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Structural Characterization and Physicochemical Stability Profile of a Double Mutant Heat Labile Toxin Protein Based Adjuvant. J Pharm Sci 2017; 106:3474-3485. [PMID: 28780391 PMCID: PMC5690273 DOI: 10.1016/j.xphs.2017.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 01/07/2023]
Abstract
A novel protein adjuvant double-mutant Escherichia coli heat-labile toxin, LT (R192G/L211A) or dmLT, is in preclinical and early clinical development with various vaccine candidates. Structural characterization and formulation development of dmLT will play a key role in its successful process development, scale-up/transfer, and commercial manufacturing. This work describes extensive analytical characterization of structural integrity and physicochemical stability profile of dmLT from a lyophilized clinical formulation. Reconstituted dmLT contained a heterogeneous mixture of intact holotoxin (AB5, ∼75%) and free B5 subunit (∼25%) as assessed by analytical ultracentrifugation and hydrophobic interaction chromatography. Intact mass spectrometry (MS) analysis revealed presence of Lys84 glycation near the native sugar-binding site in dmLT, and forced degradation studies using liquid chromatography-MS peptide mapping demonstrated specific Asn deamidation and Met oxidation sites. Using multiple biophysical measurements, dmLT was found most stable between pH 6.5 and 7.5 and at temperatures ≤50°C. In addition, soluble aggregates and particle formation were observed upon shaking stress. By identifying the physicochemical degradation pathways of dmLT using newly developed stability-indicating analytical methods from this study, we aim at developing more stable candidate formulations of dmLT that will minimize the formation of degradants and improve storage stability, as both a frozen bulk substance and eventually as a liquid final dosage form.
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52
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Monocyte adhesion to atherosclerotic matrix proteins is enhanced by Asn-Gly-Arg deamidation. Sci Rep 2017; 7:5765. [PMID: 28720870 PMCID: PMC5515959 DOI: 10.1038/s41598-017-06202-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/09/2017] [Indexed: 12/25/2022] Open
Abstract
Atherosclerosis arises from leukocyte infiltration and thickening of the artery walls and constitutes a major component of vascular disease pathology, but the molecular events underpinning this process are not fully understood. Proteins containing an Asn-Gly-Arg (NGR) motif readily undergo deamidation of asparagine to generate isoDGR structures that bind to integrin αvβ3 on circulating leukocytes. Here we report the identification of isoDGR motifs in human atherosclerotic plaque components including extracellular matrix (ECM) proteins fibronectin and tenascin C, which have been strongly implicated in human atherosclerosis. We further demonstrate that deamidation of NGR motifs in fibronectin and tenascin C leads to increased adhesion of the monocytic cell line U937 and enhanced binding of primary human monocytes, except in the presence of a αvβ3-blocking antibody or the αv-selective inhibitor cilengitide. In contrast, under the same deamidating conditions monocyte-macrophages displayed only weak binding to the alternative ECM component vitronectin which lacks NGR motifs. Together, these findings confirm a critical role for isoDGR motifs in mediating leukocyte adhesion to the ECM via integrin αvβ3 and suggest that protein deamidation may promote the pathological progression of human atherosclerosis by enhancing monocyte recruitment to developing plaques.
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53
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Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC Genomics 2017; 18:301. [PMID: 28412930 PMCID: PMC5392934 DOI: 10.1186/s12864-017-3676-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/31/2017] [Indexed: 01/24/2023] Open
Abstract
Background Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. Results We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Conclusions Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3676-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin W Brown
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Viswanadham Sridhara
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel R Boutz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Maria D Person
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Edward M Marcotte
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Jeffrey E Barrick
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA. .,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA. .,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA.
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54
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Lyon YA, Sabbah GM, Julian RR. Identification of Sequence Similarities among Isomerization Hotspots in Crystallin Proteins. J Proteome Res 2017; 16:1797-1805. [PMID: 28234481 PMCID: PMC5387677 DOI: 10.1021/acs.jproteome.7b00073] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The eye lens crystallins represent
an ideal target for studying
the effects of aging on protein structure. Herein we examine separately
the water-soluble (WS) and water-insoluble (WI) crystallin fractions
and identify sites of isomerization and epimerization. Both collision-induced
dissociation and radical-directed dissociation are needed for detection
of these non-mass-shifting post-translational modifications. Isomerization
levels differ significantly between the WS and the WI fractions from
sheep, pig, and cow eye lenses. Residues that are most susceptible
to isomerization are identified site-specifically and are found to
reside in structurally disordered regions. However, isomerization
in structured domains, although less common, often yields more dramatic
effects on solubility. Numerous isomerization hotspots were also identified
and occur in regions with aspartic acid and serine repeats. For example, 128KMEIVDDDVPSLW140 in βB3
crystallin contains three sequential aspartic acid residues and is
isomerized heavily in the WI fractions, while it is not modified at
all in the WS fractions. Potential causes for enhanced isomerization
at sites with acidic residue repeats are presented. The importance
of acidic residue repeats extends beyond the lens, as they are found
in many other long-lived proteins associated with disease.
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Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California , Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Georgette M Sabbah
- Department of Chemistry, University of California , Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California , Riverside, 501 Big Springs Road, Riverside, California 92521, United States
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55
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Succinimide Formation from an NGR-Containing Cyclic Peptide: Computational Evidence for Catalytic Roles of Phosphate Buffer and the Arginine Side Chain. Int J Mol Sci 2017; 18:ijms18020429. [PMID: 28212316 PMCID: PMC5343963 DOI: 10.3390/ijms18020429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/17/2017] [Accepted: 02/10/2017] [Indexed: 12/31/2022] Open
Abstract
The Asn-Gly-Arg (NGR) motif and its deamidation product isoAsp-Gly-Arg (isoDGR) have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the corresponding isoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual targeting strategies. It is well known that the Asn deamidation proceeds via a succinimide derivative. In the present study, we computationally investigated the mechanism of succinimide formation from a cyclic peptide, c[CH2CO-NGRC]-NH2, which has recently been shown to undergo rapid deamidation in a phosphate buffer. An H2PO4− ion was explicitly included in the calculations. We employed the density functional theory using the B3LYP functional. While geometry optimizations were performed in the gas phase, hydration Gibbs energies were calculated by the SM8 (solvation model 8) continuum model. We have found a pathway leading to the five-membered ring tetrahedral intermediate in which both the H2PO4− ion and the Arg side chain act as catalyst. This intermediate, once protonated at the NH2 group on the five-membered ring, was shown to easily undergo NH3 elimination leading to the succinimide formation. This study is the first to propose a possible catalytic role for the Arg side chain in the NGR deamidation.
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56
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Tran JC, Tran D, Hilderbrand A, Andersen N, Huang T, Reif K, Hotzel I, Stefanich EG, Liu Y, Wang J. Automated Affinity Capture and On-Tip Digestion to Accurately Quantitate in Vivo Deamidation of Therapeutic Antibodies. Anal Chem 2016; 88:11521-11526. [PMID: 27797494 DOI: 10.1021/acs.analchem.6b02766] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deamidation of therapeutic antibodies may result in decreased drug activity and undesirable changes in pharmacokinetics and immunogenicity. Therefore, it is necessary to monitor the deamidation levels [during storage] and after in vivo administration. Because of the complexity of in vivo samples, immuno-affinity capture is widely used for specific enrichment of the target antibody prior to LC-MS. However, the conventional use of bead-based methods requires large sample volumes and extensive processing steps. Furthermore, with automation difficulties and extended sample preparation time, bead-based approaches may increase artificial deamidation. To overcome these challenges, we developed an automated platform to perform tip-based affinity capture of antibodies from complex matrixes with rapid digestion and peptide elution into 96-well microtiter plates followed by LC-MS analysis. Detailed analyses showed that the new method presents high repeatability and reproducibility with both intra and inter assay CVs < 8%. Using the automated platform, we successfully quantified the levels of deamidation of a humanized monoclonal antibody in cynomolgus monkeys over a time period of 12 weeks after administration. Moreover, we found that deamidation kinetics between in vivo samples and samples stressed in vitro at neutral pH were consistent, suggesting that the in vitro stress test may be used as a method to predict the liability to deamidation of therapeutic antibodies in vivo.
