1
|
Li RX, Zhang NN, Wu B, OuYang B, Shen HB. Multiobjective heuristic algorithm for de novo protein design in a quantified continuous sequence space. Comput Struct Biotechnol J 2021; 19:2575-2587. [PMID: 34025944 PMCID: PMC8114120 DOI: 10.1016/j.csbj.2021.04.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Protein design usually involves sequence search process and evaluation criteria. Commonly used methods primarily implement the Monte Carlo or simulated annealing algorithm with a single-energy function to obtain ideal solutions, which is often highly time-consuming and limited by the accuracy of the energy function. In this report, we introduce a multiobjective algorithm named Hydra for protein design, which employs two different energy functions to optimize solutions simultaneously and makes use of the latent quantitative relationship between different amino acid types to facilitate the search process. The framework uses two kinds of prior information to transform the original disordered discrete sequence space into a relatively ordered space, and decoy sequences are searched in this ordered space through a multiobjective swarm intelligence algorithm. This algorithm features high accuracy and a high-speed search process. Our method was tested on 40 targets covering different fold classes, which were computationally verified to be well folded, and it experimentally solved the 1UBQ fold by NMR in excellent agreement with the native structure with a backbone RMSD deviation of 1.074 Å. The Hydra software package can be downloaded from: http://www.csbio.sjtu.edu.cn/bioinf/HYDRA/ for academic use.
Collapse
Affiliation(s)
- Rui-Xiang Li
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Ning-Ning Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.,Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
2
|
Piñeyro MD, Arias D, Parodi-Talice A, Guerrero S, Robello C. Trypanothione Metabolism as Drug Target for Trypanosomatids. Curr Pharm Des 2021; 27:1834-1846. [PMID: 33308115 DOI: 10.2174/1381612826666201211115329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
Chagas Disease, African sleeping sickness, and leishmaniasis are neglected diseases caused by pathogenic trypanosomatid parasites, which have a considerable impact on morbidity and mortality in poor countries. The available drugs used as treatment have high toxicity, limited access, and can cause parasite drug resistance. Long-term treatments, added to their high toxicity, result in patients that give up therapy. Trypanosomatids presents a unique trypanothione based redox system, which is responsible for maintaining the redox balance. Therefore, inhibition of these essential and exclusive parasite's metabolic pathways, absent from the mammalian host, could lead to the development of more efficient and safe drugs. The system contains different redox cascades, where trypanothione and tryparedoxins play together a central role in transferring reduced power to different enzymes, such as 2-Cys peroxiredoxins, non-selenium glutathione peroxidases, ascorbate peroxidases, glutaredoxins and methionine sulfoxide reductases, through NADPH as a source of electrons. There is sufficient evidence that this complex system is essential for parasite survival and infection. In this review, we explore what is known in terms of essentiality, kinetic and structural data, and the development of inhibitors of enzymes from this trypanothione-based redox system. The recent advances and limitations in the development of lead inhibitory compounds targeting these enzymes have been discussed. The combination of molecular biology, bioinformatics, genomics, and structural biology is fundamental since the knowledge of unique features of the trypanothione-dependent system will provide tools for rational drug design in order to develop better treatments for these diseases.
Collapse
Affiliation(s)
| | - Diego Arias
- Instituto de Agrobiotecnologia del Litoral y Facultad de Bioquimica y Ciencias Biologicas, CONICET-UNL, Santa F, Argentina
| | | | - Sergio Guerrero
- Instituto de Agrobiotecnologia del Litoral y Facultad de Bioquimica y Ciencias Biologicas, CONICET-UNL, Santa F, Argentina
| | - Carlos Robello
- Unidad de Biologia Molecular, Instituto Pasteur Montevideo, Montevideo, Uruguay
| |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Han M, Liao S, Peng X, Zhou X, Chen Q, Liu H. Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures. Protein Sci 2019; 28:1437-1447. [PMID: 31074908 DOI: 10.1002/pro.3643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/25/2022]
Abstract
Computationally designed proteins of high stability provide specimen in addition to natural proteins for the study of sequence-structure stability relationships at the very high end of protein stability spectrum. The melting temperature of E_1r26, a protein we previously designed using the A Backbone-based Amino aCid Usage Survey (ABACUS) sequence design program, is above 110 °C, more than 50 °C higher than that of the natural thioredoxin protein whose backbone (PDB ID 1R26) has been used as the design target. Using an experimental selection approach, we obtained variants of E_1r26 that remain folded but are of reduced stability, including one whose unfolding temperature and denaturing guanidine concentration are similar to those of 1r26. The mutant unfolds with a certain degree of cooperativity. Its structure solved by X-ray crystallography agrees with that of 1r26 by a root mean square deviation of 1.3 Å, adding supports to the accuracy of the ABACUS method. Analyses of intermediate mutants indicate that the substitution of two partially buried hydrophobic residues (isoleucine and leucine) by polar residues (threonine and serine, respectively) are responsible for the dramatic change in the unfolding temperature. It is suggested that the effects of mutations located in rigid secondary structure regions, but not those in loops, may be well predicted through ABACUS mutation energy analysis. The results also suggest that hydrophobic effects involving intermediately buried sidechains can be critically important for protein stability at high temperatures.
