1
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Pérez-Niño JA, Guerra Y, Díaz-Salazar AJ, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase. Protein Sci 2024; 33:e5134. [PMID: 39145435 PMCID: PMC11325190 DOI: 10.1002/pro.5134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/01/2024] [Accepted: 07/21/2024] [Indexed: 08/16/2024]
Abstract
Function and structure are strongly coupled in obligated oligomers such as Triosephosphate isomerase (TIM). In animals and fungi, TIM monomers are inactive and unstable. Previously, we used ancestral sequence reconstruction to study TIM evolution and found that before these lineages diverged, the last opisthokonta common ancestor of TIM (LOCATIM) was an obligated oligomer that resembles those of extant TIMs. Notably, calorimetric evidence indicated that ancestral TIM monomers are more structured than extant ones. To further increase confidence about the function, structure, and stability of the LOCATIM, in this work, we applied two different inference methodologies and the worst plausible case scenario for both of them, to infer four sequences of this ancestor and test the robustness of their physicochemical properties. The extensive biophysical characterization of the four reconstructed sequences of LOCATIM showed very similar hydrodynamic and spectroscopic properties, as well as ligand-binding energetics and catalytic parameters. Their 3D structures were also conserved. Although differences were observed in melting temperature, all LOCATIMs showed reversible urea-induced unfolding transitions, and for those that reached equilibrium, high conformational stability was estimated (ΔGTot = 40.6-46.2 kcal/mol). The stability of the inactive monomeric intermediates was also high (ΔGunf = 12.6-18.4 kcal/mol), resembling some protozoan TIMs rather than the unstable monomer observed in extant opisthokonts. A comparative analysis of the 3D structure of ancestral and extant TIMs shows a correlation between the higher stability of the ancestral monomers with the presence of several hydrogen bonds located in the "bottom" part of the barrel.
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Affiliation(s)
- Jorge Alejandro Pérez-Niño
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yasel Guerra
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
| | - A Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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2
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Romero-Romero S, Becerril-Sesín LA, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Structure and conformational stability of the triosephosphate isomerase from Zea mays. Comparison with the chemical unfolding pathways of other eukaryotic TIMs. Arch Biochem Biophys 2018; 658:66-76. [PMID: 30261166 DOI: 10.1016/j.abb.2018.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/18/2018] [Accepted: 09/23/2018] [Indexed: 12/16/2022]
Abstract
We studied the structure, function and thermodynamic properties for the unfolding of the Triosephosphate isomerase (TIM) from Zea mays (ZmTIM). ZmTIM shows a catalytic efficiency close to the diffusion limit. Native ZmTIM is a dimer that dissociates upon dilution into inactive and unfolded monomers. Its thermal unfolding is irreversible with a Tm of 61.6 ± 1.4 °C and an activation energy of 383.4 ± 11.5 kJ mol-1. The urea-induced unfolding of ZmTIM is reversible. Transitions followed by catalytic activity and spectroscopic properties are monophasic and superimposable, indicating that ZmTIM unfolds/refolds in a two-state behavior with an unfolding ΔG°(H20) = 99.8 ± 5.3 kJ mol-1. This contrasts with most other studied TIMs, where folding intermediates are common. The three-dimensional structure of ZmTIM was solved at 1.8 Å. A structural comparison with other eukaryotic TIMs shows a similar number of intramolecular and intermolecular interactions. Interestingly the number of interfacial water molecules found in ZmTIM is lower than those observed in most TIMs that show folding intermediates. Although with the available data, there is no clear correlation between structural properties and the number of equilibrium intermediates in the unfolding of TIM, the identification of such structural properties should increase our understanding of folding mechanisms.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Luis A Becerril-Sesín
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - Adela Rodríguez-Romero
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico.
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3
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Rodríguez-Bolaños M, Cabrera N, Perez-Montfort R. Identification of the critical residues responsible for differential reactivation of the triosephosphate isomerases of two trypanosomes. Open Biol 2017; 6:rsob.160161. [PMID: 27733588 PMCID: PMC5090059 DOI: 10.1098/rsob.160161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
The reactivation of triosephosphate isomerase (TIM) from unfolded monomers induced by guanidine hydrochloride involves different amino acids of its sequence in different stages of protein refolding. We describe a systematic mutagenesis method to find critical residues for certain physico-chemical properties of a protein. The two similar TIMs of Trypanosoma brucei and Trypanosoma cruzi have different reactivation velocities and efficiencies. We used a small number of chimeric enzymes, additive mutants and planned site-directed mutants to produce an enzyme from T. brucei with 13 mutations in its sequence, which reactivates fast and efficiently like wild-type (WT) TIM from T. cruzi, and another enzyme from T. cruzi, with 13 slightly altered mutations, which reactivated slowly and inefficiently like the WT TIM of T. brucei. Our method is a shorter alternative to random mutagenesis, saturation mutagenesis or directed evolution to find multiple amino acids critical for certain properties of proteins.