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Affiliation(s)
- John C Tran
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Daniel Tran
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Amy Hilderbrand
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Nisana Andersen
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Tao Huang
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Karin Reif
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Isidro Hotzel
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Eric G Stefanich
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Yichin Liu
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Jianyong Wang
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
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Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne. Proc Natl Acad Sci U S A 2016; 113:11162-11167. [PMID: 27638212 DOI: 10.1073/pnas.1605834113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.
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58
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Quantification of in vivo site-specific Asp isomerization and Asn deamidation of mAbs in animal serum using IP-LC–MS. Bioanalysis 2016; 8:1611-1622. [DOI: 10.4155/bio-2016-0035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background: Isomerization of aspartic acid and deamidation of asparagine are two common amino acid modifications that are of particular concern if located within the complementarity-determining region of therapeutic antibodies. Questions arise as to the extent of modification occurring in circulation due to potential exposure of the therapeutic antibody to different pH regimes. Results: To enable evaluation of site-specific isomerization and deamidation of human mAbs in vivo, immunoprecipitation (IP) has been combined with LC–MS providing selective enrichment, separation and detection of naive and modified forms of tryptic peptides comprising complementarity-determining region sequences. Conclusion: IP-LC–MS can be applied to simultaneously quantify in vivo drug concentrations and measure the extent of isomerization or deamidation in PK studies conducted during the drug discovery stage.
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59
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Thaysen-Andersen M, Chertova E, Bergamaschi C, Moh ESX, Chertov O, Roser J, Sowder R, Bear J, Lifson J, Packer NH, Felber BK, Pavlakis GN. Recombinant human heterodimeric IL-15 complex displays extensive and reproducible N- and O-linked glycosylation. Glycoconj J 2016; 33:417-33. [PMID: 26563299 PMCID: PMC7537637 DOI: 10.1007/s10719-015-9627-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 09/30/2015] [Accepted: 10/11/2015] [Indexed: 01/25/2023]
Abstract
Human interleukin 15 (IL-15) circulates in blood as a stable molecular complex with the soluble IL-15 receptor alpha (sIL-15Rα). This heterodimeric IL-15:sIL-15Rα complex (hetIL-15) shows therapeutic potential by promoting the growth, mobilization and activation of lymphocytes and is currently evaluated in clinical trials. Favorable pharmacokinetic properties are associated with the heterodimeric formation and the glycosylation of hetIL-15, which, however, remains largely uncharacterized. We report the site-specific N- and O-glycosylation of two clinically relevant large-scale preparations of HEK293-derived recombinant human hetIL-15. Intact IL-15 and sIL-15Rα and derived glycans and glycopeptides were separately profiled using multiple LC-MS/MS strategies. IL-15 Asn79 and sIL-15Rα Asn107 carried the same repertoire of biosynthetically-related N-glycans covering mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures. The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. Mass analysis of intact IL-15 confirmed its N-glycosylation and suggested that Asn79-glycosylation partially prevents Asn77-deamidation. IL-15 contained no O-glycans, whereas sIL-15Rα was heavily O-glycosylated with partially sialylated core 1 and 2-type mono- to hexasaccharides on Thr2, Thr81, Thr86, Thr156, Ser158, and Ser160. The sialoglycans displayed α2-3- and α2-6-NeuAc-type sialylation. Non-human, potentially immunogenic glycoepitopes (e.g. N-glycolylneuraminic acid and α-galactosylation) were not displayed by hetIL-15. Highly reproducible glycosylation of IL-15 and sIL-15Rα of two batches of hetIL-15 demonstrated consistent manufacturing and purification. In conclusion, we document the heterogeneous and reproducible N- and O-glycosylation of large-scale preparations of the therapeutic candidate hetIL-15. Site-specific mapping of these molecular features is important to evaluate the consistent large-scale production and clinical efficacy of hetIL-15.
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Affiliation(s)
- M Thaysen-Andersen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - E Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - C Bergamaschi
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - E S X Moh
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - O Chertov
- Cancer Research Technology Program, Leidos Biomedical, Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - J Roser
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - R Sowder
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - J Bear
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - J Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - N H Packer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - B K Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - G N Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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60
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McLaughlin RJ, de Haan A, Zaldumbide A, de Koning EJ, de Ru AH, van Veelen PA, van Lummel M, Roep BO. Human islets and dendritic cells generate post-translationally modified islet autoantigens. Clin Exp Immunol 2016; 185:133-40. [PMID: 26861694 DOI: 10.1111/cei.12775] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 02/07/2016] [Indexed: 12/14/2022] Open
Abstract
The initiation of type 1 diabetes (T1D) requires a break in peripheral tolerance. New insights into neoepitope formation indicate that post-translational modification of islet autoantigens, for example via deamidation, may be an important component of disease initiation or exacerbation. Indeed, deamidation of islet autoantigens increases their binding affinity to the T1D highest-risk human leucocyte antigen (HLA) haplotypes HLA-DR3/DQ2 and -DR4/DQ8, increasing the chance that T cells reactive to deamidated autoantigens can be activated upon T cell receptor ligation. Here we investigated human pancreatic islets and inflammatory and tolerogenic human dendritic cells (DC and tolDC) as potential sources of deamidated islet autoantigens and examined whether deamidation is altered in an inflammatory environment. Islets, DC and tolDC contained tissue transglutaminase, the key enzyme responsible for peptide deamidation, and enzyme activity increased following an inflammatory insult. Islets treated with inflammatory cytokines were found to contain deamidated insulin C-peptide. DC, heterozygous for the T1D highest-risk DQ2/8, pulsed with native islet autoantigens could present naturally processed deamidated neoepitopes. HLA-DQ2 or -DQ8 homozygous DC did not present deamidated islet peptides. This study identifies both human islets and DC as sources of deamidated islet autoantigens and implicates inflammatory activation of tissue transglutaminase as a potential mechanism for islet and DC deamidation.
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Affiliation(s)
- R J McLaughlin
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - A de Haan
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - A Zaldumbide
- Department of Molecular Cell Biology, Leiden, the Netherlands
| | - E J de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
| | - A H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - P A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - M van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - B O Roep
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands.,Department of Diabetes Immunology, Diabetes and Metabolism Research Institute at the Beckman Research Institute of the City of Hope, Duarte, CA, USA
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61
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Takahashi O, Manabe N, Kirikoshi R. A Computational Study of the Mechanism of Succinimide Formation in the Asn-His Sequence: Intramolecular Catalysis by the His Side Chain. Molecules 2016; 21:327. [PMID: 27005609 PMCID: PMC6274526 DOI: 10.3390/molecules21030327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn-His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace-Asn-His-Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH₂ group, easily releases an ammonia molecule to give the succinimide species.
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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.
| | - Noriyoshi Manabe
- 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.
