51
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Ling L, Xiao C, Ma Y, Jiang L, Wang S, Guo L, Jiang S, Guo X. 2-Phenyl-3-(p-aminophenyl) Acrylonitrile: A Reactive Matrix for Sensitive and Selective Analysis of Glycans by MALDI-MS. Anal Chem 2019; 91:8801-8807. [DOI: 10.1021/acs.analchem.9b01434] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ling Ling
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Yao Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun130012, China
| | - Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Liming Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Shimei Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun130012, China
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52
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De novo glycan structural identification from mass spectra using tree merging strategy. Comput Biol Chem 2019; 80:217-224. [DOI: 10.1016/j.compbiolchem.2019.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/23/2019] [Indexed: 11/19/2022]
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53
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Gao W, Li H, Liu L, Huang P, Wang Z, Chen W, Ye M, Yu X, Tian R. An integrated strategy for high-sensitive and multi-level glycoproteome analysis from low micrograms of protein samples. J Chromatogr A 2019; 1600:46-54. [PMID: 31036360 DOI: 10.1016/j.chroma.2019.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/26/2019] [Accepted: 04/15/2019] [Indexed: 01/09/2023]
Abstract
Glycosylation, as a biologically important protein post-translational modification, often alters on both glycosites and glycans, simultaneously. However, most of current approaches focused on biased profiling of either glycosites or glycans, and limited by time-consuming process and milligrams of starting protein material. We describe here a simple and integrated spintip-based glycoproteomics technology (termed Glyco-SISPROT) for achieving a comprehensive view of glycoproteome with shorter sample processing time and low microgram starting material. By carefully integrating and optimizing SCX, C18 and Concanavalin A (Con A) packing material and their combination in spintip format, both predigested peptides and protein lysates could be processed by Glyco-SISPROT with high efficiency. More importantly, deglycopeptide, intact glycopeptide and glycans released by multiple glycosidases could be readily collected from the same Glyco-SISPROT workflow for LC-MS analysis. In total, above 1850 glycosites in ˜1770 unique deglycopeptides were characterized from mouse liver by using either 100 μg of predigested peptides or directly using 100 μg of protein lysates, in which about 30% of glycosites were released by both PNGase F and Endos. To the best of our knowledge, this approach should be one of the most comprehensive glycoproteomic approaches by using limited protein starting material. One significant benefit of Glyco-SISPROT is that whole processing time is dramatically reduced from a few days to less than 6 h with good reproducibility when protein lysates were directly processed by Glyco-SISPROT. We expect that this method will be suitable for multi-level glycoproteome analysis of rare biological samples with high sensitivity.
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Affiliation(s)
- Weina Gao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hongjie Li
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liping Liu
- Shenzhen People's Hospital, The First affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Peiwu Huang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Zhikun Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wendong Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaofang Yu
- Shenzhen People's Hospital, The First affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Ruijun Tian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China.
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54
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Dempsey CE, Bigotti MG, Adams JC, Brancaccio A. Analysis of α-Dystroglycan/LG Domain Binding Modes: Investigating Protein Motifs That Regulate the Affinity of Isolated LG Domains. Front Mol Biosci 2019; 6:18. [PMID: 30984766 PMCID: PMC6450144 DOI: 10.3389/fmolb.2019.00018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
Dystroglycan (DG) is an adhesion complex that links the cytoskeleton to the surrounding extracellular matrix in skeletal muscle and a wide variety of other tissues. It is composed of a highly glycosylated extracellular α-DG associated noncovalently with a transmembrane β-DG whose cytodomain interacts with dystrophin and its isoforms. Alpha-dystroglycan (α-DG) binds tightly and in a calcium-dependent fashion to multiple extracellular proteins and proteoglycans, each of which harbors at least one, or, more frequently, tandem arrays of laminin-globular (LG) domains. Considerable biochemical and structural work has accumulated on the α-DG-binding LG domains, highlighting a significant heterogeneity in ligand-binding properties of domains from different proteins as well as between single and multiple LG domains within the same protein. Here we review biochemical, structural, and functional information on the LG domains reported to bind α-dystroglycan. In addition, we have incorporated bioinformatics and modeling to explore whether specific motifs responsible for α-dystroglycan recognition can be identified within isolated LG domains. In particular, we analyzed the LG domains of slits and agrin as well as those of paradigmatic α-DG non-binders such as laminin-α3. While some stretches of basic residues may be important, no universally conserved motifs could be identified. However, the data confirm that the coordinated calcium atom within the LG domain is needed to establish an interaction with the sugars of α-DG, although it appears that this alone is insufficient to mediate significant α-DG binding. We develop a scenario involving different binding modes of a single LG domain unit, or tandemly repeated units, with α-DG. A variability of binding modes might be important to generate a range of affinities to allow physiological regulation of this interaction, reflecting its crucial biological importance.
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Affiliation(s)
| | | | - Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Andrea Brancaccio
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Istituto di Chimica del Riconoscimento Molecolare - CNR, Università Cattolica del Sacro Cuore, Rome, Italy
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55
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Recent advances in glycosaminoglycan analysis by various mass spectrometry techniques. Anal Bioanal Chem 2019; 411:3731-3741. [DOI: 10.1007/s00216-019-01722-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/14/2019] [Accepted: 02/26/2019] [Indexed: 01/10/2023]
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56
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One-step fabrication of boronic-acid-functionalized carbon dots for the detection of sialic acid. Talanta 2019; 197:548-552. [PMID: 30771974 DOI: 10.1016/j.talanta.2019.01.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 01/29/2023]
Abstract
Typically, sialic acids (SA) with a nine-carbon backbone are found at the glycan chain termini on the cell membranes, which play crucial roles in various physiological and pathological processes. The expression level of SA in the blood serum has been reported to correlate with various disease states among cancer. In this study, a novel approach for preparing fluorescent boronic-acid-modified carbon dots (C-dots) for the detection of SA was developed. The functionalized C-dots were synthesized by a facile, one-step hydrothermal method using 3-pyridineboronic acid as the sole carbon source. The added SA selectively recognized the C-dots, leading to the fluorescence quenching of the C-dots in a linear range of 80-4000 μM with a detection limit of 54 μM. The as-developed boronic-acid nanoprobe was successfully applied for the detection of SA in human serum samples with satisfactory results. In addition, this method afforded results within 4 min. Compared to other methods, this new proposed approach was simpler and exhibited excellent sensitivity and selectivity, demonstrating immense potential as an alternative for SA detection.
