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Prediction and analysis of antifreeze proteins. Heliyon 2021; 7:e07953. [PMID: 34604556 PMCID: PMC8473546 DOI: 10.1016/j.heliyon.2021.e07953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Antifreeze proteins (AFPs) are proteins that protect cellular fluids and body fluids from freezing by inhibiting the nucleation and growth of ice crystals and preventing ice recrystallization, thereby contributing to the maintenance of life in living organisms. They exist in fish, insects, microorganisms, and fungi. However, the number of known AFPs is currently limited, and it is essential to construct a reliable dataset of AFPs and develop a bioinformatics tool to predict AFPs. In this work, we first collected AFPs sequences from UniProtKB considering the reliability of annotations and, based on these datasets, developed a prediction system using random forest. We achieved accuracies of 0.961 and 0.947 for non-redundant sequences with less than 90% and 30% identities and achieved the accuracy of 0.953 for representative sequences for each species. Using the ability of random forest, we identified the sequence features that contributed to the prediction. Some sequence features were common to AFPs from different species. These features include the Cys content, Ala-Ala content, Trp-Gly content, and the amino acids' distribution related to the disorder propensity. The computer program and the dataset developed in this work are available from the GitHub site: https://github.com/ryomiya/Prediction-and-analysis-of-antifreeze-proteins.
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2
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Cao W, Liu M, Kong S, Wu M, Zhang Y, Yang P. Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis. Mol Cell Proteomics 2021; 20:100060. [PMID: 33556625 PMCID: PMC8724820 DOI: 10.1074/mcp.r120.002090] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.
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Affiliation(s)
- Weiqian Cao
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China.
| | - Mingqi Liu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengxi Wu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China
| | - Yang Zhang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China.
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3
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Chen Q, Tan Z, Guan F, Ren Y. The Essential Functions and Detection of Bisecting GlcNAc in Cell Biology. Front Chem 2020; 8:511. [PMID: 32719771 PMCID: PMC7350706 DOI: 10.3389/fchem.2020.00511] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The N-glycans of mammalian glycoproteins vary greatly in structure, and the biological importance of these variations is mostly unknown. It is widely acknowledged that the bisecting N-acetylglucosamine (GlcNAc) structure, a β1,4-linked GlcNAc attached to the core β-mannose residue, represents a special type of N-glycosylated modification, and it has been reported to be involved in various biological processes, such as cell adhesion, fertilization and fetal development, neuritogenesis, and tumor development. In particular, the occurrence of N-glycans with a bisecting GlcNAc modification on proteins has been proven, with many implications for immune biology. Due to the essential functions of bisecting GlcNAc structures, analytical approaches to this modification are highly required. The traditional approach that has been used for bisecting GlcNAc determinations is based on the lectin recognition of Phaseolus vulgaris erythroagglutinin (PHA-E); however, poor binding specificity hinders the application of this method. With the development of mass spectrometry (MS) with high resolution and improved sensitivity and accuracy, MS-based glycomic analysis has provided precise characterization and quantification for glycosylation modification. In this review, we first provide an overview of the bisecting GlcNAc structure and its biological importance in neurological systems, immune tolerance, immunoglobulin G (IgG), and tumor metastasis and development and then summarize approaches to its determination by MS for performing precise functional studies. This review is valuable for those readers who are interested in the importance of bisecting GlcNAc in cell biology.
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Affiliation(s)
- Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Zengqi Tan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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4
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Glycoproteomics and Glycomics in the Biomedical Area Special Issue. Proteomics Clin Appl 2019; 12:e1800122. [PMID: 30203442 DOI: 10.1002/prca.201800122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 11/10/2022]
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5
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Zhang L, Ma S, Chen Y, Wang Y, Ou J, Uyama H, Ye M. Facile Fabrication of Biomimetic Chitosan Membrane with Honeycomb-Like Structure for Enrichment of Glycosylated Peptides. Anal Chem 2019; 91:2985-2993. [PMID: 30673210 DOI: 10.1021/acs.analchem.8b05215] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the study of glycoproteomics with mass spectrometry, certain pretreatments of samples are required for eliminating the interference of nonglycopeptides and improving the efficiency of glycopeptides detection. Although hydrophilic interaction chromatography (HILIC) has been developed for enrichment of glycosylated peptides, a plethora of hydrophilic materials always suffered from large steric hindrance, great cost, and difficulty with modifications of high-density hydrophilic groups. In this work, a 1 mm thick biomimetic honeycomb chitosan membrane (BHCM) with honeycomb-like accessible macropores was directly prepared by the freeze-casting method as an adsorbent for HILIC. The N-glycopeptides from trypsin digests of immunoglobulin G (IgG), mixture of IgG and bovine serum albumin (BSA), and serum proteins were enriched using this material and compared with a commercial material ZIC-HILIC. The biomimetic membrane could identify as many as 32 N-glycopeptides from the IgG digest, exhibiting high sensitivity (about 50 fmol) and a wide scope for glycopeptide enrichment. A molar ratio of IgG trypsin digest to bovine serum albumin trypsin digest as low as 1/500 verified the outstanding specificity and efficiency for glycopeptide enrichment. In addition, 270 unique N-glycosylation sites of 400 unique glycopeptides from 146 glycosylated proteins were identified from the triplicate analysis of 2 μL human serum. Furthermore, 48 unique O-glycosylation sites of 278 unique O-glycopeptides were identified from the triplicate analysis of 30 μg deglycosylated fetuin digest. These results indicated that the chitosan-based membrane prepared in this work had great potential for pretreatment of samples in glycoproteomics.
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Affiliation(s)
- Luwei Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Shujuan Ma
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Hiroshi Uyama
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education