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62
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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Bults P, Bischoff R, Bakker H, Gietema JA, van de Merbel NC. LC-MS/MS-Based Monitoring of In Vivo Protein Biotransformation: Quantitative Determination of Trastuzumab and Its Deamidation Products in Human Plasma. Anal Chem 2016; 88:1871-7. [DOI: 10.1021/acs.analchem.5b04276] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter Bults
- Bioanalytical
Laboratory, PRA Health Sciences, Early Development Services, Amerikaweg 18, 9407
TK Assen, The Netherlands
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
| | - Hilde Bakker
- Bioanalytical
Laboratory, PRA Health Sciences, Early Development Services, Amerikaweg 18, 9407
TK Assen, The Netherlands
| | - Jourik A. Gietema
- Faculty
of Medical Sciences, Department of Medical Oncology, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nico C. van de Merbel
- Bioanalytical
Laboratory, PRA Health Sciences, Early Development Services, Amerikaweg 18, 9407
TK Assen, The Netherlands
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
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64
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Synthesis of Novel Protected Nα(ω-Drug) Amino Acid Building Units for Facile Preparation of Anticancer Drug-Conjugates. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-015-9509-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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65
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Zacchi LF, Schulz BL. N-glycoprotein macroheterogeneity: biological implications and proteomic characterization. Glycoconj J 2015; 33:359-76. [DOI: 10.1007/s10719-015-9641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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66
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Barbariga M, Curnis F, Andolfo A, Zanardi A, Lazzaro M, Conti A, Magnani G, Volontè MA, Ferrari L, Comi G, Corti A, Alessio M. Ceruloplasmin functional changes in Parkinson's disease-cerebrospinal fluid. Mol Neurodegener 2015; 10:59. [PMID: 26537957 PMCID: PMC4634150 DOI: 10.1186/s13024-015-0055-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/29/2015] [Indexed: 01/23/2023] Open
Abstract
Background Ceruloplasmin, a ferroxidase present in cerebrospinal fluid (CSF), plays a role in iron homeostasis protecting tissues from oxidative damage. Its reduced enzymatic activity was reported in Parkinson’s disease (PD) contributing to the pathological iron accumulation. We previously showed that ceruloplasmin is modified by oxidation in vivo, and, in addition, in vitro by deamidation of specific NGR-motifs that foster the gain of integrin-binding function. Here we investigated whether the loss of ceruloplasmin ferroxidase activity in the CSF of PD patients was accompanied by NGR-motifs deamidation and gain of function. Results We have found that endogenous ceruloplasmin in the CSF of PD patients showed structural changes, deamidation of the 962NGR-motif which is usually hidden within the ceruloplasmin structure, and the gain of integrin-binding function. These effects occur owing to the presence of abnormal levels of hydrogen peroxide we detected in the CSF of PD patients. Interestingly, the pathological CSF's environment of PD patients promoted the same modifications in the exogenously added ceruloplasmin, which in turn resulted in loss of ferroxidase-activity and acquisition of integrin-binding properties. Conclusions We show that in pathological oxidative environment of PD-CSF the endogenous ceruloplasmin, in addition to loss-of-ferroxidase function, is modified as to gain integrin-binding function. These findings, beside the known role of ceruloplasmin in iron homeostasis, might have important pathogenic implications due to the potential triggering of signals mediated by the unusual integrin binding in cells of central nervous system. Furthermore, there are pharmacological implications because, based on data obtained in murine models, the administration of ceruloplasmin has been proposed as potential therapeutic treatment of PD, however, the observed CSF's pro-oxidant properties raise the possibility that in human the ceruloplasmin-based therapeutic approach might not be efficacious. Electronic supplementary material The online version of this article (doi:10.1186/s13024-015-0055-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Barbariga
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Present address: Translational Neurology group, Wallenberg Neuroscience Center, BMC A10, 221 84, Lund, Sweden.
| | - Flavio Curnis
- Tumor Biology and Vascular Targeting, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Annapaola Andolfo
- ProMiFa-Protein Microsequencing Facility, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Alan Zanardi
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Vita-Salute San Raffaele University, via Olgettina 60, 20132, Milan, Italy.
| | - Massimo Lazzaro
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Antonio Conti
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Giuseppe Magnani
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Maria Antonietta Volontè
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Laura Ferrari
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Giancarlo Comi
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Vita-Salute San Raffaele University, via Olgettina 60, 20132, Milan, Italy.
| | - Angelo Corti
- Tumor Biology and Vascular Targeting, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Massimo Alessio
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
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67
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O'Connell NE, Lelli K, Mann RS, Palmer AG. Asparagine deamidation reduces DNA-binding affinity of the Drosophila melanogaster Scr homeodomain. FEBS Lett 2015; 589:3237-41. [PMID: 26435141 DOI: 10.1016/j.febslet.2015.09.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/07/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022]
Abstract
Spontaneous deamidation of asparagine is a non-enzymatic post-translational modification of proteins. Residue Asn 321 is the main site of deamidation of the Drosophila melanogaster Hox transcription factor Sex Combs Reduced (Scr). Formation of iso-aspartate, the major deamidation product, is detected by HNCACB triple-resonance NMR spectroscopy. The rate of deamidation is quantified by fitting the decay of Asn NH2 side-chain signals in a time-series of (15)N-(1)H HSQC NMR spectra. The deamidated form of Scr binds to specific DNA target sequences with reduced affinity as determined by an electrophoretic mobility shift assay.
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Affiliation(s)
- Nichole E O'Connell
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
| | - Katherine Lelli
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
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68
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Tvardovskiy A, Wrzesinski K, Sidoli S, Fey SJ, Rogowska-Wrzesinska A, Jensen ON. Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns. Mol Cell Proteomics 2015; 14:3142-53. [PMID: 26424599 DOI: 10.1074/mcp.m115.048975] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 12/28/2022] Open
Abstract
Post-translational modifications (PTMs) of histone proteins play a fundamental role in regulation of DNA-templated processes. There is also growing evidence that proteolytic cleavage of histone N-terminal tails, known as histone clipping, influences nucleosome dynamics and functional properties. Using top-down and middle-down protein analysis by mass spectrometry, we report histone H2B and H3 N-terminal tail clipping in human hepatocytes and demonstrate a relationship between clipping and co-existing PTMs of histone H3. Histones H2B and H3 undergo proteolytic processing in primary human hepatocytes and the hepatocellular carcinoma cell line HepG2/C3A when grown in spheroid (3D) culture, but not in a flat (2D) culture. Using tandem mass spectrometry we localized four different clipping sites in H3 and one clipping site in H2B. We show that in spheroid culture clipped H3 proteoforms are mainly represented by canonical histone H3, whereas in primary hepatocytes over 90% of clipped H3 correspond to the histone variant H3.3. Comprehensive analysis of histone H3 modifications revealed a series of PTMs, including K14me1, K27me2/K27me3, and K36me1/me2, which are differentially abundant in clipped and intact H3. Analysis of co-existing PTMs revealed negative crosstalk between H3K36 methylation and H3K23 acetylation in clipped H3. Our data provide the first evidence of histone clipping in human hepatocytes and demonstrate that clipped H3 carry distinct co-existing PTMs different from those in intact H3.
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Affiliation(s)
- Andrey Tvardovskiy
- From the ‡Department of Biochemistry and Molecular Biology and §Center for Epigenetics, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK - 5230 Odense M, Denmark
| | | | - Simone Sidoli
- From the ‡Department of Biochemistry and Molecular Biology and §Center for Epigenetics, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK - 5230 Odense M, Denmark
| | - Stephen J Fey
- From the ‡Department of Biochemistry and Molecular Biology and
| | - Adelina Rogowska-Wrzesinska
- From the ‡Department of Biochemistry and Molecular Biology and §Center for Epigenetics, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK - 5230 Odense M, Denmark
| | - Ole N Jensen
- From the ‡Department of Biochemistry and Molecular Biology and §Center for Epigenetics, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK - 5230 Odense M, Denmark
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69
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Truscott RJW, Friedrich MG. The etiology of human age-related cataract. Proteins don't last forever. Biochim Biophys Acta Gen Subj 2015; 1860:192-8. [PMID: 26318017 DOI: 10.1016/j.bbagen.2015.08.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND It is probable that the great majority of human cataract results from the spontaneous decomposition of long-lived macromolecules in the human lens. Breakdown/reaction of long-lived proteins is of primary importance and recent proteomic analysis has enabled the identification of the particular crystallins, and their exact sites of amino acid modification. SCOPE OF REVIEW Analysis of proteins from cataractous lenses revealed that there are sites on some structural proteins that show a consistently greater degree of deterioration than age-matched normal lenses. MAJOR CONCLUSIONS The most abundant posttranslational modification of aged lens proteins is racemization. Deamidation, truncation and crosslinking, each arising from the spontaneous breakdown of susceptible amino acids within proteins, are also present. Fundamental to an understanding of nuclear cataract etiology, it is proposed that once a certain degree of modification at key sites occurs, that protein-protein interactions are disrupted and lens opacification ensues. GENERAL SIGNIFICANCE Since long-lived proteins are now recognized to be present in many other sites of the body, such as the brain, the information gleaned from detailed analyses of degraded proteins from aged lenses will apply more widely to other age-related human diseases. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.