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Affiliation(s)
- Monica Rodríguez-Bolaños
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Ruy Perez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
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4
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Quezada AG, Díaz-Salazar AJ, Cabrera N, Pérez-Montfort R, Piñeiro Á, Costas M. Interplay between Protein Thermal Flexibility and Kinetic Stability. Structure 2017; 25:167-179. [PMID: 28052236 DOI: 10.1016/j.str.2016.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/18/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023]
Abstract
Kinetic stability is a key parameter to comprehend protein behavior and it plays a central role to understand how evolution has reached the balance between function and stability in cell-relevant timescales. Using an approach that includes simulations, protein engineering, and calorimetry, we show that there is a clear correlation between kinetic stability determined by differential scanning calorimetry and protein thermal flexibility obtained from a novel method based on temperature-induced unfolding molecular dynamics simulations. Thermal flexibility quantitatively measures the increment of the conformational space available to the protein when energy in provided. The (β/α)8 barrel fold of two closely related by evolution triosephosphate isomerases from two trypanosomes are used as model systems. The kinetic stability-thermal flexibility correlation has predictive power for the studied proteins, suggesting that the strategy and methodology discussed here might be applied to other proteins in biotechnological developments, evolutionary studies, and the design of protein based therapeutics.
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Affiliation(s)
- Andrea G Quezada
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México
| | - A Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, México
| | - Ángel Piñeiro
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México.
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5
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Guzmán-Luna V, Quezada AG, Díaz-Salazar AJ, Cabrera N, Pérez-Montfort R, Costas M. The effect of specific proline residues on the kinetic stability of the triosephosphate isomerases of two trypanosomes. Proteins 2017; 85:571-579. [DOI: 10.1002/prot.25231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Valeria Guzmán-Luna
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica; Facultad de Química, Universidad Nacional Autónoma de México, CdMx; 04510 México
| | - Andrea G. Quezada
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica; Facultad de Química, Universidad Nacional Autónoma de México, CdMx; 04510 México
| | - A. Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica; Facultad de Química, Universidad Nacional Autónoma de México, CdMx; 04510 México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular; Universidad Nacional Autónoma de México, CdMx; 04510 México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular; Universidad Nacional Autónoma de México, CdMx; 04510 México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica; Facultad de Química, Universidad Nacional Autónoma de México, CdMx; 04510 México
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6
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Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1696-1706. [PMID: 27614148 DOI: 10.1016/j.bbapap.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/17/2016] [Accepted: 09/03/2016] [Indexed: 01/12/2023]
Abstract
Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico; Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora 83000, Mexico
| | - Jesus S Carrasco-Miranda
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Claudia D Ramirez-Aguirre
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico; Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Av. Instituto Politécnico Nacional. s/n., 23096, La Paz, Baja California Sur 23096, Mexico; Cátedras CONACyT, Dirección Adjunta de Desarrollo Científico, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de Mexico, 03940, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico.
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7
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Lara-Gonzalez S, Estrella P, Portillo C, Cruces ME, Jimenez-Sandoval P, Fattori J, Migliorini-Figueira AC, Lopez-Hidalgo M, Diaz-Quezada C, Lopez-Castillo M, Trasviña-Arenas CH, Sanchez-Sandoval E, Gómez-Puyou A, Ortega-Lopez J, Arroyo R, Benítez-Cardoza CG, Brieba LG. Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis. PLoS One 2015; 10:e0141747. [PMID: 26618356 PMCID: PMC4664265 DOI: 10.1371/journal.pone.0141747] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/11/2015] [Indexed: 11/29/2022] Open
Abstract
The dimeric nature of triosephosphate isomerases (TIMs) is maintained by an extensive surface area interface of more than 1600 Å2. TIMs from Trichomonas vaginalis (TvTIM) are held in their dimeric state by two mechanisms: a ball and socket interaction of residue 45 of one subunit that fits into the hydrophobic pocket of the complementary subunit and by swapping of loop 3 between subunits. TvTIMs differ from other TIMs in their unfolding energetics. In TvTIMs the energy necessary to unfold a monomer is greater than the energy necessary to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs, monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A) is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. As TvTIMs do not unfold upon dimer dissociation, herein we found that the high enzymatic activity of monomeric TvTIM variants is explained by the formation of catalytic dimeric competent species assisted by substrate binding.
