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Rubio-Hernández M, Alcolea V, Pérez-Silanes S. Potential of sulfur-selenium isosteric replacement as a strategy for the development of new anti-chagasic drugs. Acta Trop 2022; 233:106547. [PMID: 35667455 DOI: 10.1016/j.actatropica.2022.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
Abstract
Current treatment for Chagas disease is based on only two drugs: benznidazole and nifurtimox. Compounds containing sulfur (S) in their structure have shown promising results in vitro and in vivo against Trypanosoma cruzi, the parasite causing Chagas disease. Notably, some reports show that the isosteric replacement of S by selenium (Se) could be an interesting strategy for the development of new compounds for the treatment of Chagas disease. To date, the activity against T. cruzi of three Se- containing groups has been compared with their S counterparts: selenosemicarbazones, selenoquinones, and selenocyanates. More studies are needed to confirm the positive results of Se compounds. Therefore, we have investigated S compounds described in the literature tested against T. cruzi. We focused on those tested in vivo that allowed isosteric replacement to propose their Se counterparts as promising compounds for the future development of new drugs against Chagas disease.
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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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Quezada AG, Cabrera N, Piñeiro Á, Díaz-Salazar AJ, Díaz-Mazariegos S, Romero-Romero S, Pérez-Montfort R, Costas M. A strategy based on thermal flexibility to design triosephosphate isomerase proteins with increased or decreased kinetic stability. Biochem Biophys Res Commun 2018; 503:3017-3022. [PMID: 30143261 DOI: 10.1016/j.bbrc.2018.08.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
Abstract
Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (Eact) separating the native from the transition state in the denaturation process. The Eact was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life.
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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, Mexico.
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Ángel Piñeiro
- Soft Matter and Molecular Biophysics Group, Departamento de Física Aplicada, Facultad de Física, Universidad de Santiago de Compostela, Campus Vida s/n, E-15782, Santiago de Compostela, Spain
| | - A Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico
| | - Selma Díaz-Mazariegos
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico.
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Deng H, Vedad J, Desamero RZB, Callender R. Difference FTIR Studies of Substrate Distribution in Triosephosphate Isomerase. J Phys Chem B 2017; 121:10036-10045. [PMID: 28990791 PMCID: PMC5687254 DOI: 10.1021/acs.jpcb.7b08114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP), via an enediol(ate) intermediate. Determination of substrate population distribution in the TIM/substrate reaction mixture at equilibrium and characterization of the substrate-enzyme interactions in the Michaelis complex are ongoing efforts toward the understanding of the TIM reaction mechanism. By using isotope-edited difference Fourier transform infrared studies with unlabeled and 13C-labeled substrates at specific carbon(s), we are able to show that in the reaction mixture at equilibrium the keto DHAP is the dominant species and the populations of aldehyde GAP and enediol(ate) are very low, consistent with the results from previous X-ray structural and 13C NMR studies. Furthermore, within the DHAP side of the Michaelis complex, there is a set of conformational substates that can be characterized by the different C2═O stretch frequencies. The C2═O frequency differences reflect the different degree of the C2═O bond polarization due to hydrogen bonding from active site residues. The C2═O bond polarization has been considered as an important component for substrate activation within the Michaelis complex. We have found that in the enzyme-substrate reaction mixture with TIM from different organisms the number of substates and their population distribution within the DHAP side of the Michaelis complex may be different. These discoveries provide a rare opportunity to probe the interconversion dynamics of these DHAP substates and form the bases for the future studies to determine if the TIM-catalyzed reaction follows a simple linear reaction pathway, as previously believed, or follows parallel reaction pathways, as suggested in another enzyme system that also shows a set of substates in the Michaelis complex.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Jayson Vedad
- Programs in Chemistry and Biochemistry, CUNY Graduate Center and Department of Chemistry, York College of CUNY, Jamaica, New York 11451, United States
| | - Ruel Z. B. Desamero
- Programs in Chemistry and Biochemistry, CUNY Graduate Center and Department of Chemistry, York College of CUNY, Jamaica, New York 11451, United States
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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5
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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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6
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Olivares-Illana V, Riveros-Rosas H, Cabrera N, Tuena de Gómez-Puyou M, Pérez-Montfort R, Costas M, Gómez-Puyou A. A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Proteins 2017; 85:1190-1211. [PMID: 28378917 DOI: 10.1002/prot.25299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
Triosephosphate isomerase (TIM) is a ubiquitous enzyme, which appeared early in evolution. TIM is responsible for obtaining net ATP from glycolysis and producing an extra pyruvate molecule for each glucose molecule, under aerobic and anaerobic conditions. It is placed in a metabolic crossroad that allows a quick balance of the triose phosphate aldolase produced by glycolysis, and is also linked to lipid metabolism through the alternation of glycerol-3-phosphate and the pentose cycle. TIM is one of the most studied enzymes with more than 199 structures deposited in the PDB. The interest for this enzyme stems from the fact that it is involved in glycolysis, but also in aging, human diseases and metabolism. TIM has been a target in the search for chemical compounds against infectious diseases and is a model to study catalytic features. Until February 2017, 62% of all residues of the protein have been studied by mutagenesis and/or using other approaches. Here, we present a detailed and comprehensive recompilation of the reported effects on TIM catalysis, stability, druggability and human disease produced by each of the amino acids studied, contributing to a better understanding of the properties of this fundamental protein. The information reviewed here shows that the role of the noncatalytic residues depend on their molecular context, the delicate balance between the short and long-range interactions in concerted action determining the properties of the protein. Each protein should be regarded as a unique entity that has evolved to be functional in the organism to which it belongs. Proteins 2017; 85:1190-1211. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer. Instituto de Física, Universidad Autónoma de San Luis Potosí, SLP, 78290, México
| | - Hector Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
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7
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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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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Roland BP, Zeccola AM, Larsen SB, Amrich CG, Talsma AD, Stuchul KA, Heroux A, Levitan ES, VanDemark AP, Palladino MJ. Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics. PLoS Genet 2016; 12:e1005941. [PMID: 27031109 PMCID: PMC4816394 DOI: 10.1371/journal.pgen.1005941] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopathies, but is unique for its severe patient neuropathology and early mortality. The disease is caused by missense mutations and dysfunction in the glycolytic enzyme, TPI. Previous studies have detailed structural and catalytic changes elicited by disease-associated TPI substitutions, and samples of patient erythrocytes have yielded insight into patient hemolytic anemia; however, the neuropathophysiology of this disease remains a mystery. This study combines structural, biochemical, and genetic approaches to demonstrate that perturbations of the TPI dimer interface are sufficient to elicit TPI deficiency neuropathogenesis. The present study demonstrates that neurologic dysfunction resulting from TPI deficiency is characterized by synaptic vesicle dysfunction, and can be attenuated with catalytically inactive TPI. Collectively, our findings are the first to identify, to our knowledge, a functional synaptic defect in TPI deficiency derived from molecular changes in the TPI dimer interface.