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Affiliation(s)
- Roger J W Truscott
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Michael G Friedrich
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
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70
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Ince HH, Konuklar FAS, Ugur I, Ozcan ÖA, Sayadi M, Feig M, Aviyente V. Role of then+1 amino acid residue on the deamidation of asparagine in pentapeptides. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1068394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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71
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Xu Y, Bailey UM, Schulz BL. Automated measurement of site-specific N
-glycosylation occupancy with SWATH-MS. Proteomics 2015; 15:2177-86. [DOI: 10.1002/pmic.201400465] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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72
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Rasheed F, Newson WR, Plivelic TS, Kuktaite R, Hedenqvist MS, Gällstedt M, Johansson E. Macromolecular changes and nano-structural arrangements in gliadin and glutenin films upon chemical modification: Relation to functionality. Int J Biol Macromol 2015; 79:151-9. [PMID: 25936284 DOI: 10.1016/j.ijbiomac.2015.04.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022]
Abstract
Protein macromolecules adopted for biological and bio-based material functions are known to develop a structured protein network upon chemical modification. In this study, we aimed to evaluate the impact of chemical additives such as, NaOH, NH4OH and salicylic acid (SA), on the secondary and nano-structural transitions of wheat proteins. Further, the effect of chemically induced modifications in protein macromolecular structure was anticipated in relation to functional properties. The gliadin-NH4OH-SA film showed a supramolecular protein organization into hexagonal structures with 65 Å lattice parameter, and other not previously observed structural entities having a characteristic distance of 50 Å. Proteins in gliadin-NH4OH-SA films were highly polymerized, with increased amount of disulfide crosslinks and β-sheets, causing improved strength and stiffness. Glutenin and WG proteins with NH4OH-SA showed extensive aggregation and an increase in β-sheet content together with irreversible crosslinks. Irreversible crosslinks hindered a high order structure formation in glutenins, and this resulted in films with only moderately improved stiffness. Thus, formation of nano-hierarchical structures based on β-sheets and disulfide crosslinks are the major reasons of high strength and stiffness in wheat protein based films.
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Affiliation(s)
- Faiza Rasheed
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, SE-230 53, Box 101, Alnarp, Sweden.
| | - William R Newson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, SE-230 53, Box 101, Alnarp, Sweden
| | - Tomás S Plivelic
- MAX IV Laboratory, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Ramune Kuktaite
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, SE-230 53, Box 101, Alnarp, Sweden
| | - Mikael S Hedenqvist
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Fibre and Polymer Technology, SE-10044 Stockholm, Sweden
| | | | - Eva Johansson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, SE-230 53, Box 101, Alnarp, Sweden
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73
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Soulby AJ, Heal JW, Barrow MP, Roemer RA, O'Connor PB. Does deamidation cause protein unfolding? A top-down tandem mass spectrometry study. Protein Sci 2015; 24:850-60. [PMID: 25653127 DOI: 10.1002/pro.2659] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 01/25/2023]
Abstract
Deamidation is a nonenzymatic post-translational modification of asparagine to aspartic acid or glutamine to glutamic acid, converting an uncharged amino acid to a negatively charged residue. It is plausible that deamidation of asparagine and glutamine residues would result in disruption of a proteins' hydrogen bonding network and thus lead to protein unfolding. To test this hypothesis Calmodulin and B2M were deamidated and analyzed using tandem mass spectrometry on a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). The gas phase hydrogen bonding networks of deamidated and nondeamidated protein isoforms were probed by varying the infra-red multi-photon dissociation laser power in a linear fashion and plotting the resulting electron capture dissociation fragment intensities as a melting curve at each amino acid residue. Analysis of the unfolding maps highlighted increased fragmentation at lower laser powers localized around heavily deamidated regions of the proteins. In addition fragment intensities were decreased across the rest of the proteins which we propose is because of the formation of salt-bridges strengthening the intramolecular interactions of the central regions. These results were supported by a computational flexibility analysis of the mutant and unmodified proteins, which would suggest that deamidation can affect the global structure of a protein via modification of the hydrogen bonding network near the deamidation site and that top down FTICR-MS is an appropriate technique for studying protein folding.
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Affiliation(s)
- Andrew J Soulby
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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74
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Hao P, Ren Y, Datta A, Tam JP, Sze SK. Evaluation of the Effect of Trypsin Digestion Buffers on Artificial Deamidation. J Proteome Res 2014; 14:1308-14. [DOI: 10.1021/pr500903b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Piliang Hao
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yan Ren
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
| | - Arnab Datta
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
| | - James P. Tam
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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75
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Bergström T, Fredriksson SÅ, Nilsson C, Åstot C. Deamidation in ricin studied by capillary zone electrophoresis- and liquid chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 974:109-17. [PMID: 25463205 DOI: 10.1016/j.jchromb.2014.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/24/2014] [Accepted: 10/07/2014] [Indexed: 12/29/2022]
Abstract
Deamidation in ricin, a toxin present in castor beans from the plant Ricinus communis, was investigated using capillary zone electrophoresis (CZE) and liquid chromatography coupled to high resolution mass spectrometry. Potential sites for deamidation, converting asparagine (Asn) into aspartic or isoaspartic acid (Asp or isoAsp), were identified in silico based on the protein sequence motifs and tertiary structure. In parallel, CZE- and LC-MS-based screening were performed on the digested toxin to detect deamidated peptides. The use of CZE-MS was critical for the separation of small native/deamidated peptide pairs. Selected peptides were subjected to a detailed analysis by tandem mass spectrometry to verify the presence of deamidation and determine its exact position. In the ricin preparation studied, deamidation was confirmed and located to three asparagine residues: Asn54 in the A-chain, and Asn42 and Asn60 in the B-chain. Possible in vitro deamidation occurring during sample preparation was monitored using a synthetic peptide with a known and rapid rate of deamidation. Finally, we showed that the isoelectric diversity previously reported in ricin is related to the level of deamidation.
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Affiliation(s)
- Tomas Bergström
- Swedish Defence Research Agency, CBRN Defence and Security, Cementvägen 20, SE-901 82 Umeå, Sweden
| | - Sten-Åke Fredriksson
- Swedish Defence Research Agency, CBRN Defence and Security, Cementvägen 20, SE-901 82 Umeå, Sweden
| | - Calle Nilsson
- Swedish Defence Research Agency, CBRN Defence and Security, Cementvägen 20, SE-901 82 Umeå, Sweden
| | - Crister Åstot
- Swedish Defence Research Agency, CBRN Defence and Security, Cementvägen 20, SE-901 82 Umeå, Sweden.
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76
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Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM. Evidence for lysine acetylation in the coat protein of a polerovirus. J Gen Virol 2014; 95:2321-2327. [PMID: 24939649 PMCID: PMC4165934 DOI: 10.1099/vir.0.066514-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
Virions of the RPV strain of Cereal yellow dwarf virus-RPV were purified from infected oat tissue and analysed by MS. Two conserved residues, K147 and K181, in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional data are available for K147, K181 lies within an interfacial region critical for virion assembly and stability. The signature immonium ion at m/z 126.0919 demonstrated the presence of N-acetyllysine, and the sequence fragment ions enabled an unambiguous assignment of the epsilon-N-acetyl modification on K181. We hypothesize that selection favours acetylation of K181 in a fraction of coat protein monomers to stabilize the capsid by promoting intermonomer salt bridge formation.
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Affiliation(s)
- Michelle Cilia
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Michelle Sweeney
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Stacy L. DeBlasio
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Stewart M. Gray
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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Adav SS, Qian J, Ang YL, Kalaria RN, Lai MKP, Chen CP, Sze SK. iTRAQ quantitative clinical proteomics revealed role of Na(+)K(+)-ATPase and its correlation with deamidation in vascular dementia. J Proteome Res 2014; 13:4635-46. [PMID: 25152327 DOI: 10.1021/pr500754j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dementia is a major public health burden characterized by impaired cognition and loss of function. There are limited treatment options due to inadequate understanding of its pathophysiology and underlying causative mechanisms. Discovery-driven iTRAQ-based quantitative proteomics techniques were applied on frozen brain samples to profile the proteome from vascular dementia (VaD) and age-matched nondementia controls to elucidate the perturbed pathways contributing to pathophysiology of VaD. The iTRAQ quantitative data revealed significant up-regulation of protein-l-isoaspartate O-methyltransferase and sodium-potassium transporting ATPase, while post-translational modification analysis suggested deamidation of catalytic and regulatory subunits of sodium-potassium transporting ATPase. Spontaneous protein deamidation of labile asparagines, generating abnormal l-isoaspartyl residues, is associated with cell aging and dementia due to Alzheimer's disease and may be a cause of neurodegeneration. As ion channel proteins play important roles in cellular signaling processes, alterations in their function by deamidation may lead to perturbations in membrane excitability and neuronal function. Structural modeling of sodium-potassium transporting ATPase revealed the close proximity of these deamidated residues to the catalytic site during E2P confirmation. The deamidated residues may disrupt electrostatic interaction during E1 phosphorylation, which may affect ion transport and signal transduction. Our findings suggest impaired regulation and compromised activity of ion channel proteins contribute to the pathophysiology of VaD.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
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78
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Formolo T, Heckert A, Phinney KW. Analysis of deamidation artifacts induced by microwave-assisted tryptic digestion of a monoclonal antibody. Anal Bioanal Chem 2014; 406:6587-98. [PMID: 25080027 DOI: 10.1007/s00216-014-8043-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/08/2014] [Accepted: 07/16/2014] [Indexed: 12/17/2022]
Abstract
The thorough characterization of biopharmaceuticals is essential for ensuring their quality and safety since many potential variations can cause changes to the properties of a drug that may be detrimental to the patient such as decreased efficacy, shorter half-life or increased immunogenicity. Prior to approval and release, protein-based drugs are subject to a battery of analyses to assess the nature of those parameters that are considered critical quality attributes. In some cases the analytical method used may itself cause modifications that are impossible to distinguish from those induced by the intended test conditions (e.g. storage time/temperature, light exposure) which are used to assess drug stability. It is therefore important to develop and utilize analytical methods which impose as few artifactual modifications as possible. Asparagine deamidation is a common protein modification and it is known to be induced during tryptic digestion. Therefore we examined common tryptic digestion protocols and compared their propensities towards asparagine modification. Since microwave assisted hydrolysis techniques are often used to shorten digestion times and the effect on deamidation is unknown we sought to compare this method against alternate digestion protocols.