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Affiliation(s)
- Samuel Lara-Gonzalez
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, CP 78216, San Luis Potosí, San Luis Potosí, México
| | - Priscilla Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - Carmen Portillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - María E. Cruces
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
| | - Pedro Jimenez-Sandoval
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
| | - Juliana Fattori
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP, Brazil
| | - Ana C. Migliorini-Figueira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP, Brazil
| | - Marisol Lopez-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - Margarita Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, México
| | - Jaime Ortega-Lopez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del IPN, Col. San Pedro Zacatenco, Av. IPN, 2508, C.P. 07360, D.F., México
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Col. San Pedro Zacatenco, Av. IPN, 2508, C.P. 07360, D.F., México
| | - Claudia G. Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
- * E-mail: (LGB); (CGB)
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500, Irapuato, Guanajuato, México
- * E-mail: (LGB); (CGB)
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8
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Romero-Romero S, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp01599e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The reversible thermal unfolding of oligomeric TIM barrels results from a delicate balance of physicochemical properties related to the sequence, the native and unfolded states and the transition between them.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas
- Departamento de Bioquímica
- Facultad de Medicina
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica
- Departamento de Fisicoquímica
- Facultad de Química
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - Adela Rodríguez-Romero
- Laboratorio de Química de Biomacromoléculas 3
- Departamento de Química de Biomacromoléculas
- Instituto de Química
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas
- Departamento de Bioquímica
- Facultad de Medicina
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
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9
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Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency. Biochim Biophys Acta Mol Basis Dis 2014; 1852:61-9. [PMID: 25463631 DOI: 10.1016/j.bbadis.2014.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/01/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022]
Abstract
Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPI(I170V) elicits behavioral abnormalities in Drosophila. An examination of hTPI(I170V) enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermal stability demonstrated an increase in enzyme stability. The crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. Collectively these data reveal new observations of the structural and kinetic determinants of TPI Deficiency pathology, providing new insights into disease pathogenesis.
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De La Mora-De La Mora I, Torres-Larios A, Mendoza-Hernández G, Enriquez-Flores S, Castillo-Villanueva A, Mendez ST, Garcia-Torres I, Torres-Arroyo A, Gómez-Manzo S, Marcial-Quino J, Oria-Hernández J, López-Velázquez G, Reyes-Vivas H. The E104D mutation increases the susceptibility of human triosephosphate isomerase to proteolysis. Asymmetric cleavage of the two monomers of the homodimeric enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2702-11. [PMID: 24056040 DOI: 10.1016/j.bbapap.2013.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/27/2022]
Abstract
The deficiency of human triosephosphate isomerase (HsTIM) generates neurological alterations, cardiomyopathy and premature death. The mutation E104D is the most frequent cause of the disease. Although the wild type and mutant exhibit similar kinetic parameters, it has been shown that the E104D substitution induces perturbation of an interfacial water network that, in turn, reduces the association constant between subunits promoting enzyme inactivation. To gain further insight into the effects of the mutation on the structure, stability and function of the enzyme, we measured the sensitivity of recombinant E104D mutant and wild type HsTIM to limited proteolysis. The mutation increases the susceptibility to proteolysis as consequence of the loss of rigidity of its overall 3-D structure. Unexpectedly, it was observed that proteolysis of wild type HsTIM generated two different stable nicked dimers. One was formed in relatively short times of incubation with proteinase K; as shown by spectrometric and crystallographic data, it corresponded to a dimer containing a nicked monomer and an intact monomer. The formation of the other nicked species requires relatively long incubation times with proteinase K and corresponds to a dimer with two clipped subunits. The first species retains 50% of the original activity, whereas the second species is inactive. Collectively, we found that the E104D mutant is highly susceptible to proteolysis, which in all likelihood contributes to the pathogenesis of enzymopathy. In addition, the proteolysis data on wild type HsTIM illustrate an asymmetric conduct of the two monomers.
