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van der Linden MG, Ferreira DC, Pereira de Araújo AF. Constrained Layer Assignment for the Protein Burial Folding Code Accounting for Chain Connectivity. J Phys Chem B 2022; 126:6159-6170. [PMID: 35952378 DOI: 10.1021/acs.jpcb.2c03931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The connection between protein sequences and tertiary structures has intrigued investigators for decades. A plausible hypothesis for the coding scheme postulates that atomic burial information obtainable from the sequence could be sufficient for structural determination when combined to sequence-independent constraints. Accordingly, folding simulations using native burial information expressed by atomic central distances, discretized into a small number L of equiprobable burial layers, have indeed been successful in reaching and distinguishing the native structure of several globular proteins. Attempted predictions of layers from sequence, however, turned out to be insufficiently accurate for most proteins. Here we explore the possibility that a nonuniform assignment of layers, which is intended to account for constraints imposed by chain connectivity, might provide a more efficient burial encoding of tertiary structures. We consider the condition that adjacent Cα-atoms along the sequence cannot occupy nonadjacent layers, in which case the information required to specify sequences of burials would be smaller. It is shown that appropriate folding behavior can still be observed in this explicitly more constrained scenario with a structure-dependent assignment intended to produce the thinnest possible layers still compatible with the imposed burial constraint. This thinnest assignment turns out to be sufficiently restrictive for the observed examples and provides appropriately thinner layers or, equivalently, a larger number of layers, for examples previously observed to indeed require more restrictive constraints when compared to counterparts of similar size, as well as the appropriate increase in number of layers for larger proteins. Implications for the general understanding of the protein folding code are discussed.
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Affiliation(s)
- Marx G van der Linden
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília - UnB, Brasília-DF 70910-900, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de Brasília - IFB, SGAN quadra 610 Módulos D, E, F, G, Brasília-DF 70830-450, Brazil
| | - Diogo C Ferreira
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília - UnB, Brasília-DF 70910-900, Brazil
| | - Antônio F Pereira de Araújo
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília - UnB, Brasília-DF 70910-900, Brazil
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2
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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3
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Bravo-Chaucanés CP, Abadio AKR, Kioshima ÉS, Felipe MSS, Barbosa JARG. Crystal structure of thioredoxin 1 from Cryptococcus neoformans at 1.8 Å resolution shows unexpected plasticity of the loop preceding the catalytic site. Biochem Biophys Rep 2020; 21:100724. [PMID: 32021910 PMCID: PMC6994535 DOI: 10.1016/j.bbrep.2019.100724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/19/2019] [Accepted: 12/28/2019] [Indexed: 11/26/2022] Open
Abstract
An elevated prevalence of cryptococcal infection is a tendency in low-income countries and constitutes a global public health problem due to factors such as the limited efficacy of antifungal therapy and the AIDS/transplant immunocompromised patients. The fungus Cryptococcus neoformans, implicated in this burden, has had several genes validated as drug targets. Among them, the thioredoxin system is one of the major regulators of redox homeostasis and antioxidant defense acting on protein disulfide bonds. Thioredoxin 1 from C. neoformans (CnTrx1) was cloned and expressed in E. coli and the recombinant protein was purified and crystallized. Functional assay shows that CnTrx1 catalyzes the reduction of insulin disulfide bonds using dithiothreitol, while acting as a monomer in solution. The crystal structure of oxidized CnTrx1 at 1.80 Å resolution presents a dimer in the asymmetric unit with typical Trx-fold. Differences between the monomers in the asymmetric unit are found specially in the loop leading to the Cys-Gly-Pro-Cys active-site motif, being even larger when compared to those found between reduced and oxidized states of other thioredoxins. Although the thioredoxins have been isolated and characterized from many organisms, this new structural report provides important clues for understanding the binding and specificity of CnTrx1 to its targets.