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Affiliation(s)
- Trina Formolo
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8314, Gaithersburg, MD, 20899, USA,
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79
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Schweitzer MH, Schroeter ER, Goshe MB. Protein Molecular Data from Ancient (>1 million years old) Fossil Material: Pitfalls, Possibilities and Grand Challenges. Anal Chem 2014; 86:6731-40. [DOI: 10.1021/ac500803w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mary Higby Schweitzer
- North
Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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80
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Xu Y, Bailey UM, Punyadeera C, Schulz BL. Identification of salivary N-glycoproteins and measurement of glycosylation site occupancy by boronate glycoprotein enrichment and liquid chromatography/electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:471-482. [PMID: 24497285 DOI: 10.1002/rcm.6806] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Diseases including cancer and congenital disorders of glycosylation have been associated with changes in the site-specific extent of protein glycosylation. Saliva can be non-invasively sampled and is rich in glycoproteins, giving it the potential to be a useful biofluid for the discovery and detection of disease biomarkers associated with changes in glycosylation. METHODS Saliva was collected from healthy individuals and glycoproteins were enriched using phenylboronic acid based glycoprotein enrichment resin. Proteins were deglycosylated with peptide-N-glycosidase F and digested with AspN or trypsin. Desalted peptides and deglycosylated peptides were separated by reversed-phase liquid chromatography and detected with on-line electrospray ionization quadrupole-time-of-flight mass spectrometry using a 5600 TripleTof instrument. Site-specific glycosylation occupancy was semi-quantitatively determined from the abundance of deglycosylated and nonglycosylated versions of each given peptide. RESULTS Glycoprotein enrichment identified 67 independent glycosylation sites from 24 unique proteins, a 3.9-fold increase in the number of glycosylation sites identified. Enrichment of glycoproteins rather than glycopeptides allowed detection of both deglycosylated and nonglycosylated versions of each peptide, and thereby robust measurement of site-specific occupancy at 21 asparagines. Healthy individuals showed limited biological variability in occupancy, with partially modified sites having characteristics consistent with inefficient glycosylation by oligosaccharyltransferase. Inclusion of negative controls without enzymatic deglycosylation controlled for spontaneous chemical deamidation, and identified asparagines previously incorrectly annotated as glycosylated. CONCLUSIONS We developed a sample preparation and mass spectrometry detection strategy for rapid and efficient measurement of site-specific glycosylation occupancy on diverse salivary glycoproteins suitable for biomarker discovery and detection of changes in glycosylation occupancy in human disease.
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Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
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81
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Qin Z, Yang J, Klassen HJ, Aswad DW. Isoaspartyl protein damage and repair in mouse retina. Invest Ophthalmol Vis Sci 2014; 55:1572-9. [PMID: 24550364 DOI: 10.1167/iovs.13-13668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE To determine the propensity of retinal proteins for spontaneous damage via formation of isoaspartyl sites, a common type of protein damage that could contribute to retinal disease. METHODS Tissue extracts were obtained from retinas and brains of control mice and from mice in which the gene for protein L-isoaspartate O-methyltransferase (PIMT; an enzyme that repairs isoaspartyl protein damage) was knocked out. PIMT expression in these extracts was measured by Western blot, and its specific activity was assayed by monitoring the rate of [(3)H]methyl transfer from S-adenosyl-[methyl-(3)H]L-methionine to γ-globulin. Isoaspartate levels in extracts were measured by their capacity to accept [(3)H]methyl groups via the PIMT-catalyzed methylation reaction. To compare molecular weight distributions of isoaspartyl-rich proteins in retina versus brain, proteins from PIMT knockout (KO) and control mice were separated by SDS-PAGE and transferred to polyvinylidene difluoride (PVDF). Isoaspartyl proteins were (3)H-labeled on-blot using a PIMT overlay and imaged by autoradiography. RESULTS When normalized to the β-actin content of each tissue, retina was found to be nearly identical to brain with regard to expression and activity of PIMT and its propensity to accumulate isoaspartyl sites when PIMT is absent. The two tissues show distinct differences in the molecular weight distribution of isoaspartyl proteins. CONCLUSIONS The retina is rich in PIMT activity and contains a wide range of proteins that are highly susceptible to this type of protein damage. Recoverin may be one such protein. Isoaspartate formation, along with oxidation, should be considered as a potential source of protein dysfunction and autoimmunity in retinal disease.
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Affiliation(s)
- Zhenxia Qin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
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82
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Truscott RJW, Friedrich MG. Old proteins and the Achilles heel of mass spectrometry. The role of proteomics in the etiology of human cataract. Proteomics Clin Appl 2014; 8:195-203. [PMID: 24458544 DOI: 10.1002/prca.201300044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 12/10/2013] [Accepted: 12/16/2013] [Indexed: 11/09/2022]
Abstract
Proteomics may have enabled the root cause of a major human-blinding condition, age-related cataract, to be established. Cataract appears to result from the spontaneous decomposition of long-lived macromolecules in the human lens, and recent proteomic analysis has enabled both the particular crystallins, and the specific sites of amino acid modification within each polypeptide, to be identified. Analysis of proteins from cataract lenses has demonstrated that there are key sites on some structural proteins that show a consistently greater degree of deterioration than age-matched normal lenses. Proteomic analysis, using MS, revealed that the most abundant posttranslational modification of aged lens proteins is racemization. This is somewhat ironic, since structural isomers can be viewed as the "Achilles heel" of MS and there are typically few, if any, differences in the MS/MS spectra of tryptic peptides containing one d-amino acid. It is proposed that once a certain level of spontaneous PTM at key sites occurs, that protein-protein interactions are disrupted, and binding of complexes to cell membranes takes place that impairs cell-to-cell communication. These findings may apply more widely to age-related human diseases, in particular where the deterioration of long-lived proteins is a crucial component in the etiology.