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Lara-González S, Estrella-Hernández P, Ochoa-Leyva A, Del Carmen Portillo-Téllez M, Caro-Gómez LA, Figueroa-Angulo EE, Salgado-Lugo H, Miranda Ozuna JFT, Ortega-López J, Arroyo R, Brieba LG, Benítez-Cardoza CG. Structural and thermodynamic folding characterization of triosephosphate isomerases from Trichomonas vaginalis reveals the role of destabilizing mutations following gene duplication. Proteins 2013; 82:22-33. [PMID: 23733417 DOI: 10.1002/prot.24333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 05/01/2013] [Accepted: 05/03/2013] [Indexed: 11/07/2022]
Abstract
We report the structures and thermodynamic analysis of the unfolding of two triosephosphate isomerases (TvTIM1 and TvTIM2) from Trichomonas vaginalis. Both isoforms differ by the character of four amino acids: E/Q 18, I/V 24, I/V 45, and P/A 239. Despite the high sequence and structural similarities between both isoforms, they display substantial differences in their stabilities. TvTIM1 (E18, I24, I45, and P239) is more stable and less dissociable than TvTIM2 (Q18, V24, V45, and A239). We postulate that the identities of residues 24 and 45 are responsible for the differences in monomer stability and dimer dissociability, respectively. The structural difference between both amino acids is one methyl group. In TvTIMs, residue 24 is involved in packing α-helix 1 against α-helix 2 of each monomer and residue 45 is located at the center of the dimer interface forming a "ball and socket" interplay with a hydrophobic cavity. The mutation of valine at position 45 for an alanine in TvTIM2 produces a protein that migrates as a monomer by gel filtration. A comparison with known TIM structures indicates that this kind of interplay is a conserved feature that stabilizes dimeric TIM structures. In addition, TvTIMs are located in the cytoplasm and in the membrane. As TvTIM2 is an easily dissociable dimer, the dual localization of TvTIMs may be related to the acquisition of a moonlighting activity of monomeric TvTIM2. To our knowledge, this is the simplest example of how a single amino acid substitution can provide alternative function to a TIM barrel protein.
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Affiliation(s)
- Samuel Lara-González
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, San Luis Potosí, San Luis Potosí, México, CP 78216
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12
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Guzman-Luna V, Garza-Ramos G. The folding pathway of glycosomal triosephosphate isomerase: Structural insights into equilibrium intermediates. Proteins 2012; 80:1669-82. [DOI: 10.1002/prot.24063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 02/09/2012] [Accepted: 02/23/2012] [Indexed: 11/12/2022]
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13
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Merlino A, Russo Krauss I, Rossi B, Vergara A, De Vendittis A, Marco S, De Vendittis E, Sica F. Identification of an active dimeric intermediate populated during the unfolding process of the cambialistic superoxide dismutase from Streptococcus mutans. Biochimie 2012; 94:768-75. [DOI: 10.1016/j.biochi.2011.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/18/2011] [Indexed: 10/15/2022]
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14
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Di Venere A, Nicolai E, Rosato N, Rossi A, Finazzi Agrò A, Mei G. Characterization of monomeric substates of ascorbate oxidase. FEBS J 2011; 278:1585-93. [DOI: 10.1111/j.1742-4658.2011.08084.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Nolan MJ, Hofmann A, Jex AR, Gasser RB. A theoretical study to establish the relationship between the three-dimensional structure of triose-phosphate isomerase of Giardia duodenalis and point mutations in the respective gene. Mol Cell Probes 2010; 24:281-5. [DOI: 10.1016/j.mcp.2010.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/01/2010] [Accepted: 06/03/2010] [Indexed: 11/15/2022]
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16
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Zárate-Pérez F, Chánez-Cárdenas ME, Arreola R, Torres-Larios A, Vázquez-Contreras E. Different catalytic properties of two highly homologous triosephosphate isomerase monomers. Biochem Biophys Res Commun 2009; 382:626-30. [PMID: 19303397 DOI: 10.1016/j.bbrc.2009.03.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 03/16/2009] [Indexed: 11/26/2022]
Abstract
It is assumed that amino acid sequence differences in highly homologous enzymes would be found at the peripheral level, subtle changes that would not necessarily affect catalysis. Here, we demonstrate that, using the same set of mutations at the level of the interface loop 3, the activity of a triosephosphate isomerase monomeric enzyme is ten times higher than that of a homologous enzyme with 74% identity and 86% similarity, whereas the activity of the native, dimeric enzymes is essentially the same. This is an example of how the dimeric biological unit evolved to compensate for the intrinsic differences found at the monomeric species level. Biophysical techniques of size exclusion chromatography, dynamic light scattering, X-ray crystallography, fluorescence and circular dichroism, as well as denaturation/renaturation assays with guanidinium hydrochloride and ANS binding, allowed us to fully characterize the properties of the new monomer.
