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Babalola JA, Stracke A, Loeffler T, Schilcher I, Sideromenos S, Flunkert S, Neddens J, Lignell A, Prokesch M, Pazenboeck U, Strobl H, Tadic J, Leitinger G, Lass A, Hutter-Paier B, Hoefler G. Effect of astaxanthin in type-2 diabetes -induced APPxhQC transgenic and NTG mice. Mol Metab 2024; 85:101959. [PMID: 38763496 PMCID: PMC11153249 DOI: 10.1016/j.molmet.2024.101959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024] Open
Abstract
OBJECTIVES Aggregation and misfolding of amyloid beta (Aβ) and tau proteins, suggested to arise from post-translational modification processes, are thought to be the main cause of Alzheimer's disease (AD). Additionally, a plethora of evidence exists that links metabolic dysfunctions such as obesity, type 2 diabetes (T2D), and dyslipidemia to the pathogenesis of AD. We thus investigated the combinatory effect of T2D and human glutaminyl cyclase activity (pyroglutamylation), on the pathology of AD and whether astaxanthin (ASX) treatment ameliorates accompanying pathophysiological manifestations. METHODS Male transgenic AD mice, APPxhQC, expressing human APP751 with the Swedish and the London mutation and human glutaminyl cyclase (hQC) enzyme and their non-transgenic (NTG) littermates were used. Both APPxhQC and NTG mice were allocated to 3 groups, control, T2D-control, and T2D-ASX. Mice were fed control or high fat diet ± ASX for 13 weeks starting at an age of 11-12 months. High fat diet fed mice were further treated with streptozocin for T2D induction. Effects of genotype, T2D induction, and ASX treatment were evaluated by analysing glycemic readouts, lipid concentration, Aβ deposition, hippocampus-dependent cognitive function and nutrient sensing using immunosorbent assay, ELISA-based assays, western blotting, immunofluorescence staining, and behavioral testing via Morris water maze (MWM), respectively. RESULTS APPxhQC mice presented a higher glucose sensitivity compared to NTG mice. T2D-induced brain dysfunction was more severe in NTG compared to the APPxhQC mice. T2D induction impaired memory functions while increasing hepatic LC3B, ABCA1, and p65 levels in NTG mice. T2D induction resulted in a progressive shift of Aβ from the soluble to insoluble form in APPxhQC mice. ASX treatment reversed T2D-induced memory dysfunction in NTG mice and in parallel increased hepatic pAKT while decreasing p65 and increasing cerebral p-S6rp and p65 levels. ASX treatment reduced soluble Aβ38 and Aβ40 and insoluble Aβ40 levels in T2D-induced APPxhQC mice. CONCLUSIONS We demonstrate that T2D induction in APPxhQC mice poses additional risk for AD pathology as seen by increased Aβ deposition. Although ASX treatment reduced Aβ expression in T2D-induced APPxhQC mice and rescued T2D-induced memory impairment in NTG mice, ASX treatment alone may not be effective in cases of T2D comorbidity and AD.
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Affiliation(s)
| | - Anika Stracke
- Division of Immunology and Pathophysiology, Otto Loewi Research Center, Medical University of Graz, Austria
| | | | | | - Spyridon Sideromenos
- QPS Austria GmbH, Grambach, Austria; Medical University of Vienna, Vienna, Austria
| | | | | | | | | | - Ute Pazenboeck
- Division of Immunology and Pathophysiology, Otto Loewi Research Center, Medical University of Graz, Austria
| | - Herbert Strobl
- Division of Immunology and Pathophysiology, Otto Loewi Research Center, Medical University of Graz, Austria
| | - Jelena Tadic
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Gerd Leitinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Austria
| | - Achim Lass
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology Medical University of Graz, Graz, Austria.
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Wu HT, Van Orman BL, Julian RR. Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:705-713. [PMID: 38440975 PMCID: PMC10995990 DOI: 10.1021/jasms.3c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
Isomerized amino acid residues have been identified in many peptides extracted from tissues or excretions of humans and animals. These isomerized residues can play key roles by affecting biological activity or by exerting an influence on the process of aging. Isomerization occurs spontaneously and does not result in a mass shift. Thus, identifying and localizing isomerized residues in biological samples is challenging. Herein, we introduce a fast and efficient method using tandem mass spectrometry (MS) to locate isomerized residues in peptides. Although MS2 spectra are useful for identifying peptides that contain an isomerized residue, they cannot reliably localize isomerization sites. We show that this limitation can be overcome by utilizing MS3 experiments to further evaluate each fragment ion from the MS2 stage. Comparison at the MS3 level, utilizing statistical analyses, reveals which MS2 fragments differ between samples and, therefore, must contain the isomerized sites. The approach is similar to previous work relying on ion mobility to discriminate MS2 product ions by collision cross-section. The MS3 approach can be implemented using either ion-trap or beam-type collisional activation and is compatible with the quantification of isomer mixtures when coupled to a calibration curve. The method can also be implemented in combination with liquid chromatography in a targeted approach. Enabling the identification and localization of isomerized residues in peptides with an MS-only methodology will expand accessibility to this important information.
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Affiliation(s)
- Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Brielle L. Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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3
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TAKATA T. Identification of D-amino Acid Residues in Proteins Using Mass Spectrometry. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Takumi TAKATA
- Institute for Integrated Radiation and Nuclear Science, Kyoto University
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4
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Shobo A, Röntgen A, Hancock MA, Multhaup G. Biophysical characterization as a tool to predict amyloidogenic and toxic properties of amyloid-β42 peptides. FEBS Lett 2022; 596:1401-1411. [PMID: 35466397 DOI: 10.1002/1873-3468.14358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/19/2022] [Indexed: 11/06/2022]
Abstract
Amyloid-β42 (Aβ42) peptides are central to the amyloid pathology in Alzheimer's disease (AD). As biological mimetics, properties of synthetic Aβ peptides usually vary between vendors and batches, thus impacting the reproducibility of experimental studies. Here, we tested recombinantly expressed Aβ42 (Asp1 to Ala42) against synthetic Aβ42 from different suppliers using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), circular dichroism (CD) spectroscopy, thioflavin T aggregation, surface plasmon resonance and MTT cell viability assays. Overall, our recombinant Aβ42 provided a reproducible mimetic of desired properties. Across experimental approaches, the combined detection of Aβ42 dimers and random coil to β-sheet transition only correlated with aggregation-prone and cytotoxic peptides. Conclusively, combining MALDI-MS with CD appears to provide a rapid, reliable means to predict the "bioactivity" of Aβ42.