Collapse
Affiliation(s)
- Mingjie Han
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Sanhui Liao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiong Peng
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaoqun Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.,School of Data Science, University of Science and Technology of China, Hefei, Anhui, China.,Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China
| |
Collapse
|
5
|
Manta B, Bonilla M, Fiestas L, Sturlese M, Salinas G, Bellanda M, Comini MA. Polyamine-Based Thiols in Trypanosomatids: Evolution, Protein Structural Adaptations, and Biological Functions. Antioxid Redox Signal 2018; 28:463-486. [PMID: 29048199 DOI: 10.1089/ars.2017.7133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SIGNIFICANCE Major pathogenic enterobacteria and protozoan parasites from the phylum Euglenozoa, such as trypanosomatids, are endowed with glutathione (GSH)-spermidine (Sp) derivatives that play important roles in signaling and metal and thiol-redox homeostasis. For some Euglenozoa lineages, the GSH-Sp conjugates represent the main redox cosubstrates around which entire new redox systems have evolved. Several proteins underwent molecular adaptations to synthesize and utilize the new polyamine-based thiols. Recent Advances: The genomes of closely related organisms have recently been sequenced, which allows mining and analysis of gene sequences that belong to these peculiar redox systems. Similarly, the three-dimensional structures of several of these proteins have been solved, which allows for comparison with their counterparts in classical redox systems that rely on GSH/glutaredoxin and thioredoxin. CRITICAL ISSUES The evolutionary and structural aspects related to the emergence and use of GSH-Sp conjugates in Euglenozoa are reviewed focusing on unique structural specializations that proteins developed to use N1,N8-bisglutathionylspermidine (trypanothione) as redox cosubstrate. An updated overview on the biochemical and biological significance of the major enzymatic activities is also provided. FUTURE DIRECTIONS A thiol-redox system strictly dependent on trypanothione is a feature unique to trypanosomatids. The physicochemical properties of the polyamine-GSH conjugates were a major driving force for structural adaptation of proteins that use these thiols as ligand and redox cofactor. In fact, the structural differences of indispensable components of this system can be exploited toward selective drug development. Future research should clarify whether additional cellular processes are regulated by the trypanothione system. Antioxid. Redox Signal. 28, 463-486.
Collapse
Affiliation(s)
- Bruno Manta
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica , Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mariana Bonilla
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica , Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Fiestas
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Mattia Sturlese
- 3 Department of Chemical Sciences, Università degli Studi di Padova , Padova, Italy
| | - Gustavo Salinas
- 4 Worm Biology Lab, Institut Pasteur de Montevideo , Montevideo, Uruguay .,5 Departamento de Biociencias, Facultad de Química, Universidad de la República , Montevideo, Uruguay
| | - Massimo Bellanda
- 3 Department of Chemical Sciences, Università degli Studi di Padova , Padova, Italy
| | - Marcelo A Comini
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay
| |
Collapse
|
6
|
The Architecture of Thiol Antioxidant Systems among Invertebrate Parasites. Molecules 2017; 22:molecules22020259. [PMID: 28208651 PMCID: PMC6155587 DOI: 10.3390/molecules22020259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The use of oxygen as the final electron acceptor in aerobic organisms results in an improvement in the energy metabolism. However, as a byproduct of the aerobic metabolism, reactive oxygen species are produced, leaving to the potential risk of an oxidative stress. To contend with such harmful compounds, living organisms have evolved antioxidant strategies. In this sense, the thiol-dependent antioxidant defense systems play a central role. In all cases, cysteine constitutes the major building block on which such systems are constructed, being present in redox substrates such as glutathione, thioredoxin, and trypanothione, as well as at the catalytic site of a variety of reductases and peroxidases. In some cases, the related selenocysteine was incorporated at selected proteins. In invertebrate parasites, antioxidant systems have evolved in a diversity of both substrates and enzymes, representing a potential area in the design of anti-parasite strategies. The present review focus on the organization of the thiol-based antioxidant systems in invertebrate parasites. Differences between these taxa and its final mammal host is stressed. An understanding of the antioxidant defense mechanisms in this kind of parasites, as well as their interactions with the specific host is crucial in the design of drugs targeting these organisms.
