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Jesus CSH, Almeida ZL, Vaz DC, Faria TQ, Brito RMM. A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation. Int J Mol Sci 2016; 17:E1428. [PMID: 27589730 PMCID: PMC5037707 DOI: 10.3390/ijms17091428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 02/04/2023] Open
Abstract
Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer's and Parkinson's. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo.
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Affiliation(s)
- Catarina S H Jesus
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, Coimbra 3004-535, Portugal.
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
| | - Zaida L Almeida
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, Coimbra 3004-535, Portugal.
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
| | - Daniela C Vaz
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, Coimbra 3004-535, Portugal.
- Health Research Unit, School of Health Sciences, Leiria 2411-901, Portugal.
| | - Tiago Q Faria
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, Coimbra 3004-535, Portugal.
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
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Mitsuya D, Tanaka SI, Matsumura H, Urano N, Takano K, Ogasahara K, Takehira M, Yutani K, Ishida M. Strategy for cold adaptation of the tryptophan synthase α subunit from the psychrophile Shewanella frigidimarina K14-2: crystal structure and physicochemical properties. J Biochem 2013; 155:73-82. [PMID: 24163283 DOI: 10.1093/jb/mvt098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the molecular basis of cold adaptation of enzymes, we determined the crystal structure of the tryptophan synthase α subunit (SfTSA) from the psychrophile Shewanella frigidimarina K14-2 by X-ray analysis at 2.6-Å resolution and also examined its physicochemical properties. SfTSA was found to have the following characteristics: (i) The stabilities against heat and denaturant of SfTSA were lower than those of an α subunit (EcTSA) from Escherichia coli. This lower equilibrium stability originated from both a faster unfolding rate and a slower refolding rate; (ii) the heat denaturation of SfTSA was completely reversible at pH 7.0 and the solubility of denatured SfTSA was higher than that of denatured EcTSA. The two-state transition of denaturation for SfTSA was highly cooperative, whereas the denaturation process of EcTSA was considerably more complex and (iii) the global structure of SfTSA was quite similar to those of α subunits from other species. Relative to those other proteins, SfTSA exhibited an increase in cavity volume and a decrease in the number of ion pairs. SfTSA also lacks a hydrogen bond near loop B, related to catalytic function. These characteristics of SfTSA might provide the conformational flexibility required for catalytic activity at low temperatures.
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Affiliation(s)
- Daisuke Mitsuya
- Department of Ocean Sciences, Graduate school of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato, Tokyo 108-8477; Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871; Department of Life Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako-gun, Hyogo 678-1297; and RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148
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Roche J, Dellarole M, Caro JA, Norberto DR, Garcia AE, Garcia-Moreno B, Roumestand C, Royer CA. Effect of Internal Cavities on Folding Rates and Routes Revealed by Real-Time Pressure-Jump NMR Spectroscopy. J Am Chem Soc 2013; 135:14610-8. [DOI: 10.1021/ja406682e] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julien Roche
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - Mariano Dellarole
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - José A. Caro
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Douglas R. Norberto
- Department
of Biochemistry, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Angel E. Garcia
- Department
of Physics and Applied Physics and Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Bertrand Garcia-Moreno
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Christian Roumestand
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - Catherine A. Royer
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