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57
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Khanal N, Masellis C, Kamrath MZ, Clemmer DE, Rizzo TR. Cryogenic IR spectroscopy combined with ion mobility spectrometry for the analysis of human milk oligosaccharides. Analyst 2019. [PMID: 29541730 DOI: 10.1039/c8an00230d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report here our combination of cryogenic, messenger-tagging, infrared (IR) spectroscopy with ion mobility spectrometry (IMS) and mass spectrometry (MS) as a way to identify and analyze a set of human milk oligosaccharides (HMOs) ranging from trisaccharides to hexasaccharides. The added dimension of IR spectroscopy provides a diagnostic fingerprint in the OH and NH stretching region, which is crucial to identify these oligosaccharides, which are difficult to distinguish by IMS alone. These results extend our previous work in demonstrating the generality of this combined approach for distinguishing subtly different structural and regioisomers of glycans of biologically relevant size.
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Affiliation(s)
- Neelam Khanal
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA
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58
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Liu T, Qiao Z, Wang J, Zhang P, Zhang Z, Guo DS, Yang X. Molecular imprinted S-nitrosothiols nanoparticles for nitric oxide control release as cancer target chemotherapy. Colloids Surf B Biointerfaces 2019; 173:356-365. [DOI: 10.1016/j.colsurfb.2018.09.078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/16/2018] [Accepted: 09/29/2018] [Indexed: 12/14/2022]
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59
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Adua E, Memarian E, Russell A, Trbojević-Akmačić I, Gudelj I, Jurić J, Roberts P, Lauc G, Wang W. High throughput profiling of whole plasma N-glycans in type II diabetes mellitus patients and healthy individuals: A perspective from a Ghanaian population. Arch Biochem Biophys 2019; 661:10-21. [DOI: 10.1016/j.abb.2018.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022]
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60
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Khan AH, Noordin R. Strategies for humanizing glycosylation pathways and producing recombinant glycoproteins in microbial expression systems. Biotechnol Prog 2018; 35:e2752. [DOI: 10.1002/btpr.2752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/26/2018] [Accepted: 11/16/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Amjad Hayat Khan
- Inst. for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 11800 Penang Malaysia
| | - Rahmah Noordin
- Inst. for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 11800 Penang Malaysia
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61
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Sun S, Huang C, Wang Y, Liu Y, Zhang J, Zhou J, Gao F, Yang F, Chen R, Mulloy B, Chai W, Li Y, Bu D. Toward Automated Identification of Glycan Branching Patterns Using Multistage Mass Spectrometry with Intelligent Precursor Selection. Anal Chem 2018; 90:14412-14422. [DOI: 10.1021/acs.analchem.8b03967] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yaojun Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yaming Liu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jingwei Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Feng Gao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Fei Yang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Runsheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Barbara Mulloy
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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62
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Alocci D, Ghraichy M, Barletta E, Gastaldello A, Mariethoz J, Lisacek F. Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes. Glycobiology 2018. [PMID: 29518231 DOI: 10.1093/glycob/cwy019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nowadays, due to the advance of experimental techniques in glycomics, large collections of glycan profiles are regularly published. The rapid growth of available glycan data accentuates the lack of innovative tools for visualizing and exploring large amount of information. Scientists resort to using general-purpose spreadsheet applications to create ad hoc data visualization. Thus, results end up being encoded in publication images and text, while valuable curated data is stored in files as supplementary information. To tackle this problem, we have built an interactive pipeline composed with three tools: Glynsight, EpitopeXtractor and Glydin'. Glycan profile data can be imported in Glynsight, which generates a custom interactive glycan profile. Several profiles can be compared and glycan composition is integrated with structural data stored in databases. Glycan structures of interest can then be sent to EpitopeXtractor to perform a glycoepitope extraction. EpitopeXtractor results can be superimposed on the Glydin' glycoepitope network. The network visualization allows fast detection of clusters of glycoepitopes and discovery of potential new targets. Each of these tools is standalone or can be used in conjunction with the others, depending on the data and the specific interest of the user. All the tools composing this pipeline are part of the Glycomics@ExPASy initiative and are available at https://www.expasy.org/glycomics.
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Affiliation(s)
- Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Marie Ghraichy
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Elena Barletta
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Alessandra Gastaldello
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland.,Computer Science Department CUI, University of Geneva, 7 Route de Drize, 1227 Geneva, Switzerland.,Section of Biology, University of Geneva, Geneva, Switzerland
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63
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Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics. Proteomics 2018; 18:e1700150. [PMID: 29968278 DOI: 10.1002/pmic.201700150] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/23/2018] [Indexed: 01/15/2023]
Abstract
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing. This review article provides an overview of existing de novo sequencing algorithms and software tools ranging from peptide sequencing to sequence-to-protein mapping. Various use cases are described for which de novo sequencing was successfully applied. Finally, limitations of current methods are highlighted and new directions are discussed for a wider acceptance of de novo sequencing in the community.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5020, Bergen, Norway
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
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64
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Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE, Hsu KJ, Mrksich M, Jewett MC, DeLisa MP. Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nat Commun 2018; 9:2686. [PMID: 30002445 PMCID: PMC6043479 DOI: 10.1038/s41467-018-05110-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
The emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins. The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Aravind Natarajan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Cameron J Glasscock
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E Yates
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Karen J Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute B224, Evanston, IL, 60208-3120, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
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65
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Continuous Laminaribiose Production Using an Immobilized Bienzymatic System in a Packed Bed Reactor. Appl Biochem Biotechnol 2018; 186:861-876. [PMID: 29766370 DOI: 10.1007/s12010-018-2779-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/06/2018] [Indexed: 10/16/2022]
Abstract
The first continuous production system of laminaribiose from sucrose and glucose in a bienzymatic reaction is reported in this study. Immobilized laminaribiose phosphorylase and sucrose phosphorylase were used in a packed bed reactor system comprising of a 3-cm glass column at 35 °C with a steady feeding flow rate of 0.1 ml/min. Factors affecting product formation including enzyme ratio, peal concept (both enzymes in one pearl or in separate pearls), and pearl size were studied. An enzyme ratio of 2:1 of laminaribiose phosphorylase (LP) to sucrose phosphorylase (SP) when encapsulated separately in bigger size peals resulted in higher concentration of product. Laminaribiose (0.4 g/(L h)) is produced in the optimized system at steady state. The reaction system proved to be operationally stable throughout 10 days of continuous processing. A half-life time of more than 9 days was observed for both biocatalysts.