Collapse
|
7
|
Zhou X, Xiong P, Wang M, Ma R, Zhang J, Chen Q, Liu H. Proteins of well-defined structures can be designed without backbone readjustment by a statistical model. J Struct Biol 2016; 196:350-357. [DOI: 10.1016/j.jsb.2016.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022]
|
8
|
Arias DG, Herrera FE, Garay AS, Rodrigues D, Forastieri PS, Luna LE, Bürgi MDLM, Prieto C, Iglesias AA, Cravero RM, Guerrero SA. Rational design of nitrofuran derivatives: Synthesis and valuation as inhibitors of Trypanosoma cruzi trypanothione reductase. Eur J Med Chem 2016; 125:1088-1097. [PMID: 27810595 DOI: 10.1016/j.ejmech.2016.10.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/23/2016] [Indexed: 12/21/2022]
Abstract
The rational design and synthesis of a series of 5-nitro-2-furoic acid analogues are presented. The trypanocidal activity against epimastigote forms of Trypanosoma cruzi and the toxic effects on human HeLa cells were tested. Between all synthetic compounds, three of thirteen had an IC50 value in the range of Nfx, but compound 13 exhibited an improved effect with an IC50 of 1.0 ± 0.1 μM and a selective index of 70 in its toxicity against HeLa cells. We analyzed the activity of compounds 8, 12 and 13 to interfere in the central redox metabolic pathway in trypanosomatids, which is dependent of reduced trypanothione as the major pivotal thiol. The three compounds behaved as better inhibitors of trypanothione reductase than Nfx (Ki values of 118 μM, 61 μM and 68 μM for 8, 12 and 13, respectively, compared with 245 μM for Nfx), all following an uncompetitive enzyme inhibition pattern. Docking analysis predicted a binding of inhibitors to the enzyme-substrate complex with binding energy calculated in-silico that supports such molecular interaction.
Collapse
Affiliation(s)
- D G Arias
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - F E Herrera
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - A S Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - D Rodrigues
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - P S Forastieri
- Instituto de Química Rosario (CONICET) - FCByF- Universidad Nacional de Rosario, Argentina
| | - L E Luna
- Instituto de Química Rosario (CONICET) - FCByF- Universidad Nacional de Rosario, Argentina
| | - M D L M Bürgi
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - C Prieto
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - A A Iglesias
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - R M Cravero
- Instituto de Química Rosario (CONICET) - FCByF- Universidad Nacional de Rosario, Argentina
| | - S A Guerrero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Argentina; Facultad Regional Santa Fe, Universidad Tecnológica Nacional (UTN), Argentina.
| |
Collapse
|
9
|
Comini MA, Krauth-Siegel RL, Bellanda M. Mono- and dithiol glutaredoxins in the trypanothione-based redox metabolism of pathogenic trypanosomes. Antioxid Redox Signal 2013; 19:708-22. [PMID: 22978520 PMCID: PMC3739957 DOI: 10.1089/ars.2012.4932] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE Glutaredoxins are ubiquitous small thiol proteins of the thioredoxin-fold superfamily. Two major groups are distinguished based on their active sites: the dithiol (2-C-Grxs) and the monothiol (1-C-Grxs) glutaredoxins with a CXXC and a CXXS active site motif, respectively. Glutaredoxins are involved in cellular redox and/or iron sulfur metabolism. Usually their functions are closely linked to the glutathione system. Trypanosomatids, the causative agents of several tropical diseases, rely on trypanothione as principal low molecular mass thiol, and their glutaredoxins readily react with the unique bis(glutathionyl) spermidine conjugate. RECENT ADVANCES Two 2-C-Grxs and three 1-C-Grxs have been identified in pathogenic trypanosomatids. The 2-C-Grxs catalyze the reduction of glutathione disulfide by trypanothione and display reductase activity towards protein disulfides, as well as protein-glutathione mixed disulfides. In vitro, all three 1-C-Grxs as well as the cytosolic 2-C-Grx of Trypanosoma brucei can complex an iron-sulfur cluster. Recently the structure of the 1-C-Grx1 has been solved by NMR spectroscopy. The structure is very similar to those of other 1-C-Grxs, with some differences in the loop containing the conserved cis-Pro and the surface charge distribution. CRITICAL ISSUES Although four of the five trypanosomal glutaredoxins proved to coordinate an iron-sulfur cluster in vitro, the physiological role of the mitochondrial and cytosolic proteins, respectively, has only started to be unraveled. FUTURE DIRECTIONS The use of trypanothione by the glutaredoxins has established a novel role for this parasite-specific dithiol. Future work should reveal if these differences can be exploited for the development of novel antiparasitic drugs.
