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Arai S, Shibazaki C, Shimizu R, Adachi M, Ishibashi M, Tokunaga H, Tokunaga M. Catalytic mechanism and evolutionary characteristics of thioredoxin from Halobacterium salinarum NRC-1. Acta Crystallogr D Struct Biol 2020; 76:73-84. [PMID: 31909745 DOI: 10.1107/s2059798319015894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/25/2019] [Indexed: 01/08/2023] Open
Abstract
Thioredoxin (TRX) is an important antioxidant against oxidative stress. TRX from the extremely halophilic archaeon Halobacterium salinarum NRC-1 (HsTRX-A), which has the highest acidic residue content [(Asp + Glu)/(Arg + Lys + His) = 9.0] among known TRXs, was chosen to elucidate the catalytic mechanism and evolutionary characteristics associated with haloadaptation. X-ray crystallographic analysis revealed that the main-chain structure of HsTRX-A is similar to those of homologous TRXs; for example, the root-mean-square deviations on Cα atoms were <2.3 Å for extant archaeal TRXs and <1.5 Å for resurrected Precambrian TRXs. A unique water network was located near the active-site residues (Cys45 and Cys48) in HsTRX-A, which may enhance the proton transfer required for the reduction of substrates under a high-salt environment. The high density of negative charges on the molecular surface (3.6 × 10-3 e Å-2) should improve the solubility and haloadaptivity. Moreover, circular-dichroism measurements and enzymatic assays using a mutant HsTRX-A with deletion of the long flexible N-terminal region (Ala2-Pro17) revealed that Ala2-Pro17 improves the structural stability and the enzymatic activity of HsTRX-A under high-salt environments (>2 M NaCl). The elongation of the N-terminal region in HsTRX-A accompanies the increased hydrophilicity and acidic residue content but does not affect the structure of the active site. These observations offer insights into molecular evolution for haloadaptation and potential applications in halophilic protein-related biotechnology.
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Affiliation(s)
- Shigeki Arai
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Chie Shibazaki
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Rumi Shimizu
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Motoyasu Adachi
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Matsujiro Ishibashi
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Hiroko Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Esposito L, Ruggiero A, Masullo M, Ruocco MR, Lamberti A, Arcari P, Zagari A, Vitagliano L. Crystallographic and spectroscopic characterizations of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability. J Struct Biol 2012; 177:506-12. [DOI: 10.1016/j.jsb.2011.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/20/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
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Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A, Sanchez-Ruiz JM, Gaucher EA, Fernandez JM. Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nat Struct Mol Biol 2011; 18:592-6. [PMID: 21460845 PMCID: PMC3087858 DOI: 10.1038/nsmb.2020] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 01/24/2011] [Indexed: 01/01/2023]
Abstract
A journey back in time is possible at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx), dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32° C more stable than modern enzymes and the oldest show significantly higher activity than extant ones at pH 5. We probed their mechanisms of reduction using single-molecule force spectroscopy. From the force-dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs utilize chemical mechanisms of reduction similar to those of modern enzymes. While Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over a 4 Gyr time span to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth.
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Affiliation(s)
- Raul Perez-Jimenez
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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Ruggiero A, Masullo M, Marasco D, Ruocco MR, Grimaldi P, Arcari P, Zagari A, Vitagliano L. The dimeric structure of Sulfolobus solfataricus
thioredoxin A2 and the basis of its thermostability. Proteins 2009; 77:1004-8. [DOI: 10.1002/prot.22559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ruggiero A, Lanzotti MA, Ruocco MR, Grimaldi P, Marasco D, Arcari P, Masullo M, Zagari A, Vitagliano L. Crystallization and preliminary X-ray crystallographic analysis of two dimeric hyperthermostable thioredoxins isolated from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:604-7. [PMID: 19478442 PMCID: PMC2688421 DOI: 10.1107/s1744309109016200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 04/29/2009] [Indexed: 11/10/2022]
Abstract
The thioredoxin system of the archaeon Sulfolobus solfataricus involves a number of different proteins: two thioredoxin reductases (SsTrxRB2 and SsTrxRB3), two distinct thioredoxins (SsTrxA1 and SsTrxA2) and a disulfide oxidoreductase (SsPDO). Here, the crystallization and preliminary crystallographic analyses of SsTrxA1 and SsTrxA2, two dimeric proteins endowed with extraordinary thermal stability, are reported. In addition to the functional thioredoxin domain, both SsTrxA1 and SsTrxA2 present an extra N-terminal fragment of approximately 30 residues. Although crystallization trials have been conducted on both forms of the proteins, crystals that were suitable for X-ray crystallographic analyses have only been obtained for their truncated variants. The crystals of SsTrxA2 belonged to space group P2, with unit-cell parameters a = 28.27, b = 27.88, c = 62.06 A, beta = 92.34 degrees , and diffracted to 1.83 A resolution, whereas the crystals of SsTrxA1 belonged to space group P2(1), with unit-cell parameters a = 51.76, b = 75.09, c = 55.35 A, beta = 112.64 degrees , and diffracted to 1.90 A resolution. The structures of the two proteins have been solved by molecular replacement.
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Affiliation(s)
- Alessia Ruggiero
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Maria Angela Lanzotti
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Maria Rosaria Ruocco
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
| | - Pasquale Grimaldi
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- Dipartimento di Scienze Farmacobiologiche, Università degli Studi ‘Magna Graecia’ di Catanzaro, Roccelletta di Borgia, I-88021 Catanzaro, Italy
| | - Daniela Marasco
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Paolo Arcari
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate s.c.a.r.l., Via Comunale Margherita 482, I-80145 Napoli, Italy
| | - Mariorosario Masullo
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- Dipartimento di Scienze Farmacobiologiche, Università degli Studi ‘Magna Graecia’ di Catanzaro, Roccelletta di Borgia, I-88021 Catanzaro, Italy
| | - Adriana Zagari
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
- CEINGE Biotecnologie Avanzate s.c.a.r.l., Via Comunale Margherita 482, I-80145 Napoli, Italy
- CNISM Università degli Studi di Napoli Federico II, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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Duan LL, Mei Y, Zhang QG, Zhang JZH. Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. J Chem Phys 2009; 130:115102. [PMID: 19317568 DOI: 10.1063/1.3089723] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in solution using a recently developed molecular fractionation with conjugate caps-Poisson-Boltzmann (MFCC-PB) approach and therefore includes electronic polarization effect of the protein at native structure. MD simulations are performed for a number of benchmark proteins containing helix and/or beta sheet secondary structures. The computational result shows that occupancy percentage of hydrogen bonds averaged over simulation time, as well as the number of hydrogen bonds as a function of simulation time, is consistently higher under PPC than AMBER charge. In particular, some intra-protein hydrogen bonds are found broken during MD simulation using AMBER charge but they are stable using PPC. The breaking of some intra-protein hydrogen bonds in AMBER simulation is responsible for deformation or denaturing of some local structures of proteins during MD simulation. The current study provides strong evidence that hydrogen bonding is dynamically more stable using PPC than AMBER charge, highlighting the stabilizing effect of electronic polarization on protein structure.
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Affiliation(s)
- Li L Duan
- Department of Physics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
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