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66
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Jing Y, Cai M, Xu H, Zhou L, Yan Q, Gao J, Wang H. Aptamer-recognized carbohydrates on the cell membrane revealed by super-resolution microscopy. NANOSCALE 2018; 10:7457-7464. [PMID: 29637941 DOI: 10.1039/c8nr00089a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Carbohydrates are one of the most important components on the cell membrane, which participate in various physiological activities, and their aberrant expression is a consequence of pathological changes. In previous studies, carbohydrate analysis basically relied on lectins. However, discrimination between lectins still exists due to their multivalent character. Furthermore, the structures obtained by carbohydrate-lectin crosslinking confuse our direct observation to some extent. Fortunately, the emergence of aptamers, which are smaller and more flexible, has provided us an unprecedented choice. Herein, an aptamer recognition method with high precise localization was developed for imaging membrane-bound N-acetylgalactosamine (GalNAc). By using direct stochastic optical reconstruction microscopy (dSTORM), we compared this aptamer recognition method with the lectin recognition method for visualizing the detailed structure of GalNAc at the nanometer scale. The results indicated that GalNAc forms irregular clusters on the cell membrane with a resolution of 23 ± 7 nm by aptamer recognition. Additionally, when treated with N-acetylgalactosidase, the aptamer-recognized GalNAc shows a more significant decrease in cluster size and localization density, thus verifying better specificity of aptamers than lectins. Collectively, our study suggests that aptamers can act as perfect substitutes for lectins in carbohydrate labeling, which will be of great potential value in the field of super-resolution fluorescence imaging.
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Affiliation(s)
- Yingying Jing
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Research Center of Biomembranomics, Changchun, Jilin 130022, P.R. China.
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Wang DE, Yan J, Jiang J, Liu X, Tian C, Xu J, Yuan MS, Han X, Wang J. Polydiacetylene liposomes with phenylboronic acid tags: a fluorescence turn-on sensor for sialic acid detection and cell-surface glycan imaging. NANOSCALE 2018; 10:4570-4578. [PMID: 29461547 DOI: 10.1039/c7nr08557e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sialic acid (SA) located at the terminal end of glycans on cell membranes has been shown to play an important yet distinctive role in various biological and pathological processes. Effective methods for the facile, sensitive and in situ analysis of SA on living cell surfaces are of great significance in terms of clinical diagnostics and therapeutics. Here, a new polydiacetylene (PDA) liposome-based sensor system bearing phenylboronic acid (PBA) and 1,8-naphthalimide derived fluorophore moieties was developed as a fluorescence turn-on sensor for the detection of free SA in aqueous solution and the in situ imaging of SA-terminated glycans on living cell surfaces. In the sensor system, three diacetylene monomers, PCDA-pBA, PCDA-Nap and PCDA-EA, were designed and synthesized to construct the composite PDA liposome sensor. The monomer PCDA-pBA modified with PBA molecules was employed as a receptor for SA recognition, while the monomer PCDA-Nap containing a 1,8-naphthalimide derivative fluorophore was used for fluorescence signaling. When the composite PDA liposomes were formed, the energy transfer between the fluorophore and the conjugated backbone could directly quench the fluorescence of the fluorophore. In the presence of additional SA or SA abundant cells, the strong binding of SA with PBA moieties disturbed the pendent side chain conformation, resulting in the fluorescence restoration of the fluorophore. The proposed methods realized the fluorescence turn-on detection of free SA in aqueous solution and the in situ imaging of SA on living MCF-7 cell surfaces. This work provides a new potential tool for simple and selective analysis of SA on living cell membranes.
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Affiliation(s)
- Dong-En Wang
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.
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68
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Feng X, Deng C, Gao M, Yan G, Zhang X. Novel synthesis of glucose functionalized magnetic graphene hydrophilic nanocomposites via facile thiolation for high-efficient enrichment of glycopeptides. Talanta 2018; 179:377-385. [DOI: 10.1016/j.talanta.2017.11.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/30/2017] [Accepted: 11/17/2017] [Indexed: 12/21/2022]
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69
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Zhou SS, Xu J, Tsang CK, Yip KM, Yeung WP, Zhao ZZ, Zhu S, Fushimi H, Chang HY, Chen HB. Comprehensive quality evaluation and comparison of Angelica sinensis radix and Angelica acutiloba radix by integrated metabolomics and glycomics. J Food Drug Anal 2018; 26:1122-1137. [PMID: 29976405 PMCID: PMC9303037 DOI: 10.1016/j.jfda.2018.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/11/2018] [Accepted: 01/22/2018] [Indexed: 12/21/2022] Open
Abstract
Angelica radix (Danggui in Chinese) used in China and Japan is derived from two species of Angelica, namely Angelica sinensis and Angelica acutiloba, respectively. The differences in quality between A. sinensis radix (ASR) and A. acutiloba radix (AAR) should be therefore investigated to guide the medicinal and dietary applications of these two species. Secondary metabolites and carbohydrates have been demonstrated to be the two major kinds of bioactive components of Danggui. However, previously, quality comparison between ASR and AAR intensively concerned secondary metabolites but largely overlooked carbohydrates, thus failing to include or take into consideration an important aspect of the holistic quality of Danggui. In this study, untargeted/targeted metabolomics and glycomics were integrated by multiple chromatography-based analytical techniques for qualitative and quantitative characterization of secondary metabolites and carbohydrates in Danggui so as to comprehensively evaluate and compare the quality of ASR and AAR. The results revealed that not only secondary metabolites but also carbohydrates in ASR and AAR were different in type and amount, which should collectively contribute to their quality difference. By providing more comprehensive chemical information, the research results highlighted the need to assess characteristics of both carbohydrates and secondary metabolites for overall quality evaluation and comparison of ASR and AAR.
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Affiliation(s)
- Shan-Shan Zhou
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Jun Xu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Chuen-Kam Tsang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Ka-Man Yip
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Wing-Ping Yeung
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Zhong-Zhen Zhao
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Shu Zhu
- Department of Medicinal Resources, Institute of Natural Medicine, University of Toyama, Toyama, Japan
| | - Hirotoshi Fushimi
- Museum of Materia Medica, Institute of Natural Medicine, University of Toyama, Toyama, Japan
| | - Heng-Yuan Chang
- School of Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Hu-Biao Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong.