Collapse
Affiliation(s)
- Marcelo A Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | | | | |
Collapse
|
10
|
Bao R, Zhang Y, Zhou CZ, Chen Y. Structural and mechanistic analyses of yeast mitochondrial thioredoxin Trx3 reveal putative function of its additional cysteine residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:716-21. [PMID: 19166985 DOI: 10.1016/j.bbapap.2008.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 12/13/2008] [Accepted: 12/17/2008] [Indexed: 01/09/2023]
Abstract
The yeast Saccharomyces cerevisiae Trx3 is a key member of the thioredoxin system to control the cellular redox homeostasis in mitochondria. We solved the crystal structures of yeast Trx3 in oxidized and reduced forms at 1.80 and 2.10 A, respectively. Besides the active site, the additional cysteine residue Cys69 also undergoes a significant redox-correlated conformational change. Comparative structural analyses in combination with activity assays revealed that residue Cys69 could be S-nitrosylated in vitro. S-nitrosylation of Cys69 will decrease the activity of Trx3 by 20%, which is comparable to the effect of the Cys69Ser mutation. Taken together, these findings provided us some new insights into the putative function of the additional cysteine residues of Trx3.
Collapse
Affiliation(s)
- Rui Bao
- Institute of Protein Research, Tongji University, Shanghai 200092, PR China
| | | | | | | |
Collapse
|
11
|
The Fasciola hepatica thioredoxin: High resolution structure reveals two oxidation states. Mol Biochem Parasitol 2008; 161:44-8. [PMID: 18620002 DOI: 10.1016/j.molbiopara.2008.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/03/2008] [Accepted: 06/05/2008] [Indexed: 11/21/2022]
Abstract
The Fasciola hepatica thioredoxin protein structure has been determined to 1.45A resolution. This is the first example of a single crystal structure to show the active site cysteine residues in both the reduced and disulfide oxidised form. Consistent with this observation the process of oxidation appears to require very little rearrangement of the surrounding protein structure. The F. hepatica thioredoxin structure has been compared to other thioredoxin protein structures already known and is found to be highly conserved. The F. hepatica protein is most similar to that of the thioredoxin from its human and animal hosts but it resembles other parasitic thioredoxins with regard to having no additional cysteine residues and is therefore not regulated by transient disulfide bond formation as proposed for thioredoxins from higher eukaryotic species.
Collapse
|
12
|
Sotirchos IM, Hudson AL, Ellis J, Davey MW. Thioredoxins of a parasitic nematode: comparison of the 16- and 12-kDA thioredoxins from Haemonchus contortus. Free Radic Biol Med 2008; 44:2026-33. [PMID: 18410747 DOI: 10.1016/j.freeradbiomed.2008.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/07/2008] [Accepted: 03/10/2008] [Indexed: 02/07/2023]
Abstract
Thioredoxins are a family of small proteins conserved through evolution, which are essential for the maintenance of cellular homeostasis. The "classic" thioredoxin, identified in most species, is a 12-kDa protein with a Cys-Pro-Gly-Cys (CPGC) active site. However, in nematodes a larger protein, 16 kDa, with a Cys-Pro-Pro-Cys (CPPC) active site was identified. We report that in the parasitic nematode Haemonchus contortus, both the 12-kDa (HcTrx1) and the 16-kDa (HcTrx3) species are expressed through the life cycle. However, the HcTrx3 is expressed at higher concentrations. Recombinant HcTrx1 and HcTrx3 were produced and both reduced insulin at a rate similar to that observed with ovine (host) and Escherichia coli thioredoxins and both were regenerated by a mammalian thioredoxin reductase, demonstrating that they have similar thioredoxin activity. Unlike mammalian thioredoxins, both proteins were able to reduce oxidised glutathione and hydrogen peroxide. This suggests essential roles for these proteins in response to oxidative stress and the host immune attack. Analysis of ivermectin-resistant H. contortus showed that expression of both genes were increased in a drug-resistant strain relative to a sensitive strain. Involvement in drug resistance identifies these thioredoxin proteins as potential drug targets for parasite control.
