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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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Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
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Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
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Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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Nika H, Nieves E, Hawke DH, Angeletti RH. Phosphopeptide enrichment by covalent chromatography after derivatization of protein digests immobilized on reversed-phase supports. J Biomol Tech 2013; 24:154-77. [PMID: 23997662 PMCID: PMC3750845 DOI: 10.7171/jbt.13-2403-004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A rugged sample-preparation method for comprehensive affinity enrichment of phosphopeptides from protein digests has been developed. The method uses a series of chemical reactions to incorporate efficiently and specifically a thiol-functionalized affinity tag into the analyte by barium hydroxide catalyzed β-elimination with Michael addition using 2-aminoethanethiol as nucleophile and subsequent thiolation of the resulting amino group with sulfosuccinimidyl-2-(biotinamido) ethyl-1,3-dithiopropionate. Gentle oxidation of cysteine residues, followed by acetylation of α- and ε-amino groups before these reactions, ensured selectivity of reversible capture of the modified phosphopeptides by covalent chromatography on activated thiol sepharose. The use of C18 reversed-phase supports as a miniaturized reaction bed facilitated optimization of the individual modification steps for throughput and completeness of derivatization. Reagents were exchanged directly on the supports, eliminating sample transfer between the reaction steps and thus, allowing the immobilized analyte to be carried through the multistep reaction scheme with minimal sample loss. The use of this sample-preparation method for phosphopeptide enrichment was demonstrated with low-level amounts of in-gel-digested protein. As applied to tryptic digests of α-S1- and β-casein, the method enabled the enrichment and detection of the phosphorylated peptides contained in the mixture, including the tetraphosphorylated species of β-casein, which has escaped chemical procedures reported previously. The isolates proved highly suitable for mapping the sites of phosphorylation by collisionally induced dissociation. β-Elimination, with consecutive Michael addition, expanded the use of the solid-phase-based enrichment strategy to phosphothreonyl peptides and to phosphoseryl/phosphothreonyl peptides derived from proline-directed kinase substrates and to their O-sulfono- and O-linked β-N-acetylglucosamine (O-GlcNAc)-modified counterparts. Solid-phase enzymatic dephosphorylation proved to be a viable tool to condition O-GlcNAcylated peptide in mixtures with phosphopeptides for selective affinity purification. Acetylation, as an integral step of the sample-preparation method, precluded reduction in recovery of the thiolation substrate caused by intrapeptide lysine-dehydroalanine cross-link formation. The solid-phase analytical platform provides robustness and simplicity of operation using equipment readily available in most biological laboratories and is expected to accommodate additional chemistries to expand the scope of solid-phase serial derivatization for protein structural characterization.
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Affiliation(s)
- Heinz Nika
- Laboratory for Macromolecular Analysis and Proteomics and
- Department for Molecular and Developmental Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; and
| | - Edward Nieves
- Laboratory for Macromolecular Analysis and Proteomics and
| | - David H. Hawke
- Department of Pathology, University of Texas, M.D. Anderson Cancer Center Houston, Texas 77030, USA
| | - Ruth Hogue Angeletti
- Laboratory for Macromolecular Analysis and Proteomics and
- Department for Molecular and Developmental Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; and
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Mano N, Aoki S, Yamazaki T, Nagaya Y, Mori M, Abe K, Shimada M, Yamaguchi H, Goto T, Goto J. Analysis of Phosphorylated Peptides by Double Pseudoneutral Loss Extraction Coupled with Derivatization Using N-(4-Bromobenzoyl)aminoethanethiol. Anal Chem 2009; 81:9395-401. [DOI: 10.1021/ac9017988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Sayaka Aoki
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Takuma Yamazaki
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Yoko Nagaya
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Masaru Mori
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Kohei Abe
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Miki Shimada
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Hiroaki Yamaguchi
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Takaaki Goto
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
| | - Junichi Goto
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, Laboratory of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan, and Laboratory of Bioanalytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai 980-8578, Japan
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