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70
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AlJadda K, Korayem M, Ortiz C, Grainger T, Miller JA, Rasheed KM, Kochut KJ, Peng H, York WS, Ranzinger R, Porterfield M. Mining massive hierarchical data using a scalable probabilistic graphical model. Inf Sci (N Y) 2018. [DOI: 10.1016/j.ins.2017.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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71
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Matsumoto A, Miyahara Y. 'Borono-lectin' based engineering as a versatile platform for biomedical applications. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2018; 19:18-30. [PMID: 29296128 PMCID: PMC5738650 DOI: 10.1080/14686996.2017.1411143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 05/23/2023]
Abstract
Boronic acids are well known for their ability to reversibly interact with the diol groups, a common motif of biomolecules including sugars and ribose. Due to their ability to interact with carbohydrates, they can be regarded as synthetic mimics of lectins, termed 'borono-lectins'. The borono-lectins can be tailored to elicit a broad profile of binding strength and specificity. This special property has been translated into many creative biomedical applications in a way interactive with biology. This review provides a brief overview of recent efforts of polymeric materials-based engineering taking advantage of such virtue of 'borono-lectins' chemistry, related to the field of biomaterials and drug delivery applications.
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Affiliation(s)
- Akira Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC-KAST), Kawasaki, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
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72
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Piña B, Raldúa D, Barata C, Portugal J, Navarro-Martín L, Martínez R, Fuertes I, Casado M. Functional Data Analysis: Omics for Environmental Risk Assessment. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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73
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Zhang J, Ju N, Yang X, Chen L, Yu C. The α1,3-fucosyltransferase FUT7 regulates IL-1β-induced monocyte-endothelial adhesion via fucosylation of endomucin. Life Sci 2017; 192:231-237. [PMID: 29138114 DOI: 10.1016/j.lfs.2017.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/07/2017] [Accepted: 11/10/2017] [Indexed: 01/04/2023]
Abstract
Monocyte-endothelial adhesion is a hallmark feature of atherosclerosis at early stage and emerging evidence suggests that the glycosylation of vascular adhesive molecules and its ligands is involved in this process. Nevertheless, the mechanism underlying this process remains incompletely elucidated. In this study, we reported that treatment with inflammatory factors interleukin-1β (IL-1β) pronouncedly upregulated α1,3-fucosyltransferase VII gene (FUT7) mRNA and protein expression level in EA.hy926 endothelial cells. Moreover, FUT7 overexpression significantly promoted monocyte-endothelial adhesion, while FUT7 knockdown obviously inhibited IL-1β-induced monocyte-endothelial adhesion. Further analysis demonstrated that fucosylation of selectin ligand endomucin was directly involved in IL-1β-induced monocyte-endothelial adhesion. Finally, we demonstrated that p38 and extracellular signal-regulated kinase (ERK) MAPK signaling pathway was activated by IL-1β, while inhibition of p38/ERK signaling pathway decreased FUT7 expression level and IL-1β-induced monocyte-endothelial adhesion. In summary, these results provide a novel insight that FUT7-mediated fucosylation contribute to the initiation and progression of atherosclerosis.
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Affiliation(s)
- Jun Zhang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Nana Ju
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Xi Yang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Linmu Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Chao Yu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, PR China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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74
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Deniaud-Bouët E, Hardouin K, Potin P, Kloareg B, Hervé C. A review about brown algal cell walls and fucose-containing sulfated polysaccharides: Cell wall context, biomedical properties and key research challenges. Carbohydr Polym 2017; 175:395-408. [PMID: 28917882 DOI: 10.1016/j.carbpol.2017.07.082] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/04/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
Studies on brown algal cell walls have entered a new phase with the concomitant discovery of novel polysaccharides present in cell walls and the establishment of a comprehensive generic model for cell wall architecture. Brown algal cell walls are composites of structurally complex polysaccharides. In this review we discuss the most recent progress in the structural composition of brown algal cell walls, emphasizing the significance of extraction and screening techniques, and the biological activities of the corresponding polysaccharides, with a specific focus on the fucose-containing sulfated polysaccharides. They include valuable marine molecules that exert a broad range of pharmacological properties such as antioxidant and anti-inflammatory activities, functions in the regulation of immune responses and of haemostasis, anti-infectious and anticancer actions. We identify the key remaining challenges in this research field.
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Affiliation(s)
- Estelle Deniaud-Bouët
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Kevin Hardouin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Philippe Potin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Bernard Kloareg
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
| | - Cécile Hervé
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
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75
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Tiwari N, Srivastava A, Kundu B, Munde M. Biophysical insight into the heparin-peptide interaction and its modulation by a small molecule. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/28/2017] [Accepted: 09/03/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Neha Tiwari
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
| | - Ankit Srivastava
- School of Biological Sciences; Indian Institute of Technology; New Delhi India
| | - Bishwajit Kundu
- School of Biological Sciences; Indian Institute of Technology; New Delhi India
| | - Manoj Munde
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
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76
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Ting CY, Lin YW, Wu CY, Wong CH. Design of Disaccharide Modules for a Programmable One-Pot Synthesis of Building Blocks with LacNAc Repeating Units for Asymmetric N-Glycans. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Cheng-Yueh Ting
- Genomics Research Center; Academia Sinica; No. 128, Academia Road, Section 2, Nankang District Taipei 11529 Taiwan
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Rd., Daan District Taipei 106 Taiwan
| | - Yu-Wei Lin
- Genomics Research Center; Academia Sinica; No. 128, Academia Road, Section 2, Nankang District Taipei 11529 Taiwan
| | - Chung-Yi Wu
- Genomics Research Center; Academia Sinica; No. 128, Academia Road, Section 2, Nankang District Taipei 11529 Taiwan
| | - Chi-Huey Wong
- Genomics Research Center; Academia Sinica; No. 128, Academia Road, Section 2, Nankang District Taipei 11529 Taiwan
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Rd., Daan District Taipei 106 Taiwan
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77
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Lee HHL, Kim HI. Supramolecular Analysis of Monosaccharide Derivatives Using Cucurbit[7]uril and Electrospray Ionization Tandem Mass Spectrometry. Isr J Chem 2017. [DOI: 10.1002/ijch.201700073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hyun Hee L. Lee
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
| | - Hugh I. Kim
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
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78
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Liu MQ, Zeng WF, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY. pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nat Commun 2017; 8:438. [PMID: 28874712 PMCID: PMC5585273 DOI: 10.1038/s41467-017-00535-2] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with 15N/13C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues. Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.