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Okada J, Koga Y, Takano K, Kanaya S. Slow unfolding pathway of hyperthermophilic Tk-RNase H2 examined by pulse proteolysis using the stable protease Tk-subtilisin. Biochemistry 2012; 51:9178-91. [PMID: 23106363 DOI: 10.1021/bi300973n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The unfolding speed of some hyperthermophilic proteins is significantly slower than those of their mesostable homologues. Ribonuclease H2 from the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-RNase H2) is stabilized by its remarkably slow unfolding rate. In this work, we examined the slow unfolding pathway of Tk-RNase H2 by pulse proteolysis using a superstable subtilisin-like serine protease from T. kodakarensis (Tk-subtilisin). Tk-subtilisin has enzymatic activity in highly concentrated guanidine hydrochloride (GdnHCl), in which Tk-RNase H2 unfolds slowly. The native state of Tk-RNase H2 was completely resistant to Tk-subtilisin, whereas the unfolded state (induced by 4 M GdnHCl) was degraded by Tk-subtilisin. Degradation products of Tk-RNase H2 created from pulse proteolysis during its unfolding were detected by tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis. We identified the cleavage sites in Tk-RNase H2 by N-terminal sequencing and mass spectrometry and constructed mimics of the unfolding intermediate of Tk-RNase H2 by protein engineering. The mimics were biophysically characterized. We found that the native state of Tk-RNase H2 (N-state) changed to the I(A)-state that was digested by Tk-subtilisin in the early stage of unfolding. In the slow unfolding pathway, the I(A)-state shifted to two intermediate forms, I(B)-state and I(C)-state. The I(B)-state was digested by Tk-subtilisin in the C-terminal region, but the I(C)-state was a Tk-subtilisin resistant form. These states gradually unfolded through the I(D)-state, in which the N-terminal region was digested. The results indicate that pulse proteolysis, by a superstable protease, was a suitable strategy and an effective tool for analyzing intermediate structures of proteins with slow unfolding properties. We also showed that the N-terminal region contributes to the slow unfolding of Tk-RNase H2, and the C-terminal region is important for folding and stability.
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Affiliation(s)
- Jun Okada
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Mizuguchi M, Takeuchi M, Ohki S, Nabeshima Y, Kouno T, Aizawa T, Demura M, Kawano K, Yutani K. Structural characterization of a trapped folding intermediate of pyrrolidone carboxyl peptidase from a hyperthermophile. Biochemistry 2012; 51:6089-96. [PMID: 22799522 DOI: 10.1021/bi300608e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The refolding of cysteine-free pyrrolidone carboxyl peptidase (PCP-0SH) from a hyperthermophile is unusually slow. PCP-0SH is trapped in the denatured (D1) state at 4 °C and pH 2.3, which is different from the highly denatured state in the presence of concentrated denaturant. In order to elucidate the mechanism of the unusually slow folding, we investigated the structure of the D1 state using NMR techniques with amino acid selectively labeled PCP-0SH. The HSQC spectrum of the D1 state showed that most of the resonances arising from the 114-208 residues are broadened, indicating that conformations of the 114-208 residues are in intermediate exchange on the microsecond to millisecond time scale. Paramagnetic relaxation enhancement data indicated the lack of long-range interactions between the 1-113 and the 114-208 segments in the D1 state. Furthermore, proline scanning mutagenesis showed that the 114-208 segment in the D1 state forms a loosely packed hydrophobic core composed of α4- and α6-helices. From these findings, we conclude that the 114-208 segment of PCP-0SH folds into a stable compact structure with non-native helix-helix association in the D1 state. Therefore, in the folding process from the D1 state to the native state, the α4- and α6-helices become separated and the central β-sheet is folded between these helices. That is, the non-native interaction between the α4- and α6-helices may be responsible for the unusually slow folding of PCP-0SH.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630, Sugitani, Toyama 930-0194, Japan.