Collapse
Affiliation(s)
- Irene M Sotirchos
- Institute for the Biotechnology of Infectious Diseases, University of Technology, Sydney, P.O. Box 123, Broadway NSW 2007, Australia
| | | | | | | |
Collapse
|
13
|
Koh CS, Navrot N, Didierjean C, Rouhier N, Hirasawa M, Knaff DB, Wingsle G, Samian R, Jacquot JP, Corbier C, Gelhaye E. An atypical catalytic mechanism involving three cysteines of thioredoxin. J Biol Chem 2008; 283:23062-72. [PMID: 18552403 DOI: 10.1074/jbc.m802093200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Unlike other thioredoxins h characterized so far, a poplar thioredoxin of the h type, PtTrxh4, is reduced by glutathione and glutaredoxin (Grx) but not NADPH:thioredoxin reductase (NTR). PtTrxh4 contains three cysteines: one localized in an N-terminal extension (Cys(4)) and two (Cys(58) and Cys(61)) in the classical thioredoxin active site ((57)WCGPC(61)). The property of a mutant in which Cys(58) was replaced by serine demonstrates that it is responsible for the initial nucleophilic attack during the catalytic cycle. The observation that the C4S mutant is inactive in the presence of Grx but fully active when dithiothreitol is used as a reductant indicates that Cys(4) is required for the regeneration of PtTrxh4 by Grx. Biochemical and x-ray crystallographic studies indicate that two intramolecular disulfide bonds involving Cys(58) can be formed, linking it to either Cys(61) or Cys(4). We propose thus a four-step disulfide cascade mechanism involving the transient glutathionylation of Cys(4) to convert this atypical thioredoxin h back to its active reduced form.
Collapse
Affiliation(s)
- Cha San Koh
- Equipe Biocristallographie, UMR 7036 CNRS-Université Henri Poincaré, URAFPA, Equipe PB2P, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre Cedex France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Maeda K, Hägglund P, Finnie C, Svensson B, Henriksen A. Crystal structures of barley thioredoxin h isoforms HvTrxh1 and HvTrxh2 reveal features involved in protein recognition and possibly in discriminating the isoform specificity. Protein Sci 2008; 17:1015-24. [PMID: 18424513 DOI: 10.1110/ps.083460308] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
H-type thioredoxins (Trxs) constitute a particularly large Trx sub-group in higher plants. Here, the crystal structures are determined for the two barley Trx h isoforms, HvTrxh1 and HvTrxh2, in the partially radiation-reduced state to resolutions of 1.7 A, and for HvTrxh2 in the oxidized state to 2.0 A. The two Trxs have a sequence identity of 51% and highly similar fold and active-site architecture. Interestingly, the four independent molecules in the crystals of HvTrxh1 form two relatively large and essentially identical protein-protein interfaces. In each interface, a loop segment of one HvTrxh1 molecule is positioned along a shallow hydrophobic groove at the primary nucleophile Cys40 of another HvTrxh1 molecule. The association mode can serve as a model for the target protein recognition by Trx, as it brings the Met82 Cgamma atom (gamma position as a disulfide sulfur) of the bound loop segment in the proximity of the Cys40 thiol. The interaction involves three characteristic backbone-backbone hydrogen bonds in an antiparallel beta-sheet-like arrangement, similar to the arrangement observed in the structure of an engineered, covalently bound complex between Trx and a substrate protein, as reported by Maeda et al. in an earlier paper. The occurrence of an intermolecular salt bridge between Glu80 of the bound loop segment and Arg101 near the hydrophobic groove suggests that charge complementarity plays a role in the specificity of Trx. In HvTrxh2, isoleucine corresponds to this arginine, which emphasizes the potential for specificity differences between the coexisting barley Trx isoforms.