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Affiliation(s)
- Ming-Qi Liu
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China.,Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, 20032, China
| | - Wen-Feng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Fang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Wei-Qian Cao
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Chao Liu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Guo-Quan Yan
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Yang Zhang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Chao Peng
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 201210, China
| | - Jian-Qiang Wu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Jin Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Jun Tu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Rui-Xiang Sun
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Yong Cao
- National Institute of Biological Sciences (Beijing), Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (Beijing), Beijing, 102206, China
| | - Bi-Yun Jiang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Jiang-Ming Huang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Hua-Li Shen
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Catherine C L Wong
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 201210, China.
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Yuan Yang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China. .,Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, 20032, China.
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79
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Wang L, Hu L, Yan S, Jiang T, Fang S, Wang G, Zhao J, Zhang H, Chen W. Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation. Food Funct 2017; 8:1966-1978. [PMID: 28475191 DOI: 10.1039/c7fo00031f] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aim of this study was to evaluate the effects of three different kinds of oligosaccharides (a fructo-oligosaccharide (FOS) formulation consisting of 95% FOS (FOS95); a galacto-oligosaccharide (GOS) formulation consisting of 90% GOS (GOS90) and an isomalto-oligosaccharide (IMO) formulation consisting of 90% IMO (IMO90)) at dosages of 0.8, 4 g per d per kg bw and 8 g per d per kg bw on the composition and activity of the microbiota in the gut of mice with constipation induced by loperamide. Oligosaccharides were intragastrically administered to specific pathogen-free BALB/c mice once per day for 17 days. Feces were collected during a feeding trial and subjected to 16S rDNA amplicon analysis. Constipation indices, changes in gut microbiota and metabolic activity were measured to evaluate the effects of the oligosaccharides. The results show that oligosaccharides treated constipation by increasing both the water content of the feces and the small intestinal transit rate. The dosage required to treat constipation was different for different oligosaccharides. High-dose GOS90 was the most effective in relieving constipation, followed by medium-dose FOS95 and IMO90. The fecal samples were investigated after the oligosaccharide treatment. All three oligosaccharides increased the ratio of acetic acid and decreased the ratio of propionic and butyric acids in the feces. The increase in the ratio of acetic acid and the concentration of butyric acid were found to have relatively larger effects on constipation. After treatment with oligosaccharides, the gut microbiotas of the mice were dominated by Firmicutes, Bacteroidetes and Actinobacteria. At the genus level, oligosaccharide treatment increased the levels of Lactobacillus and Bifidobacterium and decreased the levels of Odoribacter, Alistipes and Bacteroides. In conclusion, our results demonstrate that oligosaccharides administered as a dietary supplement increase the water content of feces, reduce intestinal transit time, modulate the composition of the gut microbiota and increase the concentration of short-chain fatty acids in the feces of mice with constipation.
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Affiliation(s)
- Linlin Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China.
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80
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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81
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Native glycan fragments detected by MALDI-FT-ICR mass spectrometry imaging impact gastric cancer biology and patient outcome. Oncotarget 2017; 8:68012-68025. [PMID: 28978092 PMCID: PMC5620232 DOI: 10.18632/oncotarget.19137] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 06/02/2017] [Indexed: 01/23/2023] Open
Abstract
Glycosylation in cancer is a highly dynamic process that has a significant impact on tumor biology. Further, the attachment of aberrant glycan forms is already considered a hallmark of the disease state. Mass spectrometry has become a prominent approach to analyzing glycoconjugates. Specifically, matrix-assisted laser desorption/ionisation -mass spectrometric imaging (MALDI-MSI) is a powerful technique that combines mass spectrometry with histology and enables the spatially resolved and label-free detection of glycans. The most common approach to the analysis of glycans is the use of mass spectrometry adjunct to PNGase F digestion and other chemical reactions. In the current study, we perform the analysis of formalin-fixed, paraffin-embedded (FFPE) tissues for natively occurring bioactive glycan fragments without prior digestion or chemical reactions using MALDI-FT-ICR-MSI. We examined 106 primary resected gastric cancer patient tissues in a tissue microarray and correlated native-occurring fragments with clinical endpoints, therapeutic targets such as epidermal growth factor receptor (EGFR) and HER2/neu expressions and the proliferation marker MIB1. The detection of a glycosaminoglycan fragment in tumor stroma regions was determined to be an independent prognostic factor for gastric cancer patients. Native glycan fragments were significantly linked to the expression of EGFR, HER2/neu and MIB1. In conclusion, we are the first to report the in situ detection of native-occurring bioactive glycan fragments in FFPE tissues that influence patient outcomes. These findings highlight the significance of glycan fragments in gastric cancer tumor biology and patient outcome.
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82
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Geng F, Wang J, Liu D, Jin Y, Ma M. Identification of N-Glycosites in Chicken Egg White Proteins Using an Omics Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5357-5364. [PMID: 28587447 DOI: 10.1021/acs.jafc.7b01706] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chicken egg white (CEW) is a perfect source of natural proteins that possesses outstanding functional properties and various bioactivities. The glycosylation structure of CEW proteins plays important roles in their functions, bioactivities, and allergies. The present work attempted to identify N-glycosites of CEW proteins using an omics strategy. CEW proteins were digested with trypsin and chymotrypsin; glycopeptides were enriched and deglycosylated using PNGase F in H218O water, followed by analysis using high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS). A total of 71 N-glycosites in 26 CEW glycoproteins were identified. Web-Logo analysis showed that most of the N-glycosites were at N-X-T (55%) and N-X-S (32%). Furthermore, two-dimensional electrophoresis of CEW clusterin demonstrated a series of spots horizontally distributed at 35-37 kDa with an extremely wide isoelectric point range of 4.54-6.68, indicating the heterogeneity of glycosylation of CEW clusterin. These results provided important information for the understanding of the structures, functions, and bioactivities of CEW glycoproteins.