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Okada J, Okamoto T, Mukaiyama A, Tadokoro T, You DJ, Chon H, Koga Y, Takano K, Kanaya S. Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins. BMC Evol Biol 2010; 10:207. [PMID: 20615256 PMCID: PMC2927913 DOI: 10.1186/1471-2148-10-207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 07/09/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. Ribonuclease HII from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-RNase HII) is stabilized by its remarkably slow unfolding rate, whereas RNase HI from the thermophilic bacterium Thermus thermophilus (Tt-RNase HI) unfolds rapidly, comparable with to that of RNase HI from Escherichia coli (Ec-RNase HI). RESULTS To clarify whether the difference in the unfolding rate is due to differences in the types of RNase H or differences in proteins from archaea and bacteria, we examined the equilibrium stability and unfolding reaction of RNases HII from the hyperthermophilic bacteria Thermotoga maritima (Tm-RNase HII) and Aquifex aeolicus (Aa-RNase HII) and RNase HI from the hyperthermophilic archaeon Sulfolobus tokodaii (Sto-RNase HI). These proteins from hyperthermophiles are more stable than Ec-RNase HI over all the temperature ranges examined. The observed unfolding speeds of all hyperstable proteins at the different denaturant concentrations studied are much lower than those of Ec-RNase HI, which is in accordance with the familiar slow unfolding of hyperstable proteins. However, the unfolding rate constants of these RNases H in water are dispersed, and the unfolding rate constant of thermophilic archaeal proteins is lower than that of thermophilic bacterial proteins. CONCLUSIONS These results suggest that the nature of slow unfolding of thermophilic proteins is determined by the evolutionary history of the organisms involved. The unfolding rate constants in water are related to the amount of buried hydrophobic residues in the tertiary structure.
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Affiliation(s)
- Jun Okada
- Department of Material and Life Science, Osaka University, Suita, Japan
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Mukaiyama A, Takano K. Slow unfolding of monomeric proteins from hyperthermophiles with reversible unfolding. Int J Mol Sci 2009; 10:1369-1385. [PMID: 19399254 PMCID: PMC2672035 DOI: 10.3390/ijms10031369] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 03/19/2009] [Accepted: 03/23/2009] [Indexed: 01/22/2023] Open
Abstract
Based on the differences in their optimal growth temperatures microorganisms can be classified into psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Proteins from hyperthermophiles generally exhibit greater stability than those from other organisms. In this review, we collect data about the stability and folding of monomeric proteins from hyperthermophilies with reversible unfolding, from the equilibrium and kinetic aspects. The results indicate that slow unfolding is a general strategy by which proteins from hyperthermophiles adapt to higher temperatures. Hydrophobic interaction is one of the factors in the molecular mechanism of the slow unfolding of proteins from hyperthermophiles.
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Affiliation(s)
- Atsushi Mukaiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; E-Mail:
| | - Kazufumi Takano
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST, JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +81-6-6879-4157; Fax: +81-6-6879-4157
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Takano K, Higashi R, Okada J, Mukaiyama A, Tadokoro T, Koga Y, Kanaya S. Proline effect on the thermostability and slow unfolding of a hyperthermophilic protein. J Biochem 2008; 145:79-85. [PMID: 18977771 DOI: 10.1093/jb/mvn144] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribonuclease HII from hyperthermophile Thermococcus kodakaraensis (Tk-RNase HII) is a robust monomeric protein under kinetic control, which possesses some proline residues at the N-terminal of alpha-helices. Proline residue at the N-terminal of an alpha-helix is thought to stabilize a protein. In this work, the thermostability and folding kinetics of Tk-RNase HII were measured for mutant proteins in which a proline residue is introduced (Xaa to Pro) or removed (Pro to Ala) at the N-terminal of alpha-helices. In the folding experiments, the mutant proteins examined exhibit little influence on the remarkably slow unfolding of Tk-RNase HII. In contrast, E111P and K199P exhibit some thermostabilization, whereas P46A, P70A and P174A have some thermodestabilization. E111P/K199P and P46A/P70A double mutations cause cumulative changes in stability. We conclude that the proline effect on protein thermostability is observed in a hyperthermophilic protein, but each proline residue at the N-terminal of an alpha-helix slightly contributes to the thermostability. The present results also mean that even a natural hyperthermophilic protein can acquire improved thermostability.
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Affiliation(s)
- Kazufumi Takano
- Department of Material and Life Science, Osaka University, Yamadaoka, Suita 565-0871, Japan.
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Umezaki T, Iimura S, Noda Y, Segawa SI, Yutani K. The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions: Difference in helix propensity of two synthetic peptides with single amino acid substitution. Proteins 2008; 71:737-42. [DOI: 10.1002/prot.21742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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