Collapse
Affiliation(s)
- Kenji Maeda
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | | | | | | |
Collapse
|
15
|
Krauth-Siegel RL, Comini MA. Redox control in trypanosomatids, parasitic protozoa with trypanothione-based thiol metabolism. Biochim Biophys Acta Gen Subj 2008; 1780:1236-48. [PMID: 18395526 DOI: 10.1016/j.bbagen.2008.03.006] [Citation(s) in RCA: 294] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 02/26/2008] [Accepted: 03/11/2008] [Indexed: 01/09/2023]
Abstract
Trypanosomes and leishmania, the causative agents of several tropical diseases, possess a unique redox metabolism which is based on trypanothione. The bis(glutathionyl)spermidine is the central thiol that delivers electrons for the synthesis of DNA precursors, the detoxification of hydroperoxides and other trypanothione-dependent pathways. Many of the reactions are mediated by tryparedoxin, a distant member of the thioredoxin protein family. Trypanothione is kept reduced by the parasite-specific flavoenzyme trypanothione reductase. Since glutathione reductases and thioredoxin reductases are missing, the reaction catalyzed by trypanothione reductase represents the only connection between the NADPH- and the thiol-based redox metabolisms. Thus, cellular thiol redox homeostasis is maintained by the biosynthesis and reduction of trypanothione. Nearly all proteins of the parasite-specific trypanothione metabolism have proved to be essential.
Collapse
|
16
|
Melchers J, Dirdjaja N, Ruppert T, Krauth-Siegel RL. Glutathionylation of Trypanosomal Thiol Redox Proteins. J Biol Chem 2007; 282:8678-94. [PMID: 17242409 DOI: 10.1074/jbc.m608140200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosomatids, the causative agents of several tropical diseases, lack glutathione reductase and thioredoxin reductase but have a trypanothione reductase instead. The main low molecular weight thiols are trypanothione (N(1),N(8)-bis-(glutathionyl)spermidine) and glutathionyl-spermidine, but the parasites also contain free glutathione. To elucidate whether trypanosomes employ S-thiolation for regulatory or protection purposes, six recombinant parasite thiol redox proteins were studied by ESI-MS and MALDI-TOF-MS for their ability to form mixed disulfides with glutathione or glutathionylspermidine. Trypanosoma brucei mono-Cys-glutaredoxin 1 is specifically thiolated at Cys(181). Thiolation of this residue induced formation of an intramolecular disulfide bridge with the putative active site Cys(104). This contrasts with mono-Cys-glutaredoxins from other sources that have been reported to be glutathionylated at the active site cysteine. Both disulfide forms of the T. brucei protein were reduced by tryparedoxin and trypanothione, whereas glutathione cleaved only the protein disulfide. In the glutathione peroxidase-type tryparedoxin peroxidase III of T. brucei, either Cys(47) or Cys(95) became glutathionylated but not both residues in the same protein molecule. T. brucei thioredoxin contains a third cysteine (Cys(68)) in addition to the redox active dithiol/disulfide. Treatment of the reduced protein with GSSG caused glutathionylation of Cys(68), which did not affect its capacity to catalyze reduction of insulin disulfide. Reduced T. brucei tryparedoxin possesses only the redox active Cys(32)-Cys(35) couple, which upon reaction with GSSG formed a disulfide. Also glyoxalase II and Trypanosoma cruzi trypanothione reductase were not sensitive to thiolation at physiological GSSG concentrations.
Collapse
|
17
|
Abstract
Like other actinomycetes Mycobacterium tuberculosis lacks glutathione and, consequently, the glutathione peroxidases that dominate the antioxidant defence of its mammalian hosts. The hydrogen peroxide metabolism of the pathogen has for long been recognised to depend on a heme-containing catalase/peroxidase. Clinical isolates lacking the catalase were virulent and proved to be resistant to the first line tuberculostatic isoniazid, because the enzyme is evidently required to activate this drug. The survival and virulence of such strains are attributed to the peroxiredoxin-type peroxidases alkyl hydroperoxide reductase (AhpC) and thioredoxin peroxidase (TPx). The most common AhpC reductant in bacteria, the disulfide reductase AhpF, is deleted in M. tuberculosis. Instead, AhpC can be reduced by AhpD, a CXXC-motif-containing protein, or by one of the mycobacterial thioredoxins, TrxC. TPx is reduced by thioredoxins B and C. Mycobacteria contain three more peroxiredoxins, the 1-Cys-Prx AhpE, Bcp and BcpB, whose function and reductants are still unknown.