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Affiliation(s)
- Fang Geng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Jinqiu Wang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Dayu Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Yongguo Jin
- National R&D Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan 430070, P. R. China
| | - Meihu Ma
- National R&D Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan 430070, P. R. China
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83
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Matsumoto A, Stephenson-Brown AJ, Khan T, Miyazawa T, Cabral H, Kataoka K, Miyahara Y. Heterocyclic boronic acids display sialic acid selective binding in a hypoxic tumor relevant acidic environment. Chem Sci 2017; 8:6165-6170. [PMID: 28989647 PMCID: PMC5627601 DOI: 10.1039/c7sc01905j] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 01/02/2023] Open
Abstract
A group of heterocyclic boronic acids demonstrating unusually high affinity and selectivity for sialic acids are described, with strong interactions under the weakly acidic pH conditions associated with a hypoxic tumoral microenvironment.
Boronic acids are well known for their ability to reversibly interact with the diol groups found in sugars and glycoproteins. However, they are generally indiscriminate in their binding. Herein we describe the discovery of a group of heterocyclic boronic acids demonstrating unusually high affinity and selectivity for sialic acids (SAs or N-acetylneuraminic acid), which are sugar residues that are intimately linked with tumor growth and cancer progression. Remarkably, these interactions strengthen under the weakly acidic pH conditions associated with a hypoxic tumoral microenvironment. In vitro competitive binding assays uncovered a significantly higher ability of 5-boronopicolinic acid, one of the derivatives identified in this work as a strong SA-binder, to interact with cell surface SA in comparison to a gold-standard structure, 3-propionamidophenylboronic acid, which has proven to be an efficient SA-binder in numerous reports. This structure also proved to be suitable for further chemical conjugation with a well-preserved SA-binding capability. These findings suggest an attractive alternative to other ongoing boronic acid based chemistry techniques aiming to achieve tumor-specific chemotherapies and diagnoses.
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Affiliation(s)
- A Matsumoto
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University , 2-3-10 Kanda-Surugadai, Chiyoda-ku , Tokyo 101-0062 , Japan .
| | - A J Stephenson-Brown
- School of Chemical Engineering , University of Birmingham , Edgbaston , Birmingham , B15 2TT , UK
| | - T Khan
- Department of Bioengineering , Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - T Miyazawa
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University , 2-3-10 Kanda-Surugadai, Chiyoda-ku , Tokyo 101-0062 , Japan .
| | - H Cabral
- Department of Bioengineering , Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - K Kataoka
- School of Chemical Engineering , University of Birmingham , Edgbaston , Birmingham , B15 2TT , UK.,Department of Materials Engineering , Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Y Miyahara
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University , 2-3-10 Kanda-Surugadai, Chiyoda-ku , Tokyo 101-0062 , Japan .
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84
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017. [PMID: 28585084 DOI: 10.1007/s00216-017-04067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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85
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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86
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Le C, Stuckey DC. Influence of Feed Composition on the Monomeric Structure of Free Bacterial Extracellular Polysaccharides in Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7009-7017. [PMID: 28564536 DOI: 10.1021/acs.est.7b00925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Six 5.0-L fill-and-draw batch reactors were used with different feed compositions containing a range of carbohydrates (glucose, sucrose, fructose) and nitrogen sources (urea, NH4Cl) at various concentrations to investigate free extracellular polysaccharide (EPS) production during anaerobic digestion (AD). This work analyzed not only their monosaccharide components, but also their specific linkage patterns and the change associated with different chemical nature in carbon substrates or nitrogen sources; all of these parameters can have profound biological consequences, and were correlated to macronutrients present in the feed. It is believed that feed composition is a major factor which determines the physicochemical characteristics of the free EPS. Our findings also suggest that the differences associated with the digestion of various carbon substrates and/or nitrogen sources could alter monomeric saccharide composition and concentrations of the free EPS. Such insights demonstrate that previous studies on feed C/N ratios tended to overestimate EPS production, while variations in the chemical nature of the nitrogen source were overlooked. Our results also link the physiochemical properties of free EPS with underlying biofouling mechanisms, and demonstrate that membrane fouling is to some extent dependent upon the prevailing nutritional environment and feed composition.
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Affiliation(s)
- Chencheng Le
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University , 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
- Division of Environmental and Water Resources Engineering, School of Civil and Environmental Engineering, Nanyang Technological University , 50 Nanyang Avenue, Singapore 639798, Singapore
| | - David C Stuckey
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University , 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
- Department of Chemical Engineering, Imperial College London , London SW7 2AZ, U.K
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87
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Hui J, Bao L, Li S, Zhang Y, Feng Y, Ding L, Ju H. Localized Chemical Remodeling for Live Cell Imaging of Protein-Specific Glycoform. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jingjing Hui
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Lei Bao
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Siqiao Li
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Yi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Yimei Feng
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P.R. China
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88
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Hui J, Bao L, Li S, Zhang Y, Feng Y, Ding L, Ju H. Localized Chemical Remodeling for Live Cell Imaging of Protein-Specific Glycoform. Angew Chem Int Ed Engl 2017; 56:8139-8143. [PMID: 28557363 DOI: 10.1002/anie.201703406] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Indexed: 11/07/2022]
Abstract
Live cell imaging of protein-specific glycoforms is important for the elucidation of glycosylation mechanisms and identification of disease states. The currently used metabolic oligosaccharide engineering (MOE) technology permits routinely global chemical remodeling (GCM) for carbohydrate site of interest, but can exert unnecessary whole-cell scale perturbation and generate unpredictable metabolic efficiency issue. A localized chemical remodeling (LCM) strategy for efficient and reliable access to protein-specific glycoform information is reported. The proof-of-concept protocol developed for MUC1-specific terminal galactose/N-acetylgalactosamine (Gal/GalNAc) combines affinity binding, off-on switchable catalytic activity, and proximity catalysis to create a reactive handle for bioorthogonal labeling and imaging. Noteworthy assay features associated with LCM as compared with MOE include minimum target cell perturbation, short reaction timeframe, effectiveness as a molecular ruler, and quantitative analysis capability.
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Affiliation(s)
- Jingjing Hui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Lei Bao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Siqiao Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Yi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Yimei Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P.R. China
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89
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Immobilization of concanavalin A lectin on a reduced graphene oxide-thionine surface by glutaraldehyde crosslinking for the construction of an impedimetric biosensor. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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90
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Adua E, Russell A, Roberts P, Wang Y, Song M, Wang W. Innovation Analysis on Postgenomic Biomarkers: Glycomics for Chronic Diseases. ACTA ACUST UNITED AC 2017; 21:183-196. [DOI: 10.1089/omi.2017.0035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Alyce Russell
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Peter Roberts
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
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91
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Villadsen K, Martos-Maldonado MC, Jensen KJ, Thygesen MB. Chemoselective Reactions for the Synthesis of Glycoconjugates from Unprotected Carbohydrates. Chembiochem 2017; 18:574-612. [DOI: 10.1002/cbic.201600582] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Klaus Villadsen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Manuel C. Martos-Maldonado
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Mikkel B. Thygesen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
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92
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Gu X, Fang Z. A novel Hg 2+-selective fluorescent chemprobe based on thiooxorhodamine-B and β-C-glycoside. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:495-501. [PMID: 27728878 DOI: 10.1016/j.saa.2016.09.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
In this paper, two novel easily available probes based on rhodamine B and β-C-glycoside were synthesized and characterized by 1H NMR, 13C NMR and elemental analysis. Sensor 1 exhibited very high sensitivity and selectivity toward Hg2+ over other metal ions, due to the opening of the spiro ring in thiooxorhodamine B caused by Hg2+ through desulfurization. The binding analysis using Job's plot suggested 1:1 stoichiometry for the complexes formed for Hg2+. The fluorescent probe is pH independent in medium condition and common interferent ions do not show any interference with the Hg2+ determination. It is anticipated that 1 could be a good candidate probe and has potential application for Hg2+ determination.
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Affiliation(s)
- Xiaomin Gu
- School of Chemical Engineering, Nanjing University of Science & Technology, 200 Xiaolingwei St, Nanjing, JiangSu 210 094, PR China
| | - Zhijie Fang
- School of Chemical Engineering, Nanjing University of Science & Technology, 200 Xiaolingwei St, Nanjing, JiangSu 210 094, PR China.
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93
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Liu R, Cui Q, Wang C, Wang X, Yang Y, Li L. Preparation of Sialic Acid-Imprinted Fluorescent Conjugated Nanoparticles and Their Application for Targeted Cancer Cell Imaging. ACS APPLIED MATERIALS & INTERFACES 2017; 9:3006-3015. [PMID: 28051302 DOI: 10.1021/acsami.6b14320] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fluorescent conjugated polymer nanoparticles have attracted great interest for applications in biological imaging owing to their excellent optical properties and low cytotoxicity; however, a lack of effective targeting limits their use. In this work, we design and synthesize a fluorescent conjugated polymer modified with a phenylboronic acid group, which can covalently bind with cis-diol-containing compounds, such as sialic acid (SA), by forming a cyclic ester. However, the obtained conjugated polymer nanoparticles failed to discriminate between cancer cells, with or without SA overexpressed surfaces (such as DU 145 and HeLa cells, respectively). To address this problem, we introduced SA template molecules into the polymer nanoparticles during the reprecipitation process and then removed the template by adjusting the solution pH. The SA-imprinted nanoparticles showed a uniform size around 30 nm and enhanced fluorescence intensity compared with unmodified polymer nanoparticles. The SA-imprinted nanoparticles exhibited selective staining for DU 145 cancer cells and did not enter HeLa cells even after long incubation times. Thus, we present a facile method to prepare fluorescent nanoparticles for applications in targeted cancer cell imaging.
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Affiliation(s)
- Ronghua Liu
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
| | - Qianling Cui
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
| | - Chun Wang
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
| | - Xiaoyu Wang
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
| | - Yu Yang
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
| | - Lidong Li
- State Key Lab for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, China
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94
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Kanie Y, Kanie O. Addressing the glycan complexity by using mass spectrometry: In the pursuit of decoding glycologic. ACTA ACUST UNITED AC 2017. [DOI: 10.7243/2052-9341-5-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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95
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Monti D, Ostan R, Borelli V, Castellani G, Franceschi C. Inflammaging and human longevity in the omics era. Mech Ageing Dev 2016; 165:129-138. [PMID: 28038993 DOI: 10.1016/j.mad.2016.12.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/21/2016] [Indexed: 11/24/2022]
Abstract
Inflammaging is a recent theory of aging originally proposed in 2000 where data and conceptualizations regarding the aging of the immune system (immunosenescence) and the evolution of immune responses from invertebrates to mammals converged. This theory has received an increasing number of citations and experimental confirmations. Here we present an updated version of inflammaging focused on omics data - particularly on glycomics - collected on centenarians, semi-supercentenarians and their offspring. Accordingly, we arrived to the following conclusions: i) inflammaging has a structure where specific combinations of pro- and anti-inflammatory mediators are involved; ii) inflammaging is systemic and more complex than we previously thought, as many organs, tissues and cell types participate in producing pro- and anti-inflammatory stimuli defined "molecular garbage"; iii) inflammaging is dynamic, can be propagated locally to neighboring cells and systemically from organ to organ by circulating products and microvesicles, and amplified by chronic age-related diseases constituting a "local fire", which in turn produces additional inflammatory stimuli and molecular garbage; iv) an integrated Systems Medicine approach is urgently needed to let emerge a robust and highly informative set/combination of omics markers able to better grasp the complex molecular core of inflammaging in elderly and centenarians.
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Affiliation(s)
- Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Rita Ostan
- Interdepartmental Centre "L. Galvani" (CIG) and Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via San Giacomo 12, 40126 Bologna, Italy.
| | - Vincenzo Borelli
- Interdepartmental Centre "L. Galvani" (CIG) and Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via San Giacomo 12, 40126 Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy DIFA, University of Bologna, Viale Berti Pichat 6/2, 40127, Bologna, Italy
| | - Claudio Franceschi
- IRCCS, Institute of Neurological Sciences of Bologna, Via Altura 3, 40139 Bologna, Italy
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96
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Xu G, Liu X, Liu QY, Li J, Zhou Y. Automatic annotation and visualization tool for mass spectrometry based glycomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2471-2479. [PMID: 27599464 DOI: 10.1002/rcm.7735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/03/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE With the development of glycomics, a large number of glycan structures have been determined by using mass spectrometry (MS)-based techniques. However, most glycan MS data needs to be manually annotated which is time-consuming, unreliable and inaccurate. METHODS Herein we report a tool for automatically annotating and browsing N-glycan masses and isotopic distributions. We first constructed a training dataset using the Consortium for Functional Glycomics database, in conjunction with data preprocessing and filtering by composition matching. In addition, we improved a matching glycan isotope abundance algorithm through identifying potential overlap region and constructing an optimization model so that it can deconvolute the overlapped glycan isotopic clusters. RESULTS In the matching process, if the m/z difference of two detected ions was close to an integer from 1 to 5, the m/z range was considered as a potential overlapped region, from the lower m/z to m/z + 5. It was found that there were more than 20 potential overlap regions in each group of data from CHO sample and human testing sample. Because the training dataset was imbalanced, we combined the Supporting Vector Machines (SVMs) algorithm with different sampling techniques, including Synthetic Minority Over-sampling Technique (SMOTE), to classify all potential candidate compositions. The results demonstrated an average of 26.8% increase in annotation sensitivity through the SMOTE-SVMs algorithm. The source code can be obtained from https://sourceforge.net/projects/glycomaid/. CONCLUSIONS We have developed a new tool which facilities high-throughput glycomics research and assists mass spectrometrists in the interpretation and annotation of glycan samples. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Guang Xu
- Hubei Co-Innovation Center of Basic Education Information Technology Services, Hubei University of Education, 430205, Wuhan, China
| | - Xin Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Qing Yan Liu
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada, K1A 0R6
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H 8M5
| | - Jianjun Li
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada, K1A 0R6
| | - Yanhong Zhou
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
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97
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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98
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Zaporozhets T, Besednova N. Prospects for the therapeutic application of sulfated polysaccharides of brown algae in diseases of the cardiovascular system: review. PHARMACEUTICAL BIOLOGY 2016; 54:3126-3135. [PMID: 27252012 DOI: 10.1080/13880209.2016.1185444] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/22/2015] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
CONTEXT Fucoidans are water-soluble, highly sulfated, branched homo- and hetero-polysaccharides derived from the fibrillar cell walls and intercellular spaces of brown seaweeds of the class Phaeophyceae. Fucoidans possess mimetic properties of the natural ligands of protein receptors and regulate functions of biological systems via key signaling molecules. OBJECTIVES The aim of this review was to collect and combine all available scientific literature about the potential use of the fucoidans for diseases of cardiovascular system. MATERIALS AND METHODS The review has been compiled using references from major databases such as Web of Science, PubMed, Scopus, Elsevier, Springer and Google Scholar (up to September 2015). After obtaining all reports from database (a total number is about 580), the papers were carefully analyzed in order to find data related to the topic of this review (129 references). RESULTS An exhaustive survey of literature revealed that fucoidans possess a broad spectrum of biological activity, including anti-coagulant, hypolipidemic, anti-thrombotic, anti-inflammatory, immunomodulatory, anti-tumor, anti-adhesive and anti-hypertensive properties. Numerous investigations of fucoidans in diseases of the cardiovascular system mainly focus on pleiotropic anti-inflammatory effects. Fucoidans also possess pro-angiogenic and pro-vasculogenic properties. CONCLUSION A great number of investigations in the past years have demonstrated that fucoidans has great potential for in-depth investigation of their effects on cardiovascular system. Through this review, the authors hope to attract the attention of researchers to use fucoidan as mimetic of natural ligand receptor protein with the view of developing new formulations with an improved therapeutic value.
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Affiliation(s)
- Tatyana Zaporozhets
- a Somov Institute of Epidemiology and Microbiology , Vladivostok , Russian Federation
| | - Natalia Besednova
- a Somov Institute of Epidemiology and Microbiology , Vladivostok , Russian Federation
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99
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Hu W, Su X, Zhu Z, Go EP, Desaire H. GlycoPep MassList: software to generate massive inclusion lists for glycopeptide analyses. Anal Bioanal Chem 2016; 409:561-570. [PMID: 27614974 DOI: 10.1007/s00216-016-9896-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022]
Abstract
Protein glycosylation drives many biological processes and serves as markers for disease; therefore, the development of tools to study glycosylation is an essential and growing area of research. Mass spectrometry can be used to identify both the glycans of interest and the glycosylation sites to which those glycans are attached, when proteins are proteolytically digested and their glycopeptides are analyzed by a combination of high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) methods. One major challenge in these experiments is collecting the requisite MS/MS data. The digested glycopeptides are often present in complex mixtures and in low abundance, and the most commonly used approach to collect MS/MS data on these species is data-dependent acquisition (DDA), where only the most intense precursor ions trigger MS/MS. DDA results in limited glycopeptide coverage. Semi-targeted data acquisition is an alternative experimental approach that can alleviate this difficulty. However, due to the massive heterogeneity of glycopeptides, it is not obvious how to expediently generate inclusion lists for these types of analyses. To solve this problem, we developed the software tool GlycoPep MassList, which can be used to generate inclusion lists for liquid chromatography tandem-mass spectrometry (LC-MS/MS) experiments. The utility of the software was tested by conducting comparisons between semi-targeted and untargeted data-dependent analysis experiments on a variety of proteins, including IgG, a protein whose glycosylation must be characterized during its production as a biotherapeutic. When the GlycoPep MassList software was used to generate inclusion lists for LC-MS/MS experiments, more unique glycopeptides were selected for fragmentation. Generally, ∼30 % more unique glycopeptides can be analyzed per protein, in the simplest cases, with low background. In cases where background ions from proteins or other interferents are high, usage of an inclusion list is even more advantageous. The software is freely publically accessible. Graphical abstract Software increases the number of glycopeptides that get selected for MS/MS analysis.
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Affiliation(s)
- Wenting Hu
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Xiaomeng Su
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Zhikai Zhu
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Eden P Go
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA.
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100
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Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses. Anal Bioanal Chem 2016; 409:467-476. [PMID: 27604268 DOI: 10.1007/s00216-016-9866-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/27/2016] [Accepted: 08/06/2016] [Indexed: 02/01/2023]
Abstract
Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules, such as proteins and lipids, and alter their properties and functions, so glycan characterization is essential for understanding the effects they have on cellular systems. However, the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycan standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest that specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS. Graphical abstract Glycan isomers, such as fructose and glucose, show distinct separations in positive and negative ion mode.
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