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Affiliation(s)
- Roger J W Truscott
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
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83
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Halim MA, Almatarneh MH, Poirier RA. Mechanistic Study of the Deamidation Reaction of Glutamine: A Computational Approach. J Phys Chem B 2014; 118:2316-30. [DOI: 10.1021/jp4107266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohammad A. Halim
- Department
of Chemistry, Memorial University, St. John’s, NL, Canada A1B 3X7
| | | | - Raymond A. Poirier
- Department
of Chemistry, Memorial University, St. John’s, NL, Canada A1B 3X7
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84
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Gerlei KZ, Élő L, Fiser B, Owen MC, Jákli I, Knak Jensen SJ, Csizmadia IG, Perczel A, Viskolcz B. Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide Cα-radical foldamers. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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85
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Glutamatergic autoencephalitides: an emerging field. J Neural Transm (Vienna) 2014; 121:957-68. [PMID: 24402576 DOI: 10.1007/s00702-013-1152-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/20/2013] [Indexed: 12/19/2022]
Abstract
Autoimmune responses targeting synaptic proteins are associated with a wide range of neurologic symptoms. Among these disorders are those associated with antibodies to ionotropic glutamate receptors, including the NMDAR (N-methyl-D-aspartate receptor) and AMPAR (α-amino-3-hydrozy-5-methyl-4-isoxazolepropionic acid receptor). Patients with anti-NMDAR encephalitis present with psychiatric symptoms, seizures, movement disorders, impaired consciousness, and autonomic derangements; half of patients have an associated ovarian teratoma, and most patients respond to immunosuppressive therapies. Patients' antibodies bind to the amino terminal domain of the NMDAR, and result in loss of NMDARs from synapses with subsequent NMDAR hypofunction. Anti-NMDAR antibodies have now been reported in other neuropsychiatric conditions, including psychosis, dementia, and HSV encephalitis. The pathophysiologic relevance of anti-NMDAR antibodies in these disorders is not yet clear, but their presence may indicate a role for immunotherapy in some patients. Although considerable work remains to be done, our understanding of disorders associated with anti-glutamate receptor antibodies has grown exponentially since they were first described just over 7 years ago, revolutionizing neurology. These antibodies, by interfering with synaptic function, readily link basic science and clinical medicine, and have revealed the impact of sudden but sustained loss of specific neurotransmitter receptors in humans. Improved understanding of their pathophysiology will lead to better treatments for these diseases while providing novel insights regarding the roles of glutamate receptors in learning, memory, and neuropsychiatric disease.
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86
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Barbariga M, Curnis F, Spitaleri A, Andolfo A, Zucchelli C, Lazzaro M, Magnani G, Musco G, Corti A, Alessio M. Oxidation-induced structural changes of ceruloplasmin foster NGR motif deamidation that promotes integrin binding and signaling. J Biol Chem 2013; 289:3736-48. [PMID: 24366863 DOI: 10.1074/jbc.m113.520981] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asparagine deamidation occurs spontaneously in proteins during aging; deamidation of Asn-Gly-Arg (NGR) sites can lead to the formation of isoAsp-Gly-Arg (isoDGR), a motif that can recognize the RGD-binding site of integrins. Ceruloplasmin (Cp), a ferroxidase present in the cerebrospinal fluid (CSF), contains two NGR sites in its sequence: one exposed on the protein surface ((568)NGR) and the other buried in the tertiary structure ((962)NGR). Considering that Cp can undergo oxidative modifications in the CSF of neurodegenerative diseases, we investigated the effect of oxidation on the deamidation of both NGR motifs and, consequently, on the acquisition of integrin binding properties. We observed that the exposed (568)NGR site can deamidate under conditions mimicking accelerated Asn aging. In contrast, the hidden (962)NGR site can deamidate exclusively when aging occurs under oxidative conditions, suggesting that oxidation-induced structural changes foster deamidation at this site. NGR deamidation in Cp was associated with gain of integrin-binding function, intracellular signaling, and cell pro-adhesive activity. Finally, Cp aging in the CSF from Alzheimer disease patients, but not in control CSF, causes Cp deamidation with gain of integrin-binding function, suggesting that this transition might also occur in pathological conditions. In conclusion, both Cp NGR sites can deamidate during aging under oxidative conditions, likely as a consequence of oxidative-induced structural changes, thereby promoting a gain of function in integrin binding, signaling, and cell adhesion.
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87
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Solazzo C, Wilson J, Dyer JM, Clerens S, Plowman JE, von Holstein I, Walton Rogers P, Peacock EE, Collins MJ. Modeling Deamidation in Sheep α-Keratin Peptides and Application to Archeological Wool Textiles. Anal Chem 2013; 86:567-75. [DOI: 10.1021/ac4026362] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Solazzo
- BioArCh, Biology
(S Block), Wentworth Way, University of York, York YO10 5DD, U.K
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | - Julie Wilson
- Department
of Mathematics, University of York, York YO10 5YW, U.K
- Department
of Chemistry, University of York, York YO10 5YW, U.K
| | - Jolon M. Dyer
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
- Biomolecular Interaction
Centre, School of Biological Sciences, University of Canterbury, Private Bag
4800, Christchurch 8140, New Zealand
- Riddet Institute, Massey University, Private
Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Clerens
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | - Jeffrey E. Plowman
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | | | | | - Elizabeth E. Peacock
- NTNU
University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Department
of Conservation, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Matthew J. Collins
- BioArCh, Biology
(S Block), Wentworth Way, University of York, York YO10 5DD, U.K
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88
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Qin Z, Kaufman RS, Khoury RN, Khoury MK, Aswad DW. Isoaspartate accumulation in mouse brain is associated with altered patterns of protein phosphorylation and acetylation, some of which are highly sex-dependent. PLoS One 2013; 8:e80758. [PMID: 24224061 PMCID: PMC3818261 DOI: 10.1371/journal.pone.0080758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/14/2013] [Indexed: 12/05/2022] Open
Abstract
Isoaspartate (isoAsp) formation is a major source of protein damage that is kept in check by the repair function of protein L-isoaspartyl methyltransferase (PIMT). Mice deficient in PIMT accumulate isoAsp-containing proteins, resulting in cognitive deficits, abnormal neuronal physiology and cytoarchitecture, and fatal epileptic seizures 30–60 days after birth. Synapsins I and II, dynamin-1, collapsin response mediator protein 2 (CRMP2), and α/β-tubulin are major targets of PIMT in brain. To investigate links between isoAsp accumulation and the neurological phenotype of the KO mice, we used Western blotting to compare patterns of in vivo phosphorylation or acetylation of the major PIMT targets listed above. Phosphorylations of synapsins I and II at Ser-9 were increased in female KO vs. WT mice, and acetylation of tubulin at Lys-40 was decreased in male KO vs. WT mice. Average levels of dynamin-1 phosphorylation at Ser-778 and Ser-795 were higher in male KO vs. WT mice, but the statistical significance (P>0.1) was low. No changes in phosphorylation were found in synapsins I and II at Ser-603, in CRMP2 at Ser-522 or Thr-514, in DARPP-32 at Thr-34, or in PDK1 at Ser-241. General levels of phosphorylation assessed with Pro-Q Diamond stain, or an anti-phosphotyrosine antibody, appeared similar in the WT and KO mice. We conclude that isoAsp accumulation is associated with altered functional status of several neuronal proteins that are highly susceptible to this type of damage. We also uncovered unexpected differences in how male and female mice respond to isoAsp accumulation in the brain.
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Affiliation(s)
- Zhenxia Qin
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Rachel S. Kaufman
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Rana N. Khoury
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Mitri K. Khoury
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Dana W. Aswad
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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89
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Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2013; 97:265-86. [PMID: 23994099 DOI: 10.1016/j.jprot.2013.08.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/08/2013] [Accepted: 08/10/2013] [Indexed: 12/12/2022]
Abstract
The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Joel A Cain
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Nestor Solis
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006, Australia.
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90
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Dho SH, Deverman BE, Lapid C, Manson SR, Gan L, Riehm JJ, Aurora R, Kwon KS, Weintraub SJ. Control of cellular Bcl-xL levels by deamidation-regulated degradation. PLoS Biol 2013; 11:e1001588. [PMID: 23823868 PMCID: PMC3692414 DOI: 10.1371/journal.pbio.1001588] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 05/07/2013] [Indexed: 02/07/2023] Open
Abstract
Deamidation of two asparagines activates a conditional PEST sequence to target Bcl-xL for degradation. The cellular concentration of Bcl-xL is among the most important determinants of treatment response and overall prognosis in a broad range of tumors as well as an important determinant of the cellular response to several forms of tissue injury. We and others have previously shown that human Bcl-xL undergoes deamidation at two asparaginyl residues and that DNA-damaging antineoplastic agents as well as other stimuli can increase the rate of deamidation. Deamidation results in the replacement of asparginyl residues with aspartyl or isoaspartyl residues. Thus deamidation, like phosphorylation, introduces a negative charge into proteins. Here we show that the level of human Bcl-xL is constantly modulated by deamidation because deamidation, like phosphorylation in other proteins, activates a conditional PEST sequence to target Bcl-xL for degradation. Additionally, we show that degradation of deamidated Bcl-xL is mediated at least in part by calpain. Notably, we present sequence and biochemical data that suggest that deamidation has been conserved from the simplest extant metazoans through the human form of Bcl-xL, underscoring its importance in Bcl-xL regulation. Our findings strongly suggest that deamidation-regulated Bcl-xL degradation is an important component of the cellular rheostat that determines susceptibility to DNA-damaging agents and other death stimuli. Cellular levels of the pro-survival protein Bcl-xL are an important determinant of cellular susceptibility to many death stimuli, including most cancer therapies. We previously showed that human Bcl-xL undergoes deamidation – the conversion of two neutral asparaginyl side-chains into negatively charged aspartyl side-chains – a process that occurs spontaneously but is accelerated by the treatment of tumor cells with DNA-damaging agents. Here, we show that deamidation activates a hitherto undetected signal sequence within Bcl-xL that targets it for degradation by a pathway involving the proteolytic enzyme calpain. This increased degradation of Bcl-xL, and the consequent enhanced cellular susceptibility to programmed cell death, may contribute to the ability of DNA-damaging agents to kill tumors. We also demonstrate that deamidation of Bcl-xL has likely been conserved from the simplest metazoans to humans, underscoring the importance of deamidation in the regulation of Bcl-xL.