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Affiliation(s)
- Claudia Patricia Bravo-Chaucanés
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | | | | | - Maria Sueli Soares Felipe
- Universidade Católica de Brasília, Pós-Graduação em Ciências Genômicas e Biotecnologia, Brasília, DF, Brazil
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Buchko GW, Hewitt SN, Van Voorhis WC, Myler PJ. Solution NMR structures of oxidized and reduced Ehrlichia chaffeensis thioredoxin: NMR-invisible structure owing to backbone dynamics. Acta Crystallogr F Struct Biol Commun 2018; 74:46-56. [PMID: 29372907 PMCID: PMC5947692 DOI: 10.1107/s2053230x1701799x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/16/2017] [Indexed: 11/10/2022] Open
Abstract
Thioredoxins are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site. Here, the NMR solution structures of a reduced and oxidized thioredoxin from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, are described. The overall topology of the calculated structures is similar in both redox states and is similar to those of other thioredoxins: a five-stranded, mixed β-sheet (β1-β3-β2-β4-β5) surrounded by four α-helices. Unlike other thioredoxins studied by NMR in both redox states, the 1H-15N HSQC spectrum of reduced Ec-Trx was missing eight additional amide cross peaks relative to the spectrum of oxidized Ec-Trx. These missing amides correspond to residues Cys35-Glu39 in the active-site-containing helix (α2) and Ser72-Ile75 in a loop near the active site, and suggest a change in backbone dynamics on the millisecond-to-microsecond timescale associated with the breakage of an intramolecular Cys32-Cys35 disulfide bond in a thioredoxin. A consequence of the missing amide resonances is the absence of observable or unambiguous NOEs to provide the distance restraints necessary to define the N-terminal end of the α-helix containing the CPGC active site in the reduced state. This region adopts a well defined α-helical structure in other reported reduced thioredoxin structures, is mostly helical in oxidized Ec-Trx and CD studies of Ec-Trx in both redox states suggests there is no significant difference in the secondary structure of the protein. The NMR solution structure of reduced Ec-Trx illustrates that the absence of canonical structure in a region of a protein may be owing to unfavorable dynamics prohibiting NOE observations or unambiguous NOE assignments.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Infectious Disease Research, Seattle, Washington, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, USA
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5
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Yang J, Hamid S, Liu Q, Cai J, Xu S, Zhang Z. Gene expression of selenoproteins can be regulated by thioredoxin(Txn) silence in chicken cardiomyocytes. J Inorg Biochem 2017; 177:118-126. [PMID: 28957736 DOI: 10.1016/j.jinorgbio.2017.08.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 02/06/2023]
Abstract
Thioredoxin (Txn) system is the most crucial antioxidant defense mechanism in myocardium. The aim of this study was to clarify the effect of Txn low expression on 25 selenoproteins in chicken cardiomyocytes. We developed a Se-deficient model (0.033mg/kg) and Txn knock down cardiomyocytes model (siRNA) studies. Western Blot, Quantitative Real-time PCR (qPCR) were performed, and correlation analysis, heat map were used for further analysis. Both low expression of Txn models are significantly decreased (P<0.05) the mRNA levels of Deiodinase 1, 2 (Dio 1, 2), Glutathione Peroxidase 1, 2, 3, 4 (Gpx 1, 2, 3, 4), Thioredoxin Reductase 1, 2, 3 (TR 1, 2, 3), Selenoprotein t (Selt), Selenoprotein w (Selw), Selenoprotein k (Selk), selenoprotein x1 (Sepx1), and significantly increased (P<0.05) the mRNA levels of the rest of selenoproteins. Correlation analysis showed that Deiodinase 3 (Dio 3), Selenoprotein m (Selm), 15-kDa Selenoprotein (Selp15), Selenoprotein h (Selh), Selenoprotein u (Selu), Selenoprotein i (Seli), Selenoprotein n (Seln), Selenoprotein p1 (Sepp1), Selenoprotein o (Selo), Selenoprotein s (Sels), Selenoprotein synthetase 2 (Sels2) and Selenoprotein p (Selp) had a negative correlation with Txn, while the rest of selenoproteins had a positive correlation with Txn. Combined in vivo and in vitro we can know that hamper Txn expression can inhibit Gpx 1, 2, 3, 4, TR 1, 2, 3, Dio 1, 2, Selt, Selw, Selk, Sepx1, meanwhile, over expression the rest of selenoproteins. In conclusion, the different selenoproteins possess and exhibit distinct responses to silence of Txn in chicken cardiomyocytes.
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Affiliation(s)
- Jie Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Sattar Hamid
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Qi Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Jingzeng Cai
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China.
| | - Ziwei Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China.