Collapse
Affiliation(s)
- Timo Jaeger
- MOLISA GmbH, Molecular Links Sachsen-Anhalt, Magdeburg, Germany
| |
Collapse
|
18
|
Bao R, Chen YX, Zhang Y, Zhou CZ. Expression, purification, crystallization and preliminary X-ray diffraction analysis of mitochondrial thioredoxin Trx3 from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1161-3. [PMID: 17077505 PMCID: PMC2225218 DOI: 10.1107/s1744309106041467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 10/08/2006] [Indexed: 11/10/2022]
Abstract
There are three thioredoxin isoforms in the yeast Saccharomyces cerevisiae: two cytosolic/nuclear thioredoxins, Trx1 and Trx2, and one mitochondrial thioredoxin, Trx3. In the present work, S. cerevisiae Trx3 overexpressed in Escherichia coli was purified and crystallized. The Trx3 crystals were obtained by the hanging-drop vapour-diffusion method. A data set diffracting to 2.0 A resolution was collected from a single crystal. The crystal belongs to space group P3(1), with unit-cell parameters a = b = 49.57, c = 94.55 A, alpha = beta = 90, gamma = 120 degrees. The asymmetric unit is assumed to contain two subunits of Trx3, with a V(M) value of 2.62 A(3) Da(-1) and a solvent content of 53%.
Collapse
Affiliation(s)
- Rui Bao
- Institute of Protein Research, Tongji University, Shanghai 200092, People’s Republic of China
| | - Yu-xing Chen
- Institute of Protein Research, Tongji University, Shanghai 200092, People’s Republic of China
| | - Yaru Zhang
- Institute of Protein Research, Tongji University, Shanghai 200092, People’s Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| |
Collapse
|
19
|
Bao R, Chen Y, Tang YJ, Janin J, Zhou CZ. Crystal structure of the yeast cytoplasmic thioredoxin Trx2. Proteins 2006; 66:246-9. [PMID: 17044062 DOI: 10.1002/prot.21194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rui Bao
- Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China
| | | | | | | | | |
Collapse
|
20
|
Zhang X, Hu Y, Guo X, Lescop E, Li Y, Xia B, Jin C. The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity. J Biol Chem 2006; 281:8296-304. [PMID: 16418167 DOI: 10.1074/jbc.m512015200] [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: 11/06/2022] Open
Abstract
The Bacillus subtilis YkuV responds to environmental oxidative stress and plays an important role for the bacteria to adapt to the environment. Bioinformatic analysis suggests that YkuV is a homolog of membrane-anchored proteins and belongs to the thioredoxin-like protein superfamily containing the typical Cys-Xaa-Xaa-Cys active motif. However, the biological function of this protein remains unknown thus far. In order to elucidate the biological function, we have determined the solution structures of both the oxidized and reduced forms of B. subtilis YkuV by NMR spectroscopy and performed biochemical studies. Our results demonstrated that the reduced YkuV has a low midpoint redox potential, allowing it to reduce a variety of protein substrates. The overall structures of both oxidized and reduced forms are similar, with a typical thioredoxin-like fold. However, significant conformational changes in the Cys-Xaa-Xaa-Cys active motif of the tertiary structures are observed between the two forms. In addition, the backbone dynamics provide further insights in understanding the strong redox potential of the reduced YkuV. Furthermore, we demonstrated that YkuV is able to reduce different protein substrates in vitro. Together, our results clearly established that YkuV may function as a general thiol:disulfide oxidoreductase, which acts as an alternative for thioredoxin or thioredoxin reductase to maintain the reducing environment in the cell cytoplasm.