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Affiliation(s)
- Bartholomew P. Roland
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Alison M. Zeccola
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Samantha B. Larsen
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Christopher G. Amrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aaron D. Talsma
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kimberly A. Stuchul
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Annie Heroux
- Energy Sciences Directorate/Photon Science Division, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Edwin S. Levitan
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Andrew P. VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Carcamo-Noriega EN, Saab-Rincon G. Identification of fibrillogenic regions in human triosephosphate isomerase. PeerJ 2016; 4:e1676. [PMID: 26870617 PMCID: PMC4748702 DOI: 10.7717/peerj.1676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/20/2016] [Indexed: 12/31/2022] Open
Abstract
Background. Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to structural features, such is the case of TIM barrel topology. Methods. This work was aimed to study the fibrillogenic propensity of human triosephosphate isomerase (HsTPI) as a model of TIM barrels. In order to do so, aggregation of HsTPI was evaluated under native-like and destabilizing conditions. Fibrillogenic regions were identified by bioinformatics approaches, protein fragmentation and peptide aggregation. Results. We identified four fibrillogenic regions in the HsTPI corresponding to the β3, β6, β7 y α8 of the TIM barrel. From these, the β3-strand region (residues 59–66) was highly fibrillogenic. In aggregation assays, HsTPI under native-like conditions led to amorphous assemblies while under partially denaturing conditions (urea 3.2 M) formed more structured aggregates. This slightly structured aggregates exhibited residual cross-β structure, as demonstrated by the recognition of the WO1 antibody and ATR-FTIR analysis. Discussion. Despite the fibrillogenic regions present in HsTPI, the enzyme maintained under native-favoring conditions displayed low fibrillogenic propensity. This amyloid-resistance can be attributed to the three-dimensional arrangement of the protein, where β-strands, susceptible to aggregation, are protected in the core of the molecule. Destabilization of the protein structure may expose inner regions promoting β-aggregation, as well as the formation of hydrophobic disordered aggregates. Being this last pathway kinetically favored over the thermodynamically more stable fibril aggregation pathway.
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Affiliation(s)
- Edson N Carcamo-Noriega
- Instituto de Biotecnología, Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México , Cuernavaca, Morelos , Mexico
| | - Gloria Saab-Rincon
- Instituto de Biotecnología, Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México , Cuernavaca, Morelos , Mexico
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11
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Aguirre C, Goto Y, Costas M. Thermal and chemical unfolding pathways of PaSdsA1 sulfatase, a homo-dimer with topologically interlinked chains. FEBS Lett 2016; 590:202-14. [PMID: 26823168 DOI: 10.1002/1873-3468.12041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/17/2015] [Accepted: 12/07/2015] [Indexed: 11/11/2022]
Abstract
Understanding the mechanisms as to how interlinked proteins entangle and fold is a challenge. PaSdsA1 sulfatase is a homo-dimer containing two zinc atoms per monomer. The monomer chains are interlinked in a dimerization domain. To study the unfolding pathways denaturation experiments were performed. In the native protein three forms coexist in chemical equilibrium, each with a different number of zinc atoms. In the chemical unfolding of the holo-dimers the entanglement of the chains is preserved and acts as a 'folding seed', allowing the unfolding process to be reversible. Thermal irreversible unfolding of the holo-dimers favours dissociation, producing monomers that are SDS-stabilized. The thermal unfolding of these monomers is reversible. However, it is not possible to form dimers from unfolded monomers.
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Affiliation(s)
- César Aguirre
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F, México
| | - Yuji Goto
- Protein Folding Laboratory, Institute for Protein Research, Osaka University, Japan
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F, México
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12
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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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Pey AL, Majtan T, Kraus JP. The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1453-62. [PMID: 24780582 DOI: 10.1016/j.bbapap.2014.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/06/2014] [Accepted: 04/21/2014] [Indexed: 11/25/2022]
Abstract
Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.
| | - Tomas Majtan
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
| | - Jan P Kraus
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
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