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6
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Selenium deficiency-induced thioredoxin suppression and thioredoxin knock down disbalanced insulin responsiveness in chicken cardiomyocytes through PI3K/Akt pathway inhibition. Cell Signal 2017; 38:192-200. [PMID: 28734787 DOI: 10.1016/j.cellsig.2017.07.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/26/2017] [Accepted: 07/16/2017] [Indexed: 01/15/2023]
Abstract
Thioredoxin (Txn) system is the most crucial antioxidant defense mechanism in cell consisting of Txn, thioredoxin reductase (TR) and Nicotinamide Adenine Dinucleotide Phosphate (NADPH). Perturbations in Txn system may compromise cell survival through oxidative stress induction. Metabolic activity of insulin plays important roles in fulfilling the stable and persistent demands of heart through glucose metabolism. However, the roles of Txn and Txn system in insulin modulated cardiac energy metabolism have been less reported. Therefore, to investigate the role of Txn in myocardial metabolism, we developed a Se-deficient chicken model (0.033mg/kg) for in-vivo and Txn knock down cardiomyocytes culture model (siRNA) for in-vitro studies. Quantitative real time PCR and western blotting was performed. Se deficiency suppressed Txn and TR in cardiac tissues. Significant increases in ROS (P<0.05) levels signify the onset of oxidative stress and in both models. Se deficiency-induced Txn suppression model and Txn knock down cardiomyocytes models significantly decreased (P<0.05), the mRNA and protein levels of insulin-like growth factors (IGF1, IGF2), IGF-binding proteins (IGFBP2, IGFBP4), insulin receptor (IR), insulin receptor substrates (IRS1, IRS2), and glucose transporters (GLUT1, GLUT3, GLUT8), however, IGFBP3 expression increased in Txn knock down cardiomyocytes. In addition, in contrast to their respective controls, Se deficiency-induced Txn depleted tissues and Txn deleted cardiomyocytes showed suppression in mRNA and protein levels of PI3K, AKT, P-PI3K, and repression in FOX, P-FOX JNK genes. Combing the in vitro and in vivo experiments, we demonstrate that Txn gene suppression can cause dysfunction of insulin-modulated cardiac energy metabolism and increase insulin resistance through PI3K-Akt pathway inhibition. Herein, we conclude that inactivation of Txn system can alter cellular insulin response through IRS/PI3K/Akt pathway repression and JNK and FOX expression. These findings point out that Txn system can redox regulate the insulin dependent glucose metabolism in heart and is essential for cell vitality. Moreover, the increased expression of IGFBP3 indicates that it can be a potential negative modulator of metabolic activity of insulin in Txn deficient cells.
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Campos-Acevedo AA, Sotelo-Mundo RR, Pérez J, Rudiño-Piñera E. Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:326-339. [PMID: 28375144 DOI: 10.1107/s2059798317002066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/08/2017] [Indexed: 11/10/2022]
Abstract
The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo. Crystallographic data for shrimp thioredoxin (LvTrx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx. Through the analysis of five mutants located at the crystallographic interface, this study provides structural and biochemical evidence for the existence in solution of monomeric and dimeric populations of wild-type LvTrx and five mutants. Based on the results of biochemical assays, SAXS studies and the crystallographic structures of three of the studied mutants (Cys73Ser, Asp60Ser and Trp31Ala), it is clear that the Cys73 residue is essential for dimerization. However, its mutation to Ser produces an enzyme which has similar redox activity in vitro to the wild type. A putative regulatory function of dimerization is proposed based on structural analysis. Nonetheless, the biological role of LvTrx dimerization needs to be experimentally unveiled. Additionally, the findings of this work reopen the discussion regarding the existence of similar behaviour in human thioredoxin, which shares a Cys at position 73 with LvTrx, a structural feature that is also present in some Trxs from vertebrates and crustaceans.