Collapse
Affiliation(s)
- Xinxin Zhang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | | | | | | | | | | | | |
Collapse
|
21
|
Piattoni CV, Blancato VS, Miglietta H, Iglesias AA, Guerrero SA. On the occurrence of thioredoxin in Trypanosoma cruzi. Acta Trop 2006; 97:151-60. [PMID: 16310752 DOI: 10.1016/j.actatropica.2005.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 09/27/2005] [Accepted: 10/21/2005] [Indexed: 11/26/2022]
Abstract
The full coding sequence for thioredoxin from Trypanosoma cruzi (TcTRX) strain Tulahuen O has been cloned into the pRSETA vector. The protein was expressed in Escherichia coli with an N-terminal extension of six histidine residues for purification through metal ion chromatography. The biological activity of recombinant TcTRX was proved utilizing the insulin reduction assay. Amino acid sequence alignment indicates a high identity of TcTRX with thioredoxins from different sources. Immunocytochemistry assays showed that TcTRX is present in epimastigote forms of T. cruzi, thus, indicating that the gene is expressed in vivo, rather than being a pseudogene. The in vivo occurrence of TcTRX points out the necessity of considering this protein as a molecular component of the redox metabolism in trypanosomatids.
Collapse
Affiliation(s)
- Claudia V Piattoni
- Laboratorio de Bioquímica Microbiana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Paraje El Pozo, CC 242, S 3000ZAA Santa Fe, Argentina
| | | | | | | | | |
Collapse
|
22
|
Kato M, Yamamoto H, Okamura TA, Maoka N, Masui R, Kuramitsu S, Ueyama N. Inhibition of Thermus thermophilus HB8 thioredoxin activity by platinum(II). Dalton Trans 2005:1023-6. [PMID: 15739003 DOI: 10.1039/b419119f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 1:1 thioredoxin-Pt(bpy) complex was prepared by adding [Pt(bpy)(en)]Cl(2)(bpy = 2,2'-bipyridine, en = ethylenediamine) to Thermus thermophilus HB8 thioredoxin in pH 8 phosphate buffer. Matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) and UV spectra of indicate the formation of Pt(bpy)(cys-Ala-Pro-cys-containing peptide fragment). These findings suggest that the Pt(bpy)(2+) unit binds to the active site of thioredoxin. The thioredoxin-platinum complex has no catalytic activity for the reduction of glutathione disulfide in the presence of NADPH and thioredoxin reductase, so that the platinum complex functions as an inhibitor.
Collapse
Affiliation(s)
- Masahiro Kato
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | | | | | | | | | | | | |
Collapse
|
23
|
Wahl MC, Irmler A, Hecker B, Schirmer RH, Becker K. Comparative structural analysis of oxidized and reduced thioredoxin from Drosophila melanogaster. J Mol Biol 2004; 345:1119-30. [PMID: 15644209 DOI: 10.1016/j.jmb.2004.11.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 11/01/2004] [Accepted: 11/02/2004] [Indexed: 10/26/2022]
Abstract
Thioredoxins (Trx) participate in essential antioxidant and redox-regulatory processes via a pair of conserved cysteine residues. In dipteran insects like Drosophila and Anopheles, which lack a genuine glutathione reductase (GR), thioredoxins fuel the glutathione system with reducing equivalents. Thus, characterizing Trxs from these organisms contributes to our understanding of redox control in GR-free systems and provides information on novel targets for insect control. Cytosolic Trx of Drosophila melanogaster (DmTrx) is the first thioredoxin that was crystallized for X-ray diffraction analysis in the reduced and in the oxidized form. Comparison of the resulting structures shows rearrangements in the active-site regions. Formation of the C32-C35 disulfide bridge leads to a rotation of the side-chain of C32 away from C35 in the reduced form. This is similar to the situation in human Trx and Trx m from spinach chloroplasts but differs from Escherichia coli Trx, where it is C35 that moves upon change of the redox state. In all four crystal forms that were analysed, DmTrx molecules are engaged in a non-covalent dimer interaction. However, as demonstrated by gel-filtration analyses, DmTrx does not dimerize under quasi in vivo conditions and there is no redox control of a putative monomer/dimer equilibrium. The dimer dissociation constants K(d) were found to be 2.2mM for reduced DmTrx and above 10mM for oxidized DmTrx as well as for the protein in the presence of reduced glutathione. In human Trx, oxidative dimerization has been demonstrated in vitro. Therefore, this finding may indicate a difference in redox control of GR-free and GR-containing organisms.
Collapse
Affiliation(s)
- Markus C Wahl
- Max-Planck-Institut für Biophysikalische Chemie, Arbeitsgruppe Röntgenkristallographie, Am Fassberg 11, D-37077 Göttingen, Germany.
| | | | | | | | | |
Collapse
|