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Affiliation(s)
- Francisco Zárate-Pérez
- Instituto de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de Mexico, Circuito Exterior, Mexico, DF 04510, Mexico
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17
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Costas M, Rodríguez-Larrea D, De Maria L, Borchert TV, Gómez-Puyou A, Sanchez-Ruiz JM. Between-species variation in the kinetic stability of TIM proteins linked to solvation-barrier free energies. J Mol Biol 2008; 385:924-37. [PMID: 18992756 DOI: 10.1016/j.jmb.2008.10.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 10/16/2008] [Accepted: 10/20/2008] [Indexed: 11/17/2022]
Abstract
Theoretical, computational, and experimental studies have suggested the existence of solvation barriers in protein unfolding and denaturation processes. These barriers are related to the finite size of water molecules and can be envisioned as arising from the asynchrony between water penetration and breakup of internal interactions. Solvation barriers have been proposed to play roles in protein cooperativity and kinetic stability; therefore, they may be expected to be subject to natural selection. We study the thermal denaturation, in the presence and in the absence of chemical denaturants, of triosephosphate isomerases (TIMs) from three different species: Trypanosoma cruzi, Trypanosoma brucei, and Leishmania mexicana. In all cases, denaturation was irreversible and kinetically controlled. Surprisingly, however, we found large differences between the kinetic denaturation parameters, with T. cruzi TIM showing a much larger activation energy value (and, consequently, much lower room-temperature, extrapolated denaturation rates). This disparity cannot be accounted for by variations in the degree of exposure to solvent in transition states (as measured by kinetic urea m values) and is, therefore, to be attributed mainly to differences in solvation-barrier contributions. This was supported by structure-energetics analyses of the transition states and by application of a novel procedure to estimate from experimental data the solvation-barrier impact at the entropy and free-energy levels. These analyses were actually performed with an extended protein set (including six small proteins plus seven variants of lipase from Thermomyces lanuginosus and spanning a wide range of activation parameters), allowing us to delineate the general trends of the solvation-barrier contributions. Overall, this work supports that proteins sharing the same structure and function but belonging to different organisms may show widely different solvation barriers, possibly as a result of different levels of the selection pressure associated with cooperativity, kinetic stability, and related factors.
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Affiliation(s)
- Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Cd Universitaria, México DF 04510, México.
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18
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Tellez LA, Blancas-Mejia LM, Carrillo-Nava E, Mendoza-Hernández G, Cisneros DA, Fernández-Velasco DA. Thermal Unfolding of Triosephosphate Isomerase from Entamoeba histolytica: Dimer Dissociation Leads to Extensive Unfolding. Biochemistry 2008; 47:11665-73. [DOI: 10.1021/bi801360k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis A. Tellez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Luis M. Blancas-Mejia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Ernesto Carrillo-Nava
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - Guillermo Mendoza-Hernández
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - David A. Cisneros
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, and Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF
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Shaw GS, Marlatt NM, Ferguson PL, Barber KR, Bottomley SP. Identification of a dimeric intermediate in the unfolding pathway for the calcium-binding protein S100B. J Mol Biol 2008; 382:1075-88. [PMID: 18706914 DOI: 10.1016/j.jmb.2008.07.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/30/2008] [Accepted: 07/31/2008] [Indexed: 11/18/2022]
Abstract
The S100 proteins comprise 25 calcium-signalling members of the EF-hand protein family. Unlike typical EF-hand signalling proteins such as calmodulin and troponin-C, the S100 proteins are dimeric, forming both homo- and heterodimers in vivo. One member of this family, S100B, is a homodimeric protein shown to control the assembly of several cytoskeletal proteins and regulate phosphorylation events in a calcium-sensitive manner. Calcium binding to S100B causes a conformational change involving movement of helix III in the second calcium-binding site (EF2) that exposes a hydrophobic surface enabling interactions with other proteins such as tubulin and Ndr kinase. In several S100 proteins, calcium binding also stabilizes dimerization compared to the calcium-free states. In this work, we have examined the guanidine hydrochloride (GuHCl)-induced unfolding of dimeric calcium-free S100B. A series of tryptophan substitutions near the dimer interface and the EF2 calcium-binding site were studied by fluorescence spectroscopy and showed biphasic unfolding curves. The presence of a plateau near 1.5 M GuHCl showed the presence of an intermediate that had a greater exposed hydrophobic surface area compared to the native dimer based on increased 4,4-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid fluorescence. Furthermore, (1)H-(15)N heteronuclear single quantum coherence analyses as a function of GuHCl showed significant chemical shift changes in regions near the EF1 calcium-binding loop and between the linker and C-terminus of helix IV. Together these observations show that calcium-free S100B unfolds via a dimeric intermediate.