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Affiliation(s)
- Adam A Campos-Acevedo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, 62210 Cuernavaca, MOR, 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, PO Box 1735, 83304 Hermosillo, SON, Mexico
| | - Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, Saint-Aubin, 91192 Gif sur Yvette CEDEX, France
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, 62210 Cuernavaca, MOR, Mexico
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8
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Netto LES, de Oliveira MA, Tairum CA, da Silva Neto JF. Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions. Free Radic Res 2016; 50:206-45. [DOI: 10.3109/10715762.2015.1120864] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Iqbal A, Moraes AH, Valente AP, Almeida FCL. Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insights into the mechanism for the closing of the water cavity. JOURNAL OF BIOMOLECULAR NMR 2015; 63:417-423. [PMID: 26482062 DOI: 10.1007/s10858-015-9996-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Anwar Iqbal
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS/Anexo CNRMN, Rio de Janeiro, RJ, 21941-920, Brazil
- Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adolfo Henrique Moraes
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS/Anexo CNRMN, Rio de Janeiro, RJ, 21941-920, Brazil
- Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula Valente
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS/Anexo CNRMN, Rio de Janeiro, RJ, 21941-920, Brazil
- Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS/Anexo CNRMN, Rio de Janeiro, RJ, 21941-920, Brazil.
- Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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10
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Iqbal A, Gomes-Neto F, Myiamoto CA, Valente AP, Almeida FCL. Dissection of the water cavity of yeast thioredoxin 1: the effect of a hydrophobic residue in the cavity. Biochemistry 2015; 54:2429-42. [PMID: 25830254 DOI: 10.1021/acs.biochem.5b00082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The water cavity of yeast thioredoxin 1 (yTrx1) is an ancestral, conserved structural element that is poorly understood. We recently demonstrated that the water cavity is involved in the complex protein dynamics that are responsible for the catalytically relevant event of coupling hydration, proton exchange, and motion at the interacting loops. Its main feature is the presence of the conserved polar residue, Asp24, which is buried in a hydrophobic cavity. Here, we evaluated the role of the solvation of Asp24 as the main element that is responsible for the formation of the water cavity in thioredoxins. We showed that the substitution of Asp24 with a hydrophobic residue (D24A) was not sufficient to completely close the cavity. The dynamics of the D24A mutant of yTrx1 at multiple time scales revealed that the D24A mutant presents motions at different time scales near the active site, interaction loops, and water cavity, revealing the existence of a smaller dissected cavity. Molecular dynamics simulation, along with experimental molecular dynamics, allowed a detailed description of the water cavity in wild-type yTrx1 and D24A. The cavity connects the interacting loops, the central β-sheet, and α-helices 2 and 4. It is formed by three contiguous lobes, which we call lobes A-C. Lobe A is hydrophilic and the most superficial. It is formed primarily by the conserved Lys54. Lobe B is the central lobe formed by the catalytically important residues Cys33 and Asp24, which are strategically positioned. Lobe C is the most hydrophobic and is formed by the conserved cis-Pro73. The central lobe B is closed upon introduction of the D24A mutation, revealing that independent forces other than solvation of Asp24 maintain lobes A and C in the open configuration. These data allow us to better understand the properties of this enzyme.
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Affiliation(s)
- Anwar Iqbal
- †Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francisco Gomes-Neto
- §Laboratory of Toxicology, Instituto Oswaldo Cruz, Fiocruz, 21045-900 Rio de Janeiro, Brazil
| | | | - Ana Paula Valente
- ‡Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- †Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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11
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Cruzeiro-Silva C, Gomes-Neto F, Machado LESF, Miyamoto CA, Pinheiro AS, Correa-Pereira N, de Magalhães MTQ, Valente AP, Almeida FCL. Hydration and conformational equilibrium in yeast thioredoxin 1: implication for H(+) exchange. Biochemistry 2014; 53:2890-902. [PMID: 24738963 DOI: 10.1021/bi401542v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One of the ancestral features of thioredoxins is the presence of a water cavity. Here, we report that a largely hydrated, conserved, buried aspartic acid in the water cavity modulates the dynamics of the interacting loops of yeast thioredoxin 1 (yTrx1). It is well-established that the aspartic acid, Asp24 for yTrx1, works as a proton acceptor in the reduction of the target protein. We propose a complementary role for Asp24 of coupling hydration and conformational motion of the water cavity and interacting loops. The intimate contact between the water cavity and the interacting loops means that motion at the water cavity will affect the interacting loops and vice versa. The D24N mutation alters the conformational equilibrium for both the oxidized and reduced states, quenching the conformational motion in the water cavity. By measuring the hydration and molecular dynamics simulation of wild-type yTrx1 and the D24N mutant, we showed that Asn24 is more exposed to water than Asp24 and the water cavity is smaller in the mutant, closing the inner part of the water cavity. We discuss how the conformational equilibrium contributes to the mechanism of catalysis and H(+) exchange.
