributions to the stability of hyperthermophilic proteins1. Journal of molecular biology, v. 289, p. 1435-1444, 1999. ZHURAVLEV, P. I.; PAPOIAN, G. A. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Quarterly reviews of biophysics, v. 43, p. 295-332, 2010. ZORDAN, A. B. Estudo sobre o efeito da pressão em pectinases do suco de frutas utilizando método de simulação. 2017. 102 f. Dissertação de Mestrado. Universidade Federal do Espírito Santo, Espírito Santo, 2017.
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