1
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Murata T, Ito G, Utsunomiya-Tate N. Site-specific amino acid D-isomerization of Tau R2 and R3 peptides changes the fibril morphology, resulting in attenuation of Tau aggregation inhibitor potency. Biochem Biophys Res Commun 2023; 654:18-25. [PMID: 36878036 DOI: 10.1016/j.bbrc.2023.02.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
Tau, a microtubule-binding protein, is a major component of neurofibrillary tangles in the brains of Alzheimer's disease patients. Tau aggregation following fibril formation induces Alzheimer's disease pathogenesis. The accumulation of D-isomerized amino acids in proteins that occurs in several tissues with aging is thought to be implicated in age-related diseases. D-isomerized Asp accumulation has also been found in Tau in neurofibrillary tangles. We previously demonstrated the effects of D-isomerization of Asp within microtubule-binding repeat peptides of Tau, Tau R2, and R3 on the rates of structural transition and fibril formation. Here, we investigated the potency of Tau aggregation inhibitors on fibril formation of wild-type Tau R2 and R3 peptides and D-isomerized Asp-containing Tau R2 and R3 peptides. D-isomerization of Asp within Tau R2 and R3 peptides attenuated the potency of inhibitors. We next investigated the fibril morphology of D-isomerized Asp-containing Tau R2 and R3 peptides by electron microscopy. D-isomerized Asp-containing Tau R2 and R3 fibrils showed significantly different fibril morphology from that of wild-type peptides. Our results indicate that D-isomerization of Asp within Tau R2 and R3 peptides affects fibril morphology, resulting in attenuation of the potency of Tau aggregation inhibitors.
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Affiliation(s)
- Takuya Murata
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
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2
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Sato W, Watanabe-Takahashi M, Murata T, Utsunomiya-Tate N, Motoyama J, Anzai M, Ishihara S, Nishioka N, Uchiyama H, Togashi J, Nishihara S, Kawasaki K, Saito T, Saido TC, Funamoto S, Nishikawa K. A tailored tetravalent peptide displays dual functions to inhibit amyloid β production and aggregation. Commun Biol 2023; 6:383. [PMID: 37031306 PMCID: PMC10082830 DOI: 10.1038/s42003-023-04771-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Inhibition of amyloid-β peptide (Aβ) accumulation in the brain is a promising approach for treatment of Alzheimer's disease (AD). Aβ is produced by β-secretase and γ-secretase in endosomes via sequential proteolysis of amyloid precursor protein (APP). Aβ and APP have a common feature to readily cluster to form multimers. Here, using multivalent peptide library screens, we identified a tetravalent peptide, LME-tet, which binds APP and Aβ via multivalent interactions. In cells, LME-tet-bound APP in the plasma membrane is transported to endosomes, blocking Aβ production through specific inhibition of β-cleavage, but not γ-cleavage. LME-tet further suppresses Aβ aggregation by blocking formation of the β-sheet conformation. Inhibitory effects are not observed with a monomeric peptide, emphasizing the significance of multivalent interactions for mediating these activities. Critically, LME-tet efficiently reduces Aβ levels in the brain of AD model mice, suggesting it may hold promise for treatment of AD.
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Affiliation(s)
- Waka Sato
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Miho Watanabe-Takahashi
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Takuya Murata
- Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | | | - Jun Motoyama
- Laboratory of Developmental Neurobiology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan
| | - Masataka Anzai
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Seiko Ishihara
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Nanako Nishioka
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Hina Uchiyama
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Juri Togashi
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Saeka Nishihara
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, Japan
| | - Kiyoshi Kawasaki
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, Japan
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Aichi, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, Riken Center For Brain Science, Saitama, Japan
| | - Satoru Funamoto
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.
| | - Kiyotaka Nishikawa
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.
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3
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Ozaki M, Shimotsuma M, Kuranaga T, Kakeya H, Hirose T. Separation of amyloid β fragment peptides with racemised and isomerised aspartic acid residues using an original chiral resolution labeling reagent. Analyst 2023; 148:1209-1213. [PMID: 36779274 DOI: 10.1039/d2an01885c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
We developed a system to separate and identify racemised and isomerised aspartic acid (Asp) residues in amyloid β (Aβ) by labeling with an original chiral resolution labeling reagent, 1-fluoro-2,4-dinitrophenyl-5-D-leucine-N,N-dimethylethylenediamine-amide (D-FDLDA). The racemised and isomerised Asp residues labeled with D-FDLDA in Aβ fragments generated by digesting with trypsin and endoproteinase Glu-C were separated and identified by liquid chromatography-mass spectrometry (LC-MS) under simple gradient conditions. Furthermore, the labeled Aβ fragments did not aggregate and remained stable at least for 1 week at 4 °C.
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Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Kyoto 606-8501, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Kyoto 606-8501, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
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4
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Wang J, Prajapati JD, Gao F, Ying YL, Kleinekathöfer U, Winterhalter M, Long YT. Identification of Single Amino Acid Chiral and Positional Isomers Using an Electrostatically Asymmetric Nanopore. J Am Chem Soc 2022; 144:15072-15078. [PMID: 35953064 PMCID: PMC9413207 DOI: 10.1021/jacs.2c03923] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chirality is essential in nearly all biological organizations and chemical reactions but is rarely considered due to technical limitations in identifying L/D isomerization. Using OmpF, a membrane channel from Escherichia coli with an electrostatically asymmetric constriction zone, allows discriminating chiral amino acids in a single peptide. The heterogeneous distribution of charged residues in OmpF causes a strong lateral electrostatic field at the constriction. This laterally asymmetric constriction zone forces the sidechains of the peptides to specific orientations within OmpF, causing distinct ionic current fluctuations. Using statistical analysis of the respective ionic current variations allows distinguishing the presence and position of a single amino acid with different chiralities. To explore potential applications, the disease-related peptide β-Amyloid and its d-Asp1 isoform and a mixture of the icatibant peptide drug (HOE 140) and its d-Ser7 mutant have been discriminated. Both chiral isomers were not applicable to be distinguished by mass spectroscopy approaches. These findings highlight a novel sensing mechanism for identifying single amino acids in single peptides and even for achieving single-molecule protein sequencing.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | | | - Fan Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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5
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Zhou Z, Gu YQ, Wang HX. Artificial Chiral Interfaces against Amyloid-β Peptide Aggregation: Research Progress and Challenges. ACS Chem Neurosci 2021; 12:4236-4248. [PMID: 34724384 DOI: 10.1021/acschemneuro.1c00544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by an imbalance between the production and clearance of amyloid-β (Aβ) species. AD not only influences the life quality of the patients but also heavily burdens the families and society. Therefore, it is an urgent mission to research and develop some new anti-amyloid aggregation drugs. In recent years, there were research and development of engineered nanostructures as Aβ amyloid inhibitors have attracted extensive attention and become a new frontier in nanomedicine. The effects of nanostructural surface properties (e.g., morphology, charge, hydrophobicity) on inhibition of Aβ aggregation are modulated by adsorbed Aβ peptides. Nevertheless, chirality has been seldom considered in recognition of Aβ species and modulation of Aβ aggregations. Moreover, a more relevant question for chiral inhibitors is little known about the molecular mechanism of how to interface chiral effects Aβ targeting recognition and effective mitigation of amyloidosis at the molecular level. Herein, we review recent experimental and theoretical results acquired in the specific areas of artificial chiral nanostructure inhibitors. This article will be essential to provide a microlevel insight into the effects of chiral nanointerfaces on amyloidosis processes as well as the development of chiral inhibitor drugs against Aβ fibrillation.
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Affiliation(s)
- Zhe Zhou
- Department of Neurology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - You-Quan Gu
- Department of Neurology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Hang-Xing Wang
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, China
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6
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Wang X, Wang C, Chu H, Qin H, Wang D, Xu F, Ai X, Quan C, Li G, Qing G. Molecular chirality mediated amyloid formation on phospholipid surfaces. Chem Sci 2020; 11:7369-7378. [PMID: 34123018 PMCID: PMC8159450 DOI: 10.1039/d0sc02212h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
One of the neuropathological features of Alzheimer's disease (AD) is the misfolding of amyloid-β to form amyloid aggregates, a process highly associated with biological membranes. However, how molecular chirality affects the amyloid formation on phospholipid surfaces has seldom been reported. Here, l- and d-aspartic acid-modified 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (l-/d-Asp–DPPE) is synthesized to construct chiral phospholipid bilayers. We discover that the l-Asp–DPPE liposomes slightly inhibit the Aβ(1–40) nucleation process but cannot affect the oligomer elongation process. By contrast, the d-Asp–DPPE liposomes strongly inhibit both nucleation and elongation of the peptide. Notably, l- and d-Asp–DPPE liposomes not only have good biocompatibility but can also rescue Aβ(1–40)-aggregation induced cytotoxicity with significant chiral discrimination, in which the cell viability is higher in the presence of d-Asp–DPPE liposomes. Mechanism analysis and molecular dynamics simulation clearly demonstrate that differential electrostatic interactions of Lys16 in Aβ(1–40) with l- or d-Asp on the phospholipid contribute to the remarkable chiral discrimination. This study provides a deeper understanding of the crucial amyloidosis process from the perspective of the chiral interface and reveals that the convergence of d-amino acids with the liposomes might be a feasible route for AD prevention. A remarkable inhibition effect and chiral discrimination are observed when the amyloid peptide aggregates on chiral phospholipid surfaces.![]()
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology 122 Luoshi Road Wuhan 430070 P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology Tianjin 300457 P. R. China
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Feifei Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Xuanjun Ai
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University Dalian 116600 P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
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7
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Oda A, Nakayoshi T, Kato K, Fukuyoshi S, Kurimoto E. Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality. Sci Rep 2019; 9:11594. [PMID: 31406272 PMCID: PMC6690948 DOI: 10.1038/s41598-019-48134-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Primitive proteins are likely to have been constructed from non-enzymatically generated amino acids, due to the weak enzymatic activities of primitive biomolecules such as ribozymes. On the other hand, almost all present proteins are constructed only from L-amino acids. Therefore, there must have been a mechanism early in the origins of life that selected for one of the optical isomers of amino acids. In this study, we used molecular dynamics simulations to predict the three-dimensional structures of the putative primitive proteins constructed only from glycine, alanine, aspartic acid, and valine ([GADV]-peptides). The [GADV]-peptides were generated computationally at random from L-amino acids (L-[GADV]-peptides) and from both L- and D-amino acids (DL-[GADV]-peptides). The results indicate that the tendency of secondary structure formation for L-[GADV]-peptides was larger than that for DL-[GADV]-peptides, and L-[GADV]-peptides were more rigid than DL-[GADV]-peptides. These results suggest that the proteins with rigid structure motifs were more prone to have been generated in a primordial soup that included only L-amino acids than a the soup including racemic amino acids. The tendency of the rigid structure motif formation may have played a role in selecting for the homochirality that dominates life on Earth today.
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Affiliation(s)
- Akifumi Oda
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan. .,Osaka University, Institute for Protein Research, Suita, 565-0871, Japan. .,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan.
| | - Tomoki Nakayoshi
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Koichi Kato
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kinjo Gakuin University, Faculty of Pharmacy, Nagoya, 463-8521, Japan
| | - Shuichi Fukuyoshi
- Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Eiji Kurimoto
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan
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8
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Effect of site-specific amino acid D-isomerization on β-sheet transition and fibril formation profiles of Tau microtubule-binding repeat peptides. Biochem Biophys Res Commun 2019; 508:184-190. [PMID: 30471859 DOI: 10.1016/j.bbrc.2018.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
d-amino acid-containing proteins have been found in several human tissues, and the spontaneous accumulation of d-amino acids in proteins is thought to be involved in age-dependent diseases including dementia. Tau, a microtubule-associated protein, is a major component of neurofibrillary tangles in Alzheimer's disease. Site-specific amino acid D-isomerization in Tau has been observed in the brains of patients with Alzheimer's disease. Here, we conducted amino acid D-isomerization at specific sites in microtubule-binding repeat peptides of Tau (Tau R2 and R3) and examined the effects on Tau structure and fibril formation. Our results demonstrate that amino acid D-isomerization in Tau R2 peptides decreased the rates of β-sheet transition and fibril formation compared with those of the wild-type peptide composed of all l-amino acids. In contrast, Tau R3 peptides that had undergone amino acid D-isomerization at either Asp314, Ser316, or Ser324 showed increased rates of β-sheet transition and fibril formation compared with those of the wild-type Tau R3 peptide.
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9
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Sadakane Y, Kawahara M. Implications of Metal Binding and Asparagine Deamidation for Amyloid Formation. Int J Mol Sci 2018; 19:ijms19082449. [PMID: 30126231 PMCID: PMC6121660 DOI: 10.3390/ijms19082449] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that amyloid formation, i.e., self-assembly of proteins and the resulting conformational changes, is linked with the pathogenesis of various neurodegenerative disorders such as Alzheimer’s disease, prion diseases, and Lewy body diseases. Among the factors that accelerate or inhibit oligomerization, we focus here on two non-genetic and common characteristics of many amyloidogenic proteins: metal binding and asparagine deamidation. Both reflect the aging process and occur in most amyloidogenic proteins. All of the amyloidogenic proteins, such as Alzheimer’s β-amyloid protein, prion protein, and α-synuclein, are metal-binding proteins and are involved in the regulation of metal homeostasis. It is widely accepted that these proteins are susceptible to non-enzymatic posttranslational modifications, and many asparagine residues of these proteins are deamidated. Moreover, these two factors can combine because asparagine residues can bind metals. We review the current understanding of these two common properties and their implications in the pathogenesis of these neurodegenerative diseases.
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Affiliation(s)
- Yutaka Sadakane
- Graduate School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan.
| | - Masahiro Kawahara
- Department of Bio-Analytical Chemistry, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo 202-8585, Japan.
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10
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Oda A, Nakayoshi T, Fukuyoshi S, Kurimoto E, Yamaotsu N, Hirono S, Takahashi O. Validation of molecular force field parameters for peptides including isomerized amino acids. Chirality 2018; 30:332-341. [PMID: 29393985 DOI: 10.1002/chir.22821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022]
Abstract
Recently, stereoinversions and isomerizations of amino acid residues in the proteins of living beings have been observed. Because isomerized amino acids cause structural changes and denaturation of proteins, isomerizations of amino acid residues are suspected to cause age-related diseases. In this study, AMBER molecular force field parameters were tested by using computationally generated nonapeptides and tripeptides including stereoinverted and/or isomerized amino acid residues. Energy calculations by using density functional theory were also performed for comparison. Although the force field parameters were developed by parameter fitting for l-α-amino acids, the accuracy of the computational results for d-amino acids and β-amino acids was comparable to those for l-α-amino acids. The conformational energies for tripeptides calculated by using density functional theory were reproduced more accurately than those for nonapeptides calculated by using the molecular mechanical force field. The evaluations were performed for the ff99SB, ff03, ff12SB, and the latest ff14SB force field parameters.
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Affiliation(s)
- Akifumi Oda
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan.,Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan
| | | | | | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
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11
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Nakayoshi T, Kato K, Fukuyoshi S, Takahashi O, Kurimoto E, Oda A. Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:759-766. [PMID: 29305913 DOI: 10.1016/j.bbapap.2017.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H2PO4-). We performed the study using B3LYP/6-31+G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H2PO4- catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0kcalmol-1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation.
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Affiliation(s)
- Tomoki Nakayoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan; Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan
| | - Koichi Kato
- Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan; Department of Pharmacy, Kinjo Gakuin University, 463-8521 Nagoya, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan
| | - Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan; Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan; Institute for Protein Research, Osaka University, Suita 565-0871, Japan.
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12
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Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins. Sci Rep 2017; 7:12433. [PMID: 28970487 PMCID: PMC5624888 DOI: 10.1038/s41598-017-10525-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the “downhill” folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide’s conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a “focused chiral mutant library” approach for the unbiased study of amyloid-forming IDPs.
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13
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Fukuyoshi S, Nakayoshi T, Takahashi O, Oda A. Theoretical study on keto–enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1232844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shuichi Fukuyoshi
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University , Sendai, Japan
| | - Akifumi Oda
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
- Institute for Protein Research, Osaka University , Osaka, Japan
- Faculty of Pharmacy, Meijo University , Nagoya, Japan
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Velmurugan P, Jonnalagadda RR, Unni Nair B. Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition. PLoS One 2015; 10:e0124398. [PMID: 25973613 PMCID: PMC4431724 DOI: 10.1371/journal.pone.0124398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/13/2015] [Indexed: 02/02/2023] Open
Abstract
Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of DAla in collagen like peptide (imino-poor region of type I collagen) on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD). Our findings suggest that, DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.
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Affiliation(s)
- Punitha Velmurugan
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
| | - Raghava Rao Jonnalagadda
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
- * E-mail:
| | - Balachandran Unni Nair
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
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15
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Inoue K, Hosaka D, Mochizuki N, Akatsu H, Tsutsumiuchi K, Hashizume Y, Matsukawa N, Yamamoto T, Toyo'oka T. Simultaneous determination of post-translational racemization and isomerization of N-terminal amyloid-β in Alzheimer's brain tissues by covalent chiral derivatized ultraperformance liquid chromatography tandem mass spectrometry. Anal Chem 2013; 86:797-804. [PMID: 24283798 DOI: 10.1021/ac403315h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Typical markers of protein aging are spontaneous post-translational modifications such as amino acid racemization (AAR) and amino acid isomerization (AAI) during the degradation of peptides. The post-translational AAR and AAI could significantly induce the density and localization of plaque deposition in brain tissues. Alzheimer's disease (AD) is reliably related to the formation and aggregation of amyloid-β peptide (Aβ) plaques in the human brain. No current analytical methods can simultaneously determine AAR and AAI during the degradation of Aβ from AD patients. We now report a covalent chiral derivatized ultraperformance liquid chromatography tandem mass spectrometry (CCD-UPLC-MS/MS) method for the determination of post-translational AAR and AAI of N-terminal Aβ (N-Aβ1-5) in human brain tissues. When subjected to tryptic N-Aβ1-5 from post-translationally modified natural Aβ in focal brain tissues by the CCD procedure, it was monitored at m/z 989.6→637.0/678.9 during electrospray collision-induced dissociation. These N-Aβ1-5 fragments with l-aspartic acid (l-Asp), d-Asp, l-isoAsp, and d-isoAsp could be separated using the UPLC system with a conventional reversed-phase column and mobile phase. The quantification of these peptides was determined using a stable isotope [(15)N]-labeled Aβ1-40 internal standard. The CCD-UPLC-MS/MS assay of potential N-Aβ1-5 allowed for the discovery of the present and ratio levels of these N-Aβ1-5 sequences with l-Asp, d-Asp, l-isoAsp, and d-isoAsp.
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Affiliation(s)
- Koichi Inoue
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka , Shizuoka, Japan
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16
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Sugiki T, Utsunomiya-Tate N. Site-specific aspartic acid isomerization regulates self-assembly and neurotoxicity of amyloid-β. Biochem Biophys Res Commun 2013. [DOI: 10.1016/j.bbrc.2013.10.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Sadakane Y, Fujii N, Nakagomi K. Determination of rate constants for β-linkage isomerization of three specific aspartyl residues in recombinant human αA-crystallin protein by reversed-phase HPLC. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3240-6. [DOI: 10.1016/j.jchromb.2011.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 02/20/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
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18
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Comparison of molecular dynamics simulation methods for amyloid β(1-42) monomers containing D-aspartic acid residues for predicting retention times in chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3337-43. [PMID: 21871847 DOI: 10.1016/j.jchromb.2011.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 08/01/2011] [Accepted: 08/09/2011] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations of amyloid β(1-42) containing D-aspartic acid residues were performed using several continuous solvent models to investigate the usefulness of simulation methods for D-amino acid-containing proteins and peptides. Normal molecular dynamics simulations and replica exchange molecular dynamics simulations, which are one of the generalized-ensemble algorithms, were performed. Because the β-structure contents of amyloid β(1-42) peptides obtained by replica exchange molecular dynamics simulations with Onufriev-Bashford-Case generalized Born implicit solvent were qualitatively consistent with experimental data, replica exchange molecular dynamics rather than other methods appeared to be more reasonable for calculations of amyloid β(1-42) containing D-aspartic acid residues. Computational results revealed that peptides with stereoinversion of Asp23 tend to form β-sheet structures by themselves, in contrast to the wild-type peptides that form β-sheet structures only after aggregation. These results are expected to be useful for computational investigations of proteins and peptides such as prediction of retention time of peptides and proteins containing D-aspartic acid residues.
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Takahashi O, Kobayashi K, Oda A. Modeling the enolization of succinimide derivatives, a key step of racemization of aspartic acid residues: importance of a two-H2O mechanism. Chem Biodivers 2010; 7:1349-56. [PMID: 20564551 DOI: 10.1002/cbdv.200900296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Racemization of aspartic acid residues in peptides and proteins is assumed to proceed via succinimide intermediates. An enolization of the succinimide intermediate is required for the racemization to occur. In this study, we modeled the enolization step by density-functional theory (DFT) calculations (B3LYP/6-31+G**), using two model compounds, N-methylsuccinimide (1) and its formylamino derivative 2. Three mechanisms were investigated for 1, i.e., the direct mechanism without active participation of H(2)O molecules, and one-H(2)O and two-H(2)O mechanisms, in which one or two H(2)O molecules actively participate in the reaction. We found that the two-H(2)O mechanism was the most favorable with an activation barrier of 37 kcal mol(-1). In the two-H(2)O mechanism, a concerted bond reorganization involving a triple H-atom transfer occurred in an eight-membered cyclic structure formed between the imide and two H(2)O molecules. For 2, we investigated only the two-H(2)O mechanism and found that the activation barrier was lowered to 31 kcal mol(-1) due to an H-bond between the CO O-atom of the formylamino group ('the neighboring residue') and one of the H(2)O molecules. Our results suggest that, in proteins, the Asp racemization is severely controlled by the accessibility of H(2)O molecules to the reaction site of the succinimide intermediate.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan.
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20
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Sadakane Y, Konoha K, Kawahara M, Nakagomi K. Quantification of Structural Alterations of L-Asp and L-Asn Residues in Peptides Related to Neuronal Diseases by Reversed-Phase High-Performance Liquid Chromatography. Chem Biodivers 2010; 7:1371-9. [DOI: 10.1002/cbdv.200900330] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Oda A, Kobayashi K, Takahashi O. Molecular-Dynamics Simulations for Amyloid β1-42 Monomer with D-Aspartic Acid Residues Using Continuous Solvent. Chem Biodivers 2010; 7:1357-63. [DOI: 10.1002/cbdv.200900299] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Alzheimer's disease and amyloid beta-peptide deposition in the brain: a matter of 'aging'? Biochem Soc Trans 2010; 38:539-44. [PMID: 20298218 DOI: 10.1042/bst0380539] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biomolecules can experience aging processes that limit their long-term functionality in organisms. Typical markers of protein aging are spontaneous chemical modifications, such as AAR (amino acid racemization) and AAI (amino acid isomerization), mainly involving aspartate and asparagine residues. Since these modifications may affect folding and turnover, they reduce protein functionality over time and may be linked to pathological conditions. The present mini-review describes evidence of AAR and AAI involvement in the misfolding and brain accumulation of Abeta (amyloid beta-peptide), a central event in AD (Alzheimer's disease) synaptic dysfunctions. Structural alterations introduced by site-specific modifications linked to protein aging may affect Abeta production, polymerization and clearance, and therefore play a pivotal role in the pathogenesis of sporadic and genetic forms of AD. Early changes associated with molecular aging also have significant long-term consequences for Abeta folding and turnover. New fast, reproducible and accurate methods for the screening of protein aging markers in biological samples may contribute to improve diagnostic and therapeutic approaches in AD.
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23
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Kasai A, Yamashita N, Utsunomiya-Tate N. Collagen Racemization and Deposition in the Lungs of Aged Rats. BIOCHEMISTRY INSIGHTS 2010. [DOI: 10.4137/bci.s4210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Isomerization of amino acids in proteins has recently been identified as a part of the aging process. Increases in D-amino acids as a consequence of isomerization influence the function and structure of proteins. Senescence-related pulmonary diseases, such as chronic obstructive pulmonary disease, are thought to be caused by reductions of lung function with age. We hypothesized that changes of protein structure in lung tissue induced by the isomerization of amino acids could result in decreased lung function. Therefore, we examined whether isomerization of amino acids takes place in the lungs of rats as they age. We measured the content of L- and D-amino acids in collagen 1 by HPLC using a chiral column. We found that collagen 1 was increasingly racemized with age, so that significantly higher proportions of D-Ser were present in 12- and 24-month-old rats than in 8-week-old rats. D-Asp increased slightly but not significantly. We also investigated the localization of collagen 1 in lung tissue. Stacks of collagen 1 were observed in the parenchyma and airway wall, and age-dependent changes were especially prominent in the airway wall. Racemization of collagen 1 could therefore influence lung function and contribute to pulmonary diseases.
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Affiliation(s)
- Akiko Kasai
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Naomi Yamashita
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Naoko Utsunomiya-Tate
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
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24
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Murakami K, Uno M, Masuda Y, Shimizu T, Shirasawa T, Irie K. Isomerization and/or racemization at Asp23 of Abeta42 do not increase its aggregative ability, neurotoxicity, and radical productivity in vitro. Biochem Biophys Res Commun 2007; 366:745-51. [PMID: 18078812 DOI: 10.1016/j.bbrc.2007.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 12/04/2007] [Indexed: 11/16/2022]
Abstract
Aggregation of the 42-mer amyloid beta peptide (Abeta42) plays a pivotal role in the pathogenesis of Alzheimer's disease. Recent investigations suggested the isomerization and/or racemization of Asp at position 1, 7, or 23 to be associated with the pathological role of Abeta42. Our previous study indicated that the turn at positions 22 and 23 of Abeta42 is closely related to its neurotoxicity through the formation of radicals. To clarify the contribution of these modifications at Asp23 to the pathology, three isomerized and/or racemized Abeta42 mutants were prepared. l-isoAsp23- and d-Asp23-Abeta42 showed moderate aggregative ability similar to the wild type. However, d-Asp23-Abeta42 was less neurotoxic than the wild type, while l-isoAsp23-Abeta42 was as toxic as the wild type. In contrast, d-isoAsp23-Abeta42 showed weak aggregative ability without neurotoxicity. These results suggest the isomerization and/or racemization of Asp23 not to be related to the pathogenesis, but to be a consequence of chemical reactions during the long-term deposition of fibrils.
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Affiliation(s)
- Kazuma Murakami
- Laboratory of Organic Chemistry in Life Science, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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