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Affiliation(s)
- Carolina Cruzeiro-Silva
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro-Institute of Structural Biology and Bioimaging , Rio de Janeiro, Brazil
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12
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Tommy YBW, Lim TS, Noordin R, Saadatnia G, Choong YS. Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii. BMC STRUCTURAL BIOLOGY 2012; 12:30. [PMID: 23181504 PMCID: PMC3542155 DOI: 10.1186/1472-6807-12-30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 11/23/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Toxoplasma gondii is an intracellular coccidian parasite that causes toxoplasmosis. It was estimated that more than one third of the world population is infected by T. gondii, and the disease is critical in fetuses and immunosuppressed patients. Thus, early detection is crucial for disease diagnosis and therapy. However, the current available toxoplasmosis diagnostic tests vary in their accuracy and the better ones are costly. RESULTS An earlier published work discovered a highly antigenic 12 kDa excretory-secretory (ES) protein of T. gondii which may potentially be used for the development of an antigen detection test for toxoplasmosis. However, the three-dimensional structure of the protein is unknown. Since epitope identification is important prior to designing of a specific antibody for an antigen-detection based diagnostic test, the structural elucidation of this protein is essential. In this study, we constructed a three dimensional model of the 12 kDa ES protein. The built structure possesses a thioredoxin backbone which consists of four α-helices flanking five β-strands at the center. Three potential epitopes (6-8 residues) which can be combined into one "single" epitope have been identified from the built structure as the most potential antibody binding site. CONCLUSION Together with specific antibody design, this work could contribute towards future development of an antigen detection test for toxoplasmosis.
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Affiliation(s)
- Yap Boon Wooi Tommy
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Geita Saadatnia
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
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13
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Hameed M. S. S, Sarma SP. The Structure of the Thioredoxin–Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediated Regulation of Triosephosphate Isomerase. Biochemistry 2011; 51:533-44. [DOI: 10.1021/bi201224s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shahul Hameed M. S.
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Siddhartha P. Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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14
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Netto CGCM, Nakamatsu EH, Netto LES, Novak MA, Zuin A, Nakamura M, Araki K, Toma HE. Catalytic properties of thioredoxin immobilized on superparamagnetic nanoparticles. J Inorg Biochem 2011; 105:738-44. [PMID: 21470550 DOI: 10.1016/j.jinorgbio.2011.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 10/18/2022]
Abstract
Thioredoxin (Trx1), a very important protein for regulating intracellular redox reactions, was immobilized on iron oxide superparamagnetic nanoparticles previously coated with 3-aminopropyltriethoxysilane (APTS) via covalent coupling using the EDC (1-ethyl-3-{3-dimethylaminopropyl}carbodiimide) method. The system was extensively characterized by atomic force microscopy, vibrational and magnetic techniques. In addition, gold nanoparticles were also employed to probe the exposed groups in the immobilized enzyme based on the SERS (surface enhanced Raman scattering) effect, confirming the accessibility of the cysteines residues at the catalytic site. For the single coated superparamagnetic nanoparticle, by monitoring the enzyme activity with the Ellman reagent, DTNB=5,5'-dithio-bis(2-15 nitrobenzoic acid), an inhibitory effect was observed after the first catalytic cycle. The inhibiting effect disappeared after the application of an additional silicate coating before the APTS treatment, reflecting a possible influence of unprotected iron-oxide sites in the redox kinetics. In contrast, the doubly coated system exhibited a normal in-vitro kinetic activity, allowing a good enzyme recovery and recyclability.
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Oliveira MA, Discola KF, Alves SV, Medrano FJ, Guimarães BG, Netto LES. Insights into the specificity of thioredoxin reductase-thioredoxin interactions. A structural and functional investigation of the yeast thioredoxin system. Biochemistry 2010; 49:3317-26. [PMID: 20235561 DOI: 10.1021/bi901962p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 A resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M ). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.
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Affiliation(s)
- Marcos A Oliveira
- Departamento de Biologia, Universidade Estadual Paulista, São Vicente, Brazil
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Bao R, Zhang Y, Lou X, Zhou CZ, Chen Y. Structural and kinetic analysis of Saccharomyces cerevisiae thioredoxin Trx1: Implications for the catalytic mechanism of GSSG reduced by the thioredoxin system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1218-23. [DOI: 10.1016/j.bbapap.2009.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 03/28/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
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