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Affiliation(s)
- So Hee Dho
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Laboratory of Cell Signaling, Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon, Korea
| | - Benjamin E. Deverman
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Carlo Lapid
- Department of Biology, Washington University, Saint Louis, Missouri, United States of America
| | - Scott R. Manson
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Lu Gan
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Jacob J. Riehm
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Rajeev Aurora
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ki-Sun Kwon
- Laboratory of Cell Signaling, Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon, Korea
- * E-mail: (K-SK); (SJW)
| | - Steven J. Weintraub
- Division of Urology and The Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Internal Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Internal Medicine, St. Louis VA Medical Center–John Cochran Division, Saint Louis, Missouri, United States of America
- * E-mail: (K-SK); (SJW)
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91
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Vigneswara V, Cass S, Wayne D, Bolt EL, Ray DE, Carter WG. Molecular ageing of alpha- and Beta-synucleins: protein damage and repair mechanisms. PLoS One 2013; 8:e61442. [PMID: 23630590 PMCID: PMC3632608 DOI: 10.1371/journal.pone.0061442] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 03/14/2013] [Indexed: 11/19/2022] Open
Abstract
Abnormal α-synuclein aggregates are hallmarks of a number of neurodegenerative diseases. Alpha synuclein and β-synucleins are susceptible to post-translational modification as isoaspartate protein damage, which is regulated in vivo by the action of the repair enzyme protein L-isoaspartyl O-methyltransferase (PIMT). We aged in vitro native α-synuclein, the α-synuclein familial mutants A30P and A53T that give rise to Parkinsonian phenotypes, and β-synuclein, at physiological pH and temperature for a time course of up to 20 days. Resolution of native α-synuclein and β-synuclein by two dimensional techniques showed the accumulation of a number of post-translationally modified forms of both proteins. The levels of isoaspartate formed over the 20 day time course were quantified by exogenous methylation with PIMT using S-Adenosyl-L-[3H-methyl]methionine as a methyl donor, and liquid scintillation counting of liberated 3H-methanol. All α-synuclein proteins accumulated isoaspartate at ∼1% of molecules/day, ∼20 times faster than for β-synuclein. This disparity between rates of isoaspartate was confirmed by exogenous methylation of synucleins by PIMT, protein resolution by one-dimensional denaturing gel electrophoresis, and visualisation of 3H-methyl esters by autoradiography. Protein silver staining and autoradiography also revealed that α-synucleins accumulated stable oligomers that were resistant to denaturing conditions, and which also contained isoaspartate. Co-incubation of approximately equimolar β-synuclein with α-synuclein resulted in a significant reduction of isoaspartate formed in all α-synucleins after 20 days of ageing. Co-incubated α- and β-synucleins, or α, or β synucleins alone, were resolved by non-denaturing size exclusion chromatography and all formed oligomers of ∼57.5 kDa; consistent with tetramerization. Direct association of α-synuclein with β-synuclein in column fractions or from in vitro ageing co-incubations was demonstrated by their co-immunoprecipitation. These results provide an insight into the molecular differences between α- and β-synucleins during ageing, and highlight the susceptibility of α-synuclein to protein damage, and the potential protective role of β-synuclein.
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Affiliation(s)
- Vasanthy Vigneswara
- School of Biomedical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Simon Cass
- School of Biomedical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Declan Wayne
- School of Graduate Entry Medicine and Health, University of Nottingham Medical School, Royal Derby Hospital, Derby, United Kingdom
| | - Edward L. Bolt
- School of Biomedical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - David E. Ray
- School of Biomedical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Wayne G. Carter
- School of Graduate Entry Medicine and Health, University of Nottingham Medical School, Royal Derby Hospital, Derby, United Kingdom
- * E-mail:
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92
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Jadhav S, Zilka N, Novak M. Protein truncation as a common denominator of human neurodegenerative foldopathies. Mol Neurobiol 2013; 48:516-32. [PMID: 23516100 DOI: 10.1007/s12035-013-8440-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 12/13/2022]
Abstract
Neurodegenerative foldopathies are characterized by aberrant folding of diseased modified proteins, which are major constituents of the intracellular and extracellular lesions. These lesions correlate with the cognitive and/or motor impairment seen in these diseases. The majority of the disease modified proteins in neurodegenerative foldopathies belongs to the group of proteins termed as intrinsically disordered proteins (IDPs). Several independent studies have showed that abnormal protein processing constitutes the key pathological feature of these disorders. The current review focuses on protein truncation as a common denominator of neurodegenerative foldopathies, which is considered to be the major driving force behind the pathological metamorphosis of brain IDPs. The aim of the review is to emphasize the key role of the protein truncation in the pathogenic pathways of neurodegenerative diseases. A deeper understanding of the complex downstream processing of the IDPs, resulting in the generation of pathologically modified proteins might be a prerequisite for the successful therapeutic strategies of several fatal neurodegenerative diseases.
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Affiliation(s)
- Santosh Jadhav
- Institute of Neuroimmunology, Slovak Academy of Sciences, Centre of Excellence for Alzheimer's Disease and Related Disorders, Dubravska cesta 9, 845 10, Bratislava, Slovak Republic
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93
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Chin IS, Murad AMA, Mahadi NM, Nathan S, Bakar FDA. Thermal stability engineering of Glomerella cingulata cutinase. Protein Eng Des Sel 2013; 26:369-75. [DOI: 10.1093/protein/gzt007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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94
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Bailey UM, Schulz BL. Deglycosylation systematically improves N-glycoprotein identification in liquid chromatography-tandem mass spectrometry proteomics for analysis of cell wall stress responses in Saccharomyces cerevisiae lacking Alg3p. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 923-924:16-21. [PMID: 23454304 DOI: 10.1016/j.jchromb.2013.01.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/15/2013] [Accepted: 01/19/2013] [Indexed: 12/15/2022]
Abstract
Post-translational modification of proteins with glycosylation is of key importance in many biological systems in eukaryotes, influencing fundamental biological processes and regulating protein function. Changes in glycosylation are therefore of interest in understanding these processes and are also useful as clinical biomarkers of disease. The presence of glycosylation can also inhibit protease digestion and lower the quality and confidence of protein identification by mass spectrometry. While deglycosylation can improve the efficiency of subsequent protease digest and increase protein coverage, this step is often excluded from proteomic workflows. Here, we performed a systematic analysis that showed that deglycosylation with peptide-N-glycosidase F (PNGase F) prior to protease digestion with AspN or trypsin improved the quality of identification of the yeast cell wall proteome. The improvement in the confidence of identification of glycoproteins following PNGase F deglycosylation correlated with a higher density of glycosylation sites. Optimal identification across the proteome was achieved with PNGase F deglycosylation and complementary proteolysis with either AspN or trypsin. We used this combination of deglycosylation and complementary protease digest to identify changes in the yeast cell wall proteome caused by lack of the Alg3p protein, a key component of the biosynthetic pathway of protein N-glycosylation. The cell wall of yeast lacking Alg3p showed specifically increased levels of Cis3p, a protein important for cell wall integrity. Our results showed that deglycosylation prior to protease digestion improved the quality of proteomic analyses even if protein glycosylation is not of direct relevance to the study at hand.