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Affiliation(s)
- Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1.
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20
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Hernández-Alcántara G, Rodríguez-Romero A, Reyes-Vivas H, Peon J, Cabrera N, Ortiz C, Enríquez-Flores S, De la Mora-De la Mora I, López-Velázquez G. Unraveling the mechanisms of tryptophan fluorescence quenching in the triosephosphate isomerase from Giardia lamblia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1493-500. [PMID: 18620084 DOI: 10.1016/j.bbapap.2008.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 05/09/2008] [Accepted: 05/29/2008] [Indexed: 10/21/2022]
Abstract
In the native state several proteins exhibit a quenching of fluorescence of their tryptophans. We studied triosephosphate isomerase from Giardia lamblia (GlTIM) to dissect the mechanisms that account for the quenching of fluorescence of its Trp. GlTIM contains four Trp per monomer (Trp75, Trp162, Trp173, and Trp196) distributed throughout the 3D structure. The fluorescence of the denatured enzyme is 3-fold higher than that of native GlTIM. To ascertain the origin of this phenomenon, single and triple mutants of Trp per Phe were made. The intrinsic fluorescence was determined, and the data were interpreted on the basis of the crystal structure of the enzyme. Our data show that the fluorescence of all Trp residues is quenched through two different mechanisms. In one, fluorescence is quenched by aromatic-aromatic interactions due to the proximity and orientation of the indole groups of Trp196 and Trp162. The magnitude of the quenching of fluorescence in Trp162 is higher than in the other three Trp. Fluorescence quenching is also due to energy transfer to the charged residues that surround Trp 75, 173 and 196. Further analysis of the fluorescence of GlTIM showed that, among TIMs from other parasites, Trp at position 12 exhibits rather unique properties.
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21
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Rumfeldt JAO, Galvagnion C, Vassall KA, Meiering EM. Conformational stability and folding mechanisms of dimeric proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 98:61-84. [PMID: 18602415 DOI: 10.1016/j.pbiomolbio.2008.05.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The folding of multisubunit proteins is of tremendous biological significance since the large majority of proteins exist as protein-protein complexes. Extensive experimental and computational studies have provided fundamental insights into the principles of folding of small monomeric proteins. Recently, important advances have been made in extending folding studies to multisubunit proteins, in particular homodimeric proteins. This review summarizes the equilibrium and kinetic theory and models underlying the quantitative analysis of dimeric protein folding using chemical denaturation, as well as the experimental results that have been obtained. Although various principles identified for monomer folding also apply to the folding of dimeric proteins, the effects of subunit association can manifest in complex ways, and are frequently overlooked. Changes in molecularity typically give rise to very different overall folding behaviour than is observed for monomeric proteins. The results obtained for dimers have provided key insights pertinent to understanding biological assembly and regulation of multisubunit proteins. These advances have set the stage for future advances in folding involving protein-protein interactions for natural multisubunit proteins and unnatural assemblies involved in disease.
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Affiliation(s)
- Jessica A O Rumfeldt
- Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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22
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Peimbert M, Domínguez-Ramírez L, Fernández-Velasco DA. Hydrophobic Repacking of the Dimer Interface of Triosephosphate Isomerase by in Silico Design and Directed Evolution. Biochemistry 2008; 47:5556-64. [DOI: 10.1021/bi702502k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariana Peimbert
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF, Mexico
| | - Lenin Domínguez-Ramírez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF, Mexico
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, 04510 México, DF, Mexico
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23
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24
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Mixcoha-Hernández E, Moreno-Vargas LM, Rojo-Domínguez A, Benítez-Cardoza CG. Thermal-unfolding Reaction of Triosephosphate Isomerase from Trypanosoma cruzi. Protein J 2007; 26:491-8. [PMID: 17763928 DOI: 10.1007/s10930-007-9090-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Thermal denaturation of triosephosphate isomerase from Trypanosoma cruzi was studied by circular dicrhoism and fluorescence spectroscopies. The unfolding transition was found to be highly irreversible even at the very early stages of the reaction. Kinetic studies, allowed us to identify consecutive reactions. Firstly, only the tryptophan environment is altered. Next, changes on the secondary structure and hydrophobic surface exposure measured by 1-anilino-8-naphthalenesulfonate (ANS) binding were observed. Further conformational changes imply additional modifications on the secondary and tertiary structures and release of the hydrophobic dye leading to the formation of the unfolded state that is prone to aggregate.
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Affiliation(s)
- Edgar Mixcoha-Hernández
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
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25
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Nájera H, Dagdug L, Fernández-Velasco DA. Thermodynamic and kinetic characterization of the association of triosephosphate isomerase: the role of diffusion. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:985-94. [PMID: 17644053 DOI: 10.1016/j.bbapap.2007.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 05/26/2007] [Accepted: 06/13/2007] [Indexed: 12/12/2022]
Abstract
It is known that diffusion plays a central role in the folding of small monomeric proteins and in the rigid-body association of proteins, however, the role of diffusion in the association of the folding intermediates of oligomeric proteins has been scarcely explored. In this work, catalytic activity and fluorescence measurements were used to study the effect of viscosity in the unfolding and refolding of the homodimeric enzyme triosephosphate isomerase from Saccharamyces cerevisiae. Two transitions were found by equilibrium and kinetic experiments, suggesting a three-state model with a monomeric intermediate. Glycerol barely affects DeltaG(0)(fold) whereas DeltaG(0)(assoc) becomes more favourable in the presence of the cosolvent. From 0 to 60% (v/v) glycerol, the association rate constant showed a near unitary dependence on solvent viscosity. However, at higher glycerol concentrations deviations from Kramers theory were observed. The dissociation rate constant showed a viscosity effect much higher than one. This may be related to secondary effects such as short-range glycerol-induced repulsion between monomers. Nevertheless, after comparison under isostability conditions, a slope near one was also observed for the dissociation rate. These results strongly suggest that the bimolecular association producing the native dimer is limited by diffusional events of the polypeptide chains through the solvent.
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Affiliation(s)
- Hugo Nájera
- Area Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, México.
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26
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Hurtado-Gómez E, Fernández-Ballester G, Nothaft H, Gómez J, Titgemeyer F, Neira JL. Biophysical characterization of the enzyme I of the Streptomyces coelicolor phosphoenolpyruvate:sugar phosphotransferase system. Biophys J 2006; 90:4592-604. [PMID: 16581832 PMCID: PMC1471863 DOI: 10.1529/biophysj.105.076935] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first protein in the bacterial phosphoenolpyruvate (PEP):sugar phosphotransferase system is the homodimeric 60-kDa enzyme I (EI), which autophosphorylates in the presence of PEP and Mg2+. The conformational stability and structure of the EI from Streptomyces coelicolor, EI(sc), were explored in the absence and in the presence of its effectors by using several biophysical probes (namely, fluorescence, far-ultraviolet circular dichroism, Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry) and computational approaches. The structure of EI(sc) was obtained by homology modeling of the isolated N- and C-terminal domains of other EI proteins. The experimental results indicate that at physiological pH, the dimeric EI(sc) had a well-folded structure; however, at low pH, EI(sc) showed a partially unfolded state with the features of a molten globule, as suggested by fluorescence, far-ultraviolet circular dichroism, FTIR, and 8-anilino-1-naphthalene-sulfonic acid binding. The thermal stability of EI(sc), in the absence of PEP and Mg2+, was maximal at pH 7. The presence of PEP and Mg2+ did not change substantially the secondary structure of the protein, as indicated by FTIR measurements. However, quenching experiments and proteolysis patterns suggest conformational changes in the presence of PEP; furthermore, the thermal stability of EI(sc) was modified depending on the effector added. Our approach suggests that thermodynamical analysis might reveal subtle conformational changes.
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