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Affiliation(s)
- Adeola Shobo
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Alexander Röntgen
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Mark A Hancock
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,SPR-MS Facility, McGill University, Montreal, QC, Canada
| | - Gerhard Multhaup
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
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5
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D-Amino Acids as a Biomarker in Schizophrenia. Diseases 2022; 10:diseases10010009. [PMID: 35225861 PMCID: PMC8883943 DOI: 10.3390/diseases10010009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
D-amino acids may play key roles for specific physiological functions in different organs including the brain. Importantly, D-amino acids have been detected in several neurological disorders such as schizophrenia, amyotrophic lateral sclerosis, and age-related disorders, reflecting the disease conditions. Relationships between D-amino acids and neurophysiology may involve the significant contribution of D-Serine or D-Aspartate to the synaptic function, including neurotransmission and synaptic plasticity. Gut-microbiota could play important roles in the brain-function, since bacteria in the gut provide a significant contribution to the host pool of D-amino acids. In addition, the alteration of the composition of the gut microbiota might lead to schizophrenia. Furthermore, D-amino acids are known as a physiologically active substance, constituting useful biomarkers of several brain disorders including schizophrenia. In this review, we wish to provide an outline of the roles of D-amino acids in brain health and neuropsychiatric disorders with a focus on schizophrenia, which may shed light on some of the superior diagnoses and/or treatments of schizophrenia.
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6
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Abdulbagi M, Wang L, Siddig O, Di B, Li B. D-Amino Acids and D-Amino Acid-Containing Peptides: Potential Disease Biomarkers and Therapeutic Targets? Biomolecules 2021; 11:1716. [PMID: 34827714 PMCID: PMC8615943 DOI: 10.3390/biom11111716] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
In nature, amino acids are found in two forms, L and D enantiomers, except for glycine which does not have a chiral center. The change of one form to the other will lead to a change in the primary structure of proteins and hence may affect the function and biological activity of proteins. Indeed, several D-amino acid-containing peptides (DAACPs) were isolated from patients with cataracts, Alzheimer's and other diseases. Additionally, significant levels of free D-amino acids were found in several diseases, reflecting the disease conditions. Studying the molecular mechanisms of the DAACPs formation and the alteration in D-amino acids metabolism will certainly assist in understanding these diseases and finding new biomarkers and drug targets. In this review, the presence of DAACPs and free D-amino acids and their links with disease development and progress are summarized. Similarly, we highlight some recent advances in analytical techniques that led to improvement in the discovery and analysis of DAACPs and D-amino acids.
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Affiliation(s)
- Mohamed Abdulbagi
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Liya Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Orwa Siddig
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Bin Di
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Bo Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
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7
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Readel ER, Wey M, Armstrong DW. Rapid and selective separation of amyloid beta from its stereoisomeric point mutations implicated in neurodegenerative Alzheimer's disease. Anal Chim Acta 2021; 1163:338506. [PMID: 34024415 DOI: 10.1016/j.aca.2021.338506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/25/2022]
Abstract
Extracellular deposition of amyloid beta (Aβ) peptides are a hallmark of Alzheimer's disease. The isomerization and epimerization of Aβ peptides have been linked to the enhanced deposition of Aβ plaques. Therefore, considerable effort has been expended to create effective methods to distinguish such aberrant Aβ peptides from normal Aβ peptides. Herein, we have developed chromatographic retention U-shaped curves to investigate the hydrophobicity of Aβ 1-38, 1-40, 1-42 and fourteen aberrant Aβ 1-42 peptides. Using this information, we developed the first selective and comprehensive method that can easily detect both aberrant and normal Aβ peptides simultaneously using high performance liquid chromatography-mass spectrometry (HPLC-MS). We show for the first time that D-Ser modifications to Aβ cause the peptide to be more hydrophilic, as does D-Asp and L/D-iso-Asp.
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Affiliation(s)
- Elizabeth R Readel
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Michael Wey
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Daniel W Armstrong
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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Kuang J, Tao Y, Song Y, Chemmalil L, Mussa N, Ding J, Li ZJ. Understanding the pathway and kinetics of aspartic acid isomerization in peptide mapping methods for monoclonal antibodies. Anal Bioanal Chem 2021; 413:2113-2123. [PMID: 33543314 DOI: 10.1007/s00216-021-03176-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/28/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022]
Abstract
Isomerization of aspartic acid (Asp) in therapeutic proteins could lead to safety and efficacy concerns. Thus, accurate quantitation of various Asp isomerization along with kinetic understanding of the variant formations is needed to ensure optimal process development and sufficient product quality control. In this study, we first observed Asp-succinimide conversion in complementarity-determining regions (CDRs) Asp-Gly motif of a recombinant mAb through ion exchange chromatography, intact protein analysis by mass spectrometry, and LC-MS/MS. Then, we developed a specific peptide mapping method, with optimized sample digestion conditions, to accurately quantitate Asp-succinimide-isoAsp variants at peptide level without method-induced isomerization. Various kinetics of Asp-succinimide-isoAsp isomerization pathways were elucidated using 18O labeling followed by LC-MS analysis. Molecular modeling and molecular dynamic simulation provide additional insight on the kinetics of Asp-succinimide formation and stability of succinimide intermediate. Findings of this work shed light on the molecular construct and the kinetics of the formation of isoAsp and succinimide in peptides and proteins, which facilitates analytical method development, protein engineering, and late phase development for commercialization of therapeutic proteins.
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Affiliation(s)
- June Kuang
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
| | - Yuanqi Tao
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Analytical Science Biologics, Takeda Pharmaceutical Company, Lexington, MA, 02421, USA
| | - Yuanli Song
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Process Development & Manufacture Operations, GSK, MA, 02451, Waltham, USA
| | - Letha Chemmalil
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
| | - Nesredin Mussa
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Ultragenyx, CA, 94005, Brisbane, USA
| | - Julia Ding
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA.
| | - Zheng Jian Li
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
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Kapadia A, Sharma KK, Maurya IK, Singh V, Khullar M, Jain R. Structural and mechanistic insights into the inhibition of amyloid-β aggregation by Aβ 39-42 fragment derived synthetic peptides. Eur J Med Chem 2020; 212:113126. [PMID: 33395622 DOI: 10.1016/j.ejmech.2020.113126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
The inhibition of amyloid-β (Aβ) aggregation is a promising approach towards therapeutic intervention for Alzheimer's disease (AD). Thirty eight tetrapeptides based upon Aβ39-42C-terminus fragment of the parent Aβ peptide were synthesized. The sequential replacement/modification employing unnatural amino acids imparted scaffold diversity, augmented activity, enhanced blood brain barrier permeability and offered proteolytic stability to the synthetic peptides. Several peptides exhibited promising protection against Aβ aggregation-mediated-neurotoxicity in PC-12 cells at doses ranged between 10 μM and 0.1 μM, further confirmed by the thioflavin-T fluorescence assay. CD study illustrate that these peptides restrict the β-sheet formation, and the non-appearance of Aβ42 fibrillar structures in the electron microscopy confirm the inhibition of Aβ42 aggregation. HRMS and ANS fluorescence spectroscopic analysis provided additional mechanistic insights. Two selected lead peptides 5 and 16 depicted enhanced blood-brain penetration and stability against serum and proteolytic enzyme. Structural insights into ligand-Aβ interactions on the monomeric and proto-fibrillar units of Aβ were computationally studied. Promising inhibitory potential and short sequence of the lead peptides offers new avenues for the advancement of peptide-derived therapeutics for AD.
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Affiliation(s)
- Akshay Kapadia
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Indresh Kumar Maurya
- Department of Microbial Biotechnology, Punjab University, Sector 25, Chandigarh, 160 014, India
| | - Varinder Singh
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Madhu Khullar
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India.
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11
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Foley AR, Raskatov JA. Assessing Reproducibility in Amyloid β Research: Impact of Aβ Sources on Experimental Outcomes. Chembiochem 2020; 21:2425-2430. [PMID: 32249510 PMCID: PMC7647053 DOI: 10.1002/cbic.202000125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/04/2020] [Indexed: 12/16/2022]
Abstract
The difficulty of synthesizing and purifying the amyloid β (Aβ) peptide, combined with its high aggregation propensity and low solubility under physiological conditions, leads to a wide variety of experimental results from kinetic assays to biological activity. Thus, it becomes challenging to reproduce outcomes, and this limits our ability to rely on reported results as the foundation for new research. This article examines variability of the Aβ peptide from different sources, comparing purity, and oligomer and fibril formation propensity side by side. The results highlight the importance of performing rigorous controls so that meaningful biophysical, biochemical, and neurobiological results can be obtained to improve our understanding on Aβ.
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Affiliation(s)
- Alejandro R Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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12
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Dyakin VV, Wisniewski TM, Lajtha A. Chiral Interface of Amyloid Beta (Aβ): Relevance to Protein Aging, Aggregation and Neurodegeneration. Symmetry (Basel) 2020; 12. [PMID: 34327009 PMCID: PMC8317441 DOI: 10.3390/sym12040585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biochirality is the subject of distinct branches of science, including biophysics, biochemistry, the stereochemistry of protein folding, neuroscience, brain functional laterality and bioinformatics. At the protein level, biochirality is closely associated with various post-translational modifications (PTMs) accompanied by the non-equilibrium phase transitions (PhTs NE). PTMs NE support the dynamic balance of the prevalent chirality of enzymes and their substrates. The stereoselective nature of most biochemical reactions is evident in the enzymatic (Enz) and spontaneous (Sp) PTMs (PTMs Enz and PTMs Sp) of proteins. Protein chirality, which embraces biophysics and biochemistry, is a subject of this review. In this broad field, we focus attention to the amyloid-beta (Aβ) peptide, known for its essential cellular functions and associations with neuropathology. The widely discussed amyloid cascade hypothesis (ACH) of Alzheimer’s disease (AD) states that disease pathogenesis is initiated by the oligomerization and subsequent aggregation of the Aβ peptide into plaques. The racemization-induced aggregation of protein and RNA have been extensively studied in the search for the contribution of spontaneous stochastic stereo-specific mechanisms that are common for both kinds of biomolecules. The failure of numerous Aβ drug-targeting therapies requires the reconsolidation of the ACH with the concept of PTMs Sp. The progress in methods of chiral discrimination can help overcome previous limitations in the understanding of AD pathogenesis. The primary target of attention becomes the network of stereospecific PTMs that affect the aggregation of many pathogenic agents, including Aβ. Extensive recent experimental results describe the truncated, isomerized and racemized forms of Aβ and the interplay between enzymatic and PTMs Sp. Currently, accumulated data suggest that non-enzymatic PTMs Sp occur in parallel to an existing metabolic network of enzymatic pathways, meaning that the presence and activity of enzymes does not prevent non-enzymatic reactions from occurring. PTMs Sp impact the functions of many proteins and peptides, including Aβ. This is in logical agreement with the silently accepted racemization hypothesis of protein aggregation (RHPA). Therefore, the ACH of AD should be complemented by the concept of PTMs Sp and RHPA.
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Affiliation(s)
- Victor V. Dyakin
- Departmemts: Virtual Reality Perception Lab. (VV. Dyakin) and Center for Neurochemistry (A. Lajtha), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
- Correspondence:
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Departmemts: Virtual Reality Perception Lab. (VV. Dyakin) and Center for Neurochemistry (A. Lajtha), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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13
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Kushwah N, Jain V, Yadav D. Osmolytes: A Possible Therapeutic Molecule for Ameliorating the Neurodegeneration Caused by Protein Misfolding and Aggregation. Biomolecules 2020; 10:biom10010132. [PMID: 31941036 PMCID: PMC7022651 DOI: 10.3390/biom10010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the neurological disorders in the brain are caused by the abnormal buildup of misfolded or aggregated proteins. Osmolytes are low molecular weight organic molecules usually built up in tissues at a quite high amount during stress or any pathological condition. These molecules help in providing stability to the aggregated proteins and protect these proteins from misfolding. Alzheimer’s disease (AD) is the uttermost universal neurological disorder that can be described by the deposition of neurofibrillary tangles, aggregated/misfolded protein produced by the amyloid β-protein (Aβ). Osmolytes provide stability to the folded, functional form of a protein and alter the folding balance away from aggregation and/or degradation of the protein. Moreover, they are identified as chemical chaperones. Brain osmolytes enhance the pace of Aβ aggregation, combine with the nearby water molecules more promptly, and avert the aggregation/misfolding of proteins by providing stability to them. Therefore, osmolytes can be employed as therapeutic targets and may assist in potential drug design for many neurodegenerative and other diseases.
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Affiliation(s)
- Neetu Kushwah
- Functional Genomics Unit, CSIR-institute of genomics and integrative biology, Mall road, Delhi 110007, India;
| | - Vishal Jain
- Department of ECE, Carnegie Mellon University, Pittsburgh, PA 15289, USA
- Correspondence: (V.J.); (D.Y.); Tel.: +1-412-251-3042 (V.J.); +82-10-2202-1191(D.Y.)
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
- Correspondence: (V.J.); (D.Y.); Tel.: +1-412-251-3042 (V.J.); +82-10-2202-1191(D.Y.)
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14
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Foley AR, Finn TS, Kung T, Hatami A, Lee HW, Jia M, Rolandi M, Raskatov JA. Trapping and Characterization of Nontoxic Aβ42 Aggregation Intermediates. ACS Chem Neurosci 2019; 10:3880-3887. [PMID: 31319029 DOI: 10.1021/acschemneuro.9b00340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amyloid β (Aβ) 42 is an aggregation-prone peptide and the believed seminal etiological agent of Alzheimer's disease (AD). Intermediates of Aβ42 aggregation, commonly referred to as diffusible oligomers, are considered to be among the most toxic forms of the peptide. Here, we studied the effect of the age-related epimerization of Ser26 (i.e., S26s chiral edit) in Aβ42 and discovered that this subtle molecular change led to reduced fibril formation propensity. Surprisingly, the resultant soluble aggregates were nontoxic. To gain insight into the structural changes that occurred in the peptide upon S26s substitution, the system was probed using an array of biophysical and biochemical methods. These experiments consistently pointed to the stabilization of aggregation intermediates in the Aβ42-S26s system. To better understand the changes arising as a consequence of the S26s substitution, molecular level structural studies were performed. Using a combined nuclear magnetic resonance (NMR)- and density functional theory (DFT)-computational approach, we found that the S26s chiral edit induced only local structural changes in the Gly25-Ser26-Asn27 region. Interestingly, these subtle changes enabled the formation of an intramolecular Ser26-Asn27 H-bond, which disrupted the ability of Asn27 to engage in the fibrillogenic side chain-to-side chain H-bonding pattern. This reveals that intermolecular stabilizing interactions between Asn27 side chains are a key element controlling Aβ42 aggregation and toxicity.
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Affiliation(s)
- Alejandro R. Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Thomas S. Finn
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Timothy Kung
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Asa Hatami
- Sangamo Therapeutics, Richmond, California 94804, United States
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Manping Jia
- Department of Electrical Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Marco Rolandi
- Department of Electrical Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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15
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Jia L, Wang W, Sang J, Wei W, Zhao W, Lu F, Liu F. Amyloidogenicity and Cytotoxicity of a Recombinant C-Terminal His 6-Tagged Aβ 1-42. ACS Chem Neurosci 2019; 10:1251-1262. [PMID: 30537813 DOI: 10.1021/acschemneuro.8b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aggregation of amyloid β peptide (Aβ) is closely associated with the occurrence and development of Alzheimer's disease (AD). Reproducible and detailed studies on the aggregation kinetics and structure of various aggregates have been conducted using recombinant Aβ peptides. While the His6-tag is commonly used in the purification of recombinant proteins due to its great simplicity and affinity, there is little information on the aggregation of His6-tagged Aβ and its corresponding cytotoxicity. Moreover, it is also unclear whether there is an effect of the His6-tag on the amyloidogenicity and cytotoxicity of recombinant Aβ1-42. Herein, a method to express and purify a mutant C-terminally His6-tagged Aβ1-42 (named as Aβ1-42-His6) from Escherichia coli was described. Aβ1-42-His6 aggregated into β-sheet-rich fibrils as shown by thioflavin T fluorescence, atomic force microscopy and circular dichroism spectroscopy. Moreover, the fibrillar recombinant Aβ1-42-His6 showed strong toxicity toward PC12 cells in vitro. Molecular dynamics simulations revealed that the His6-tag contributed little to the secondary structure and intermolecular interactions, including hydrophobic interactions, salt bridges, and hydrogen bonding of the fibrillar pentamer of Aβ1-42. This highlights the biological importance of modification on the molecular structure of Aβ. Thus, the easily purified high-quality Aβ1-42-His6 offers great advantages for screening aggregation inhibitors or in vitro confirmation of rationally designed drugs for the treatment of AD.
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Affiliation(s)
- Longgang Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenjuan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jingcheng Sang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Wei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenping Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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16
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Beach TG, Maarouf CL, Intorcia A, Sue LI, Serrano GE, Lu M, Joshi A, Pontecorvo MJ, Roher AE. Antemortem-Postmortem Correlation of Florbetapir (18F) PET Amyloid Imaging with Quantitative Biochemical Measures of Aβ42 but not Aβ40. J Alzheimers Dis 2019; 61:1509-1516. [PMID: 29376867 DOI: 10.3233/jad-170762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyloid imaging demonstrates the in vivo presence of amyloid-β (Aβ) deposits in the aging human brain but it is still unknown which structural forms and modifications of Aβ are detected. In Alzheimer's disease, most amyloid deposits are predominantly composed of Aβ ending at amino acid residues Val40 or Ala42. It has been reported that Aβ40 is largely restricted to neuritic plaques while Aβ42 may be deposited in amyloid plaques of all types, and is often the sole component of diffuse plaques. The distinction is important as it is mainly the neuritic plaques that correlate with cognitive impairment while diffuse plaques may be the initial type of Aβ deposited. Whether PET amyloid ligands such as florbetapir-18F (Amyvid) are partially or wholly selective for brain deposits of Aβ40 or Aβ42 is currently unknown. We compared antemortem florbetapir PET cortical/cerebellar signal intensity (SUVr) of 55 subjects with postmortem biochemical (ELISA) measurements employing specific antibodies against Aβ40 and Aβ42. Spearman's univariable correlations were significant for both Aβ40 and Aβ42, but were much stronger for Aβ42. Multiple linear regression showed significance only for Aβ42. These results suggest that florbetapir binds only weakly, if at all, to Aβ40. This may be in part due to the higher likelihood for Aβ42 to be present in a β-pleated sheet tertiary structure, or to differences between Aβ40 and Aβ42 in β-pleated sheet tertiary or quaternary structure.
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Affiliation(s)
| | | | | | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | | | - Ming Lu
- Avid Radiopharmaceuticals, Philadelphia, PA, USA
| | | | | | - Alex E Roher
- Banner Sun Health Research Institute, Sun City, AZ, USA.,Barrow Neurological Institute, Phoenix, AZ, USA
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17
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Octa-Smolin F, Niemeyer J. Stereoselective Sensing ofl- andd-Amino Acids: Development of a Fluorescence-Array Based on Readily Available Chiral Phosphoric Acids. Chemistry 2018; 24:16506-16510. [DOI: 10.1002/chem.201805003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Frescilia Octa-Smolin
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
| | - Jochen Niemeyer
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
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18
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Identification of D-Amino Acids in Light Exposed mAb Formulations. Pharm Res 2018; 35:238. [PMID: 30334107 DOI: 10.1007/s11095-018-2520-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022]
Abstract
PURPOSE We previously demonstrated that D-amino acids can form as a result of photo-irradiation of a monoclonal antibody (mAb) at both λ = 254 nm and λ > 295 nm (λmax = 305 nm), likely via reversible hydrogen transfer reactions of intermediary thiyl radicals. Here, we investigate the role of various excipients (sucrose, glucose, L-Arg, L-Met and L-Leu) on D-amino acid formation, and specifically the distribution of D-amino acids in mAb monomers and aggregates present after light exposure. METHODS The mAb-containing formulations were photo-irradiated at λ = 254 nm and λmax = 305 nm, followed by fractionation of aggregate and monomer fractions using size exclusion chromatography. These aggregate and monomer fractions were subjected to hydrolysis and subsequent amino acid analysis. RESULTS Both aggregate and monomer fractions collected from all formulations showed the formation of D-Glu and D-Val, whereas the formation of D-Ala was limited to the aggregate fraction collected from an L-Arg-containing formulation. Interestingly, quantitative analysis revealed higher yields of D-amino acids in the L-Arg-containing formulation. CONCLUSIONS Generally, D-amino acids accumulated to similar extents in monomers and aggregates.
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19
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Octa-Smolin F, Thiele M, Yadav R, Platzek A, Clever GH, Niemeyer J. Chiral Receptors for Lysine Based on Covalently Linked Bis- and Tris-binaphthylphosphoric Acids. Org Lett 2018; 20:6153-6156. [PMID: 30252491 DOI: 10.1021/acs.orglett.8b02619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The synthesis and application of three chiral receptors based on the covalent linkage of 1,1'-binaphthylphosphoric acids is reported. The binding of the lysine enantiomers to the chiral receptors was investigated by DOSY-NMR and NMR titrations, revealing that the bisphosphoric acid 1d acts as a highly stereoselective receptor for binding of d-lysine.
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Affiliation(s)
- Frescilia Octa-Smolin
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry , University of Duisburg-Essen , Universitätsstrasse 7 , 45141 Essen , Germany
| | - Maike Thiele
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry , University of Duisburg-Essen , Universitätsstrasse 7 , 45141 Essen , Germany
| | - Rohan Yadav
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry , University of Duisburg-Essen , Universitätsstrasse 7 , 45141 Essen , Germany
| | - André Platzek
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Jochen Niemeyer
- Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), Department of Chemistry , University of Duisburg-Essen , Universitätsstrasse 7 , 45141 Essen , Germany
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20
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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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21
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Nirasawa S, Nakahara K, Takahashi S. Cloning and characterization of the novel d-aspartyl endopeptidase, paenidase, from Paenibacillus sp. B38. J Biochem 2018; 164:103-112. [DOI: 10.1093/jb/mvy033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/26/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Satoru Nirasawa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuhiko Nakahara
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Saori Takahashi
- Akita Research Institute of Food and Brewing, 4-26 Sanuki, Arayamachi, Akita 010-1623, Japan
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22
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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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23
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Wang L, Jin Z, Wang X, Zeng S, Sun C, Pan Y. Pair of Stereodynamic Chiral Benzylicaldehyde Probes for Determination of Absolute Configuration of Amino Acid Residues in Peptides by Mass Spectrometry. Anal Chem 2017; 89:11902-11907. [DOI: 10.1021/acs.analchem.7b03804] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lin Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Department
of Chemistry and Chemical Engineering, Beijing University of Technology, 100124, Beijing, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Zhe Jin
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Xiayan Wang
- Department
of Chemistry and Chemical Engineering, Beijing University of Technology, 100124, Beijing, China
| | - Su Zeng
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Cuirong Sun
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuanjiang Pan
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
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24
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Morozov AV, Yurinskaya MM, Mitkevich VA, Garbuz DG, Preobrazhenskaia OV, Vinokurov MG, Evgen’ev MB, Karpov VL, Makarov AA. Heat-shock protein HSP70 decreases activity of proteasomes in human neuroblastoma cells treated by amyloid-beta 1-42 with isomerized Asp7. Mol Biol 2017. [DOI: 10.1134/s0026893316060133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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A rapid and sensitive detection of D-Aspartic acid in Crystallin by chiral derivatized liquid chromatography mass spectrometry. J Chromatogr A 2016; 1467:318-325. [PMID: 27435686 DOI: 10.1016/j.chroma.2016.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 01/23/2023]
Abstract
A method for the determination of D-Aspartic acid (D-Asp) and its D/L ratio in peptides and proteins has been developed. This method was carried out with good separation of the D/L chiral peptide pairs by combination of a chiral derivatization and an ADME column separation. Furthermore, a cationic derivatization reagent, DBD-Py-NCS, increased the sensitivity of the ESI-MS/MS detection. To confirm the comprehensive peptide analysis, synthesized α-Crystallin tryptic peptides, which included D-Asp residues, were analyzed. The 5 pairs of D/L-Asp that included peptide diastereomers were well separated. Their peak resolutions were more than 1.5 and the results were reproducible (RSD<0.05, n=5). As an application of this method, we analyzed the α-Crystallin standard and UV irradiated α-Crystallin. After trypsin digestion and DBD-Py-NCS derivatization, the tryptic peptide derivatives were applied to LC-MS/MS. Based on the results of peptide sequence identification, almost all the tryptic peptides of the αA- and αB-Crystallin homologous subunits of α-Crystallin were detected as DBD-Py NCS derivatives. However, there was no D-Asp residue in the standard proteins. In the case of the UV irradiated α-Crystallin, Asp76 and Asp84 in the αA-Crystallin and Asp96 in αB-Crystallin were racemized to D-Asp. These results show that this proposed chiral peptide LC-MS/MS method using chiral derivatization provides a rapid and sensitive analysis for post translational Asp racemization sites in aging proteins.
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26
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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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27
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Morozov AV, Kulikova AA, Astakhova TM, Mitkevich VA, Burnysheva KM, Adzhubei AA, Erokhov PA, Evgen’ev MB, Sharova NP, Karpov VL, Makarov AA. Amyloid-β Increases Activity of Proteasomes Capped with 19S and 11S Regulators. J Alzheimers Dis 2016; 54:763-76. [DOI: 10.3233/jad-160491] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Alexey V. Morozov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana M. Astakhova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia M. Burnysheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel A. Erokhov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Michail B. Evgen’ev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Natalia P. Sharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vadim L. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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28
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Ohyabu N, Kakiya K, Yokoi Y, Hinou H, Nishimura SI. Convergent Solid-Phase Synthesis of Macromolecular MUC1 Models Truly Mimicking Serum Glycoprotein Biomarkers of Interstitial Lung Diseases. J Am Chem Soc 2016; 138:8392-5. [DOI: 10.1021/jacs.6b04973] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Ohyabu
- Shionogi & Company, Ltd., 3-1-1 Futaba-cho, Toyonaka-shi, Osaka 561-0825, Japan
- Graduate School of Life Science and Faculty of Advanced
Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Kiyoshi Kakiya
- Shionogi & Company, Ltd., 2-1-3 Kuiseterashima, Amagasaki 660-0813, Japan
| | - Yasuhiro Yokoi
- Graduate School of Life Science and Faculty of Advanced
Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Hiroshi Hinou
- Graduate School of Life Science and Faculty of Advanced
Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals, Co., Ltd., N21, W12, Kita-ku, Sapporo 001-0022, Japan
| | - Shin-Ichiro Nishimura
- Graduate School of Life Science and Faculty of Advanced
Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals, Co., Ltd., N21, W12, Kita-ku, Sapporo 001-0022, Japan
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29
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Kulikova AA, Cheglakov IB, Kukharsky MS, Ovchinnikov RK, Kozin SA, Makarov AA. Intracerebral Injection of Metal-Binding Domain of Aβ Comprising the Isomerized Asp7 Increases the Amyloid Burden in Transgenic Mice. Neurotox Res 2016; 29:551-7. [PMID: 26842600 DOI: 10.1007/s12640-016-9603-y] [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: 09/25/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 11/30/2022]
Abstract
Intracerebral or intraperitoneal injections of brain extracts from the Alzheimer's disease patients result in the acceleration of cerebral β-amyloidosis in transgenic mice. Earlier, we have found that intravenous injections of synthetic full-length amyloid-β (Aβ) comprising the isomerized Asp7 trigger cerebral β-amyloidosis. In vitro studies have shown that isomerization of Asp7 promotes zinc-induced oligomerization of the Aβ metal-binding domain (Aβ1-16). Here we report that single intracerebral injection of the peptide Aβ1-16 with isomerized Asp7 (isoAβ1-16) but not the injection of Aβ1-16 significantly increases amyloid burden in 5XFAD transgenic mice. Our results provide evidence for a role of isoAβ1-16 as a minimal seeding agent of Aβ aggregation in vivo.
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Affiliation(s)
- Alexandra A Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991.
| | - Ivan B Cheglakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK.,Institute of Physiologically Active Compounds, Russian Academy of Sciences, Severniy Proezd, Chernogolovka, Moscow region, Russia, 1142432
| | - Ruslan K Ovchinnikov
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Severniy Proezd, Chernogolovka, Moscow region, Russia, 1142432
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991.
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, Russia, 119991
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Chambers JK, Tokuda T, Uchida K, Ishii R, Tatebe H, Takahashi E, Tomiyama T, Une Y, Nakayama H. The domestic cat as a natural animal model of Alzheimer's disease. Acta Neuropathol Commun 2015; 3:78. [PMID: 26651821 PMCID: PMC4674944 DOI: 10.1186/s40478-015-0258-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 12/27/2022] Open
Abstract
Introduction Alzheimer’s disease (AD) is the most dominant neurodegenerative disorder that causes dementia, and no effective treatments are available. To study its pathogenesis and develop therapeutics, animal models representing its pathologies are needed. Although many animal species develop senile plaques (SP) composed of amyloid-β (Aβ) proteins that are identical to those found in humans, none of them exhibit neurofibrillary tangles (NFT) and subsequent neurodegeneration, which are integral parts of the pathology of AD. Results The present study shows that Aβ accumulation, NFT formation, and significant neuronal loss all emerge naturally in the hippocampi of aged domestic cats. The NFT that form in the cat brain are identical to those seen in human AD in terms of their spatial distribution, the cells they affect, and the tau isoforms that comprise them. Interestingly, aged cats do not develop mature argyrophilic SP, but instead accumulate intraneuronal Aβ oligomers in their hippocampal pyramidal cells, which might be due to the amino acid sequence of felid Aβ. Conclusions These results suggest that Aβ oligomers are more important than SP for NFT formation and the subsequent neurodegeneration. The domestic cat is a unique animal species that naturally replicates various AD pathologies, especially Aβ oligomer accumulation, NFT formation, and neuronal loss. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0258-3) contains supplementary material, which is available to authorized users.
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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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Bayer TA. Proteinopathies, a core concept for understanding and ultimately treating degenerative disorders? Eur Neuropsychopharmacol 2015; 25:713-24. [PMID: 23642796 DOI: 10.1016/j.euroneuro.2013.03.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/12/2013] [Accepted: 03/24/2013] [Indexed: 10/26/2022]
Abstract
The current review covers proteinopathies an umbrella term for neurodegenerative disorders that are characterized by the accumulation of specific proteins within neurons or in the brain parenchyma. Most prevalent examples for typical proteinopathies are Alzheimer's disease and Parkinson's disease. In healthy brain, these proteins are unstructured as a monomer, serving most likely as the physiological form. In a disease condition, the unstructured proteins experience a conformational change leading to small oligomers that eventually will aggregate into higher order structures. Prion disease is an exception within the family of proteinopathies as the aggregated prion protein is highly infectious and can self-aggregate and propagate. Recent reports might implicate a prion-like spread of misfolded proteins in Alzheimer's and Parkinson's disease; however there are evident differences in comparison to prion diseases. As proteinopathies are caused by the aggregation of disease-typical proteins with an ordered structure, active and passive immunization protocols have been used to expose model systems to therapeutic antibodies that bind to the aggregates thereby inhibiting the prolongation into higher ordered fibrils or dissolving the existing fibrillar structure. While most of the immunization treatments have been only carried out in preclinical model systems overexpressing the disease-relevant aggregating protein, other approaches are already in clinical testing. Taking the core concept of proteinopathies with conformationally altered protein aggregates into account, immunization appears to be a very promising therapeutic option for neurodegenerative disorders.
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Affiliation(s)
- Thomas A Bayer
- The Georg-August-University Göttingen, University Medicine Göttingen, Division of Molecular Psychiatry, Von-Siebold-Strasse 5, 37075 Göttingen, Germany.
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Kulikova AA, Makarov AA, Kozin SA. Roles of zinc ions and structural polymorphism of β-amyloid in the development of Alzheimer’s disease. Mol Biol 2015. [DOI: 10.1134/s0026893315020065] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Takahashi O, Kirikoshi R, Manabe N. Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study. Int J Mol Sci 2015; 16:1613-26. [PMID: 25588215 PMCID: PMC4307323 DOI: 10.3390/ijms16011613] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/04/2015] [Indexed: 11/16/2022] Open
Abstract
Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:87-116. [DOI: 10.1016/bs.irn.2015.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Squeglia F, Ruggiero A, Romano M, Vitagliano L, Berisio R. Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine. ACTA ACUST UNITED AC 2014; 70:2295-300. [PMID: 25195744 DOI: 10.1107/s1399004714013674] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022]
Abstract
RipA is a key cysteine protease of Mycobacterium tuberculosis as it is responsible for bacterial daughter-cell separation. Although it is an important target for antimicrobial development, its mechanism of action and its interaction pattern with its substrate are hitherto unknown. By combining crystallographic and mutational studies with functional assays and molecular modelling, it is shown that the catalytic activity of the enzyme relies on a Cys-His-Glu triad and the impact of the mutation of each residue of the triad on the structure and function of RipA is analysed. Unexpectedly, the crystallographic analyses reveal that mutation of the glutamic acid to alanine results in inversion of the configuration of the catalytic cysteine. The consequent burial of the catalytic cysteine side chain explains the enzyme inactivation upon mutation. These data point to a novel role of the acidic residue often present in the triad of cysteine proteases as a supervisor of cysteine configuration through preservation of the local structural integrity.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
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Sivan SS, Wachtel E, Roughley P. Structure, function, aging and turnover of aggrecan in the intervertebral disc. Biochim Biophys Acta Gen Subj 2014; 1840:3181-9. [PMID: 25065289 DOI: 10.1016/j.bbagen.2014.07.013] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/11/2014] [Accepted: 07/18/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Aggrecan is the major non-collagenous component of the intervertebral disc. It is a large proteoglycan possessing numerous glycosaminoglycan chains and the ability to form aggregates in association with hyaluronan. Its abundance and unique molecular features provide the disc with its osmotic properties and ability to withstand compressive loads. Degradation and loss of aggrecan result in impairment of disc function and the onset of degeneration. SCOPE OF REVIEW This review summarizes current knowledge concerning the structure and function of aggrecan in the normal intervertebral disc and how and why these change in aging and degenerative disc disease. It also outlines how supplementation with aggrecan or a biomimetic may be of therapeutic value in treating the degenerate disc. MAJOR CONCLUSIONS Aggrecan abundance reaches a plateau in the early twenties, declining thereafter due to proteolysis, mainly by matrix metalloproteinases and aggrecanases, though degradation of hyaluronan and non-enzymic glycation may also participate. Aggrecan loss is an early event in disc degeneration, although it is a lengthy process as degradation products may accumulate in the disc for decades. The low turnover rate of the remaining aggrecan is an additional contributing factor, preventing protein renewal. It may be possible to retard the degenerative process by restoring the aggrecan content of the disc, or by supplementing with a bioimimetic possessing similar osmotic properties. GENERAL SIGNIFICANCE This review provides a basis for scientists and clinicians to understand and appreciate the central role of aggrecan in the function, degeneration and repair of the intervertebral disc.
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Affiliation(s)
- Sarit Sara Sivan
- Department of Biotechnology Engineering, ORT Braude College, Karmiel 21982 Israel.
| | - Ellen Wachtel
- Faculty of Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter Roughley
- Shriners Hospital for Children, Genetics Unit, 1529 Cedar Avenue, Montreal, Quebec H3G 1A6, Canada
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38
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Kulikova AA, Tsvetkov PO, Indeykina MI, Popov IA, Zhokhov SS, Golovin AV, Polshakov VI, Kozin SA, Nudler E, Makarov AA. Phosphorylation of Ser8 promotes zinc-induced dimerization of the amyloid-β metal-binding domain. ACTA ACUST UNITED AC 2014; 10:2590-6. [DOI: 10.1039/c4mb00332b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation of Ser8 leads to the formation of a new Zn2+ binding site and promotes zinc-induced dimerization of Aβ(1–16).
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Affiliation(s)
- Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
| | - Philipp O. Tsvetkov
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
| | - Maria I. Indeykina
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
- Emanuel Institute of Biochemical Physics
- Russian Academy of Sciences
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics
- Russian Academy of Sciences
- 119334 Moscow, Russia
| | - Sergey S. Zhokhov
- Faculty of Fundamental Medicine
- M.V. Lomonosov Moscow State University
- 119191 Moscow, Russia
| | - Andrey V. Golovin
- Bioengineering and Bioinformatics Department
- M.V. Lomonosov Moscow State University
- 119991 Moscow, Russia
| | - Vladimir I. Polshakov
- Faculty of Fundamental Medicine
- M.V. Lomonosov Moscow State University
- 119191 Moscow, Russia
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
- Orekhovich Institute of Biomedical Chemistry
- Russian Academy of Medical Sciences
| | - Evgeny Nudler
- Howard Hughes Medical Institute
- New York University School of Medicine
- New York, USA
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
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Bouter Y, Dietrich K, Wittnam JL, Rezaei-Ghaleh N, Pillot T, Papot-Couturier S, Lefebvre T, Sprenger F, Wirths O, Zweckstetter M, Bayer TA. N-truncated amyloid β (Aβ) 4-42 forms stable aggregates and induces acute and long-lasting behavioral deficits. Acta Neuropathol 2013; 126:189-205. [PMID: 23685882 PMCID: PMC3722453 DOI: 10.1007/s00401-013-1129-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/30/2022]
Abstract
N-truncated Aβ4-42 is highly abundant in Alzheimer disease (AD) brain and was the first Aβ peptide discovered in AD plaques. However, a possible role in AD aetiology has largely been neglected. In the present report, we demonstrate that Aβ4-42 rapidly forms aggregates possessing a high aggregation propensity in terms of monomer consumption and oligomer formation. Short-term treatment of primary cortical neurons indicated that Aβ4-42 is as toxic as pyroglutamate Aβ3-42 and Aβ1-42. In line with these findings, treatment of wildtype mice using intraventricular Aβ injection induced significant working memory deficits with Aβ4-42, pyroglutamate Aβ3-42 and Aβ1-42. Transgenic mice expressing Aβ4-42 (Tg4-42 transgenic line) developed a massive CA1 pyramidal neuron loss in the hippocampus. The hippocampus-specific expression of Aβ4-42 correlates well with age-dependent spatial reference memory deficits assessed by the Morris water maze test. Our findings indicate that N-truncated Aβ4-42 triggers acute and long-lasting behavioral deficits comparable to AD typical memory dysfunction.
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Affiliation(s)
- Yvonne Bouter
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
| | - Katharina Dietrich
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
| | - Jessica L. Wittnam
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | | | | | | | - Frederick Sprenger
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
| | - Oliver Wirths
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Thomas A. Bayer
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, von-Siebold-Strasse 5, 37075 Goettingen, Germany
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Kumar S, Wirths O, Theil S, Gerth J, Bayer TA, Walter J. Early intraneuronal accumulation and increased aggregation of phosphorylated Abeta in a mouse model of Alzheimer's disease. Acta Neuropathol 2013; 125:699-709. [PMID: 23525537 DOI: 10.1007/s00401-013-1107-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 12/13/2022]
Abstract
The progressive accumulation of extracellular amyloid plaques in the brain is a common hallmark of Alzheimer's disease (AD). We recently identified a novel species of Aβ phosphorylated at serine residue 8 with increased propensity to form toxic aggregates as compared to non-phosphorylated species. The age-dependent analysis of Aβ depositions using novel monoclonal phosphorylation-state specific antibodies revealed that phosphorylated Aβ variants accumulate first inside of neurons in a mouse model of AD already at 2 month of age. At higher ages, phosphorylated Aβ is also abundantly detected in extracellular plaques. Besides a large overlap in the spatiotemporal deposition of phosphorylated and non-phosphorylated Aβ species, fractionized extraction of Aβ from brains revealed an increased accumulation of phosphorylated Aβ in oligomeric assemblies as compared to non-phosphorylated Aβ in vivo. Thus, phosphorylated Aβ could represent an important species in the formation and stabilization of neurotoxic aggregates, and might be targeted for AD therapy and diagnosis.
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Affiliation(s)
- Sathish Kumar
- Department of Neurology, University of Bonn, 53127, Bonn, Germany
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Brückner C, Imhof D, Scriba GK. Capillary electrophoretic study of the degradation pathways and kinetics of the aspartyl model tetrapeptide Gly-Phe-Asp-GlyOH in alkaline solution. J Pharm Biomed Anal 2013; 76:96-103. [DOI: 10.1016/j.jpba.2012.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
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Hooi MYS, Raftery MJ, Truscott RJW. Accelerated aging of Asp 58 in αA crystallin and human cataract formation. Exp Eye Res 2012; 106:34-9. [PMID: 23142040 DOI: 10.1016/j.exer.2012.10.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 01/10/2023]
Abstract
Racemisation of amino acids is one of the most abundant modifications in long-lived proteins. In this study racemisation of Asp 58 in the small heat shock protein, αA crystallin, was investigated. In normal human lenses, levels of l-isoAsp, d-isoAsp and d-Asp increased with age, such that by age 70 they accounted for approximately half of the total Asp at this site. Levels of d-isoAsp were significantly higher in all cataract lenses than age-matched normal lenses. The introduction of d-isoAsp in αA crystallin could therefore be associated with the development of cataract. Its more rapid formation in cataract lenses may represent an example of accelerated protein aging leading to a human age-related disease.
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Affiliation(s)
- Michelle Y S Hooi
- Save Sight Institute, Sydney Eye Hospital, University of Sydney, 8 Macquarie Street, Sydney, New South Wales 2000, Australia
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Brückner C, Fahr A, Imhof D, Scriba GK. Degradation Kinetics of an Aspartyl-Tripeptide-Derived Diketopiperazine under Forced Conditions. J Pharm Sci 2012; 101:4178-90. [DOI: 10.1002/jps.23272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/13/2012] [Accepted: 07/02/2012] [Indexed: 12/23/2022]
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Sivan SS, Van El B, Merkher Y, Schmelzer CEH, Zuurmond AM, Heinz A, Wachtel E, Varga PP, Lazary A, Brayda-Bruno M, Maroudas A. Longevity of elastin in human intervertebral disc as probed by the racemization of aspartic acid. Biochim Biophys Acta Gen Subj 2012; 1820:1671-7. [PMID: 22728886 DOI: 10.1016/j.bbagen.2012.06.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 04/30/2012] [Accepted: 06/15/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Aging and degeneration of human intervertebral disc (IVD) are associated with biochemical changes, including racemization and glycation. These changes can only be counteracted by protein turnover. Little is known about the longevity of IVD elastin in health or disease. Yet, such knowledge is important for a quantitative understanding of tissue synthesis and degradation. METHODS We have measured the accumulation of d-Asp and pentosidine in IVD elastin. Samples representing a broad range of ages (28-82years) and degeneration grades (1-5) were analyzed. RESULTS d/l-Asp for elastin increased linearly with age from 3.2% (early 30s) to 14.8% (early 80s) for normal tissue (grades 1-2) and from 1.7% (late 20s) to 6.0% (until the mid 50s) for degenerate tissue (grades 3-5) with accumulation rates of 16.2±3.1×10(-4) and 11.7±3.8×10(-4)year(-1), respectively; no significant difference was found between these values (p<0.05). Above the mid 50s, a decrease in d-Asp accumulation was recorded in the degenerate tissue. d-Asp accumulation correlated well with pentosidine content for elastin from healthy and degenerate tissues combined. We conclude that IVD elastin is metabolically-stable and long-lived in both healthy and degenerate human IVDs, with signs of new synthesis in the latter. The correlation of d-Asp with pentosidine content suggests that both these agents may be used as markers in the overall aging process of IVD. GENERAL SIGNIFICANCE Accumulation of modified IVD elastin argues for its longevity and may have a negative impact on its role in disc function. Weak signs of newly synthesized molecules may act to counteract this effect in degenerate tissue.
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Affiliation(s)
- Sarit-Sara Sivan
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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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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Jawhar S, Wirths O, Bayer TA. Pyroglutamate amyloid-β (Aβ): a hatchet man in Alzheimer disease. J Biol Chem 2011; 286:38825-32. [PMID: 21965666 DOI: 10.1074/jbc.r111.288308] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pyroglutamate-modified amyloid-β (Aβ(pE3)) peptides are gaining considerable attention as potential key participants in the pathology of Alzheimer disease (AD) due to their abundance in AD brain, high aggregation propensity, stability, and cellular toxicity. Transgenic mice that produce high levels of Aβ(pE3-42) show severe neuron loss. Recent in vitro and in vivo experiments have proven that the enzyme glutaminyl cyclase catalyzes the formation of Aβ(pE3). In this minireview, we summarize the current knowledge on Aβ(pE3), discussing its discovery, biochemical properties, molecular events determining formation, prevalence in the brains of AD patients, Alzheimer mouse models, and potential as a target for therapy and as a diagnostic marker.
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Affiliation(s)
- Sadim Jawhar
- Department of Molecular Psychiatry, Georg-August-University Göttingen, University Medicine Göttingen, 37075 Göttingen, Germany
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47
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Macromolecular deterioration as the ultimate constraint on human lifespan. Ageing Res Rev 2011; 10:397-403. [PMID: 21272671 DOI: 10.1016/j.arr.2010.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/07/2010] [Accepted: 12/10/2010] [Indexed: 12/25/2022]
Abstract
A number of tissues and organs in the human body contain abundant proteins that are long-lived. This includes the heart, lung, brain, bone and connective tissues. It is proposed that the accumulation of modifications to such long-lived proteins over a period of decades alters the properties of the organs and tissues in which they reside. Such insidious processes may affect human health, fitness and ultimately may limit our lifespan. The human lens, which contains proteins that do not turnover, is used to illustrate the impact of these gradual deleterious modifications. On the basis of data derived from the lens, it is postulated that the intrinsic instability of certain amino acid residues, which leads to truncation, racemisation and deamidation, is primarily responsible for the age-related deterioration of such proteins. Since these post-translational modifications accumulate over a period of many years, they can only be studied using organisms that have lifespans measured in decades. One conclusion is that there may be important aspects of human aging that can be studied only using long-lived animals.
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Substrate stereoselectivity of mammalian D-aspartyl endopeptidase. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3349-52. [PMID: 21944696 DOI: 10.1016/j.jchromb.2011.08.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 08/20/2011] [Accepted: 08/24/2011] [Indexed: 11/24/2022]
Abstract
The formation and accumulation of D-aspartate residue (D-Asp) in proteins caused by oxidative stress leads to dysfunction and/or denaturation of proteins, and is consequently responsible for aging-related misfolding diseases such as cataracts, prion disease, and Alzheimer's disease. We sought to identify that an unknown protease selectively degrades the noxious D-Asp-containing protein, namely D-aspartyl endopeptidase (DAEP), and finally purified it from the inner mitochondrial membrane of mouse liver. In order to analyze the substrate stereoselectivity of DAEP, we synthesized a peptide corresponding to 55-65 (Thr-Val-Leu-Asp-Ser-Gly-Ile-Ser-Glu-Val-Arg) of human αA-crystallin and its corresponding diastereoisomers in which L-α-Asp was replaced with L-β-, D-α- or D-β-Asp residue at position 58. Following incubation of that peptide with purified DAEP, it was only degraded at D-α-Asp(58), independent of ATP or NAD. This result indicates that DAEP stereoselectively recognizes and degrades its substrate at the internal D-α-Asp residue. DAEP therefore seems to physiologically serve as the quality control system against the noxious D-Asp-containing protein in the long life span of mammals.
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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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Amano M, Hasegawa J, Kobayashi N, Kishi N, Nakazawa T, Uchiyama S, Fukui K. Specific Racemization of Heavy-Chain Cysteine-220 in the Hinge Region of Immunoglobulin Gamma 1 as a Possible Cause of Degradation during Storage. Anal Chem 2011; 83:3857-64. [DOI: 10.1021/ac200321v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Masato Amano
- Analytical & Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Jun Hasegawa
- Analytical & Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Naoki Kobayashi
- Analytical & Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Naoyuki Kishi
- Analytical & Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Kiichi Fukui
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
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