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Affiliation(s)
- Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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95
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Verma A, McNichol B, Domínguez-Castillo RI, Amador-Molina JC, Arciniega JL, Reiter K, Meade BD, Ngundi MM, Stibitz S, Burns DL. Use of site-directed mutagenesis to model the effects of spontaneous deamidation on the immunogenicity of Bacillus anthracis protective antigen. Infect Immun 2013; 81:278-84. [PMID: 23115046 PMCID: PMC3536148 DOI: 10.1128/iai.00863-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/25/2012] [Indexed: 12/25/2022] Open
Abstract
Long-term stability is a desired characteristic of vaccines, especially anthrax vaccines, which must be stockpiled for large-scale use in an emergency situation; however, spontaneous deamidation of purified vaccine antigens has the potential to adversely affect vaccine immunogenicity over time. In order to explore whether spontaneous deamidation of recombinant protective antigen (rPA)--the major component of new-generation anthrax vaccines--affects vaccine immunogenicity, we created a "genetically deamidated" form of rPA using site-directed mutagenesis to replace six deamidation-prone asparagine residues, at positions 408, 466, 537, 601, 713, and 719, with either aspartate, glutamine, or alanine residues. We found that the structure of the six-Asp mutant rPA was not significantly altered relative to that of the wild-type protein as assessed by circular dichroism (CD) spectroscopy and biological activity. In contrast, immunogenicity of aluminum-adjuvanted six-Asp mutant rPA, as measured by induction of toxin-neutralizing antibodies, was significantly lower than that of the corresponding wild-type rPA vaccine formulation. The six-Gln and six-Ala mutants also exhibited lower immunogenicity than the wild type. While the wild-type rPA vaccine formulation exhibited a high level of immunogenicity initially, its immunogenicity declined significantly upon storage at 25°C for 4 weeks. In contrast, the immunogenicity of the six-Asp mutant rPA vaccine formulation was low initially but did not change significantly upon storage. Taken together, results from this study suggest that spontaneous deamidation of asparagine residues predicted to occur during storage of rPA vaccines would adversely affect vaccine immunogenicity and therefore the storage life of vaccines.
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MESH Headings
- Animals
- Anthrax/immunology
- Anthrax/prevention & control
- Anthrax Vaccines/genetics
- Anthrax Vaccines/immunology
- Anthrax Vaccines/metabolism
- Antibodies, Bacterial/biosynthesis
- Antibodies, Bacterial/immunology
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Neutralizing/immunology
- Antibody Formation/genetics
- Antibody Formation/immunology
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Antigens, Bacterial/metabolism
- Asparagine/immunology
- Asparagine/metabolism
- Bacillus anthracis/genetics
- Bacillus anthracis/immunology
- Bacillus anthracis/metabolism
- Cells, Cultured
- Female
- Macrophages/immunology
- Macrophages/metabolism
- Mice
- Mutagenesis, Site-Directed/methods
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/metabolism
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Affiliation(s)
- Anita Verma
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Beth McNichol
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | | | - Juan C. Amador-Molina
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Juan L. Arciniega
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Karine Reiter
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | | | - Miriam M. Ngundi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Scott Stibitz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | - Drusilla L. Burns
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
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96
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Hurtado PP, O'Connor PB. Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:609-25. [PMID: 22322410 DOI: 10.1002/mas.20357] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Characterization and differentiation of isomers in biological macromolecules using mass spectrometry is one of the most significant challenges facing scientists in the field. The capability of high-resolution MS instruments along with the development of new fragmentation methods now provides the ability to indirectly differentiate between some isomers. This ability has enabled mass spectrometry to evolve into a multidisciplinary technique incorporating areas such as pharmaceutical research, proteomics, polymer science, medicine, environmental chemistry, and recently archeology. This article aims to review recent developments in mass spectrometry methodologies in the identification of structural and spatial isomers in biological macromolecules, such as aspartic acid and isoaspartic acid (Asp/IsoAsp), leucine and isoleucine (Leu/Ile), glutamic acid and γ-glutamic acid, and D/L enantiomers.
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97
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Anti-NMDA receptor encephalitis antibody binding is dependent on amino acid identity of a small region within the GluN1 amino terminal domain. J Neurosci 2012; 32:11082-94. [PMID: 22875940 DOI: 10.1523/jneurosci.0064-12.2012] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Anti-NMDA receptor (NMDAR) encephalitis is a newly identified autoimmune disorder that targets NMDARs, causing severe neurological symptoms including hallucinations, psychosis, and seizures, and may result in death (Dalmau et al., 2008). However, the exact epitope to which these antibodies bind is unknown. A clearly defined antigenic region could provide more precise testing, allow for comparison of immunogenicity between patients to explore potential clinically relevant variations, elucidate the functional effects of antibodies, and make patients' antibodies a more effective tool with which to study NMDAR function. Here, we use human CSF to explore the antigenic region of the NMDAR. We created a series of mutants within the amino terminal domain of GluN1 that change patient antibody binding in transfected cells in stereotyped ways. These mutants demonstrate that the N368/G369 region of GluN1 is crucial for the creation of immunoreactivity. Mass spectrometry experiments show that N368 is glycosylated in transfected cells and rat brain regions; however, this glycosylation is not directly required for epitope formation. Mutations of residues N368/G369 change the closed time of the receptor in single channel recordings; more frequent channel openings correlates with the degree of antibody staining, and acute antibody exposure prolongs open time of the receptor. The staining pattern of mutant receptors is similar across subgroups of patients, indicating consistent immunogenicity, although we have identified one region that has a variable role in epitope formation. These findings provide tools for detailed comparison of antibodies across patients and suggest an interaction between antibody binding and channel function.
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98
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Bailey UM, Jamaluddin MF, Schulz BL. Analysis of Congenital Disorder of Glycosylation-Id in a Yeast Model System Shows Diverse Site-Specific Under-glycosylation of Glycoproteins. J Proteome Res 2012; 11:5376-83. [DOI: 10.1021/pr300599f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Muhammad Fairuz Jamaluddin
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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99
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Wilson J, van Doorn NL, Collins MJ. Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal Chem 2012; 84:9041-8. [PMID: 23030643 DOI: 10.1021/ac301333t] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen peptides are analyzed using a low-cost, high-throughput method for assessing deamidation using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For each chosen peptide, the theoretical distribution is calculated and the measured distribution for each sample compared with this to determine the extent of glutamine deamidation. The deamidation of glutamine (Q) to glutamic acid (E) results in a mass shift of +0.984 Da. Thus, from the resolution of our data, the second peak in the isotope distribution for a peptide containing one glutamine residue coincides with the first peak of the isotope distribution for the peptide in which the residue is deamidated. A genetic algorithm is used to determine the extent of deamidation that gives the best fit to the measured distribution. The method can be extended to peptides containing more than one glutamine residue. The extent of protein degradation assessed in this way could be used, for example, to assess the damage of collagen, and screen samples for radiocarbon dating and DNA analysis.
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Affiliation(s)
- Julie Wilson
- Department of Mathematics, University of York, York YO10 5YW, UK.
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100
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van Doorn NL, Wilson J, Hollund H, Soressi M, Collins MJ. Site-specific deamidation of glutamine: a new marker of bone collagen deterioration. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2319-2327. [PMID: 22956324 DOI: 10.1002/rcm.6351] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Non-enzymatic deamidation accumulates in aging tissues in vivo and has been proposed to be potentially useful as a molecular clock. The process continues post mortem, and here we explore the increase in levels of deamidation in archaeological collagen, as measured during Zooarchaeology by Mass Spectrometry (ZooMS) analysis. METHODS With the high sensitivity of current generation mass spectrometers, ZooMS provides a non-destructive and highly cost-effective method to characterise collagen peptides. Deamidation can be detected by mass spectrometry as a +0.984 Da mass shift; therefore, aside from its original purpose, peptide mass-fingerprinting for bone identification, ZooMS concurrently yields a 'thermal indicator' of the samples. RESULTS By analysis of conventional ZooMS spectra, we determined the deamidation rate for glutamine residues in 911 bone collagen samples from 50 sites, with ages varying from medieval to Palaeolithic. The degree of deamidation was compared to diagenetic parameters and nearby sequence properties. CONCLUSIONS The extent of deamidation was found to be influenced more by burial conditions and thermal age than, for example, chronological age, the extent of bioerosion or crystallinity. The method lends itself mostly to screening heterogenic deposits of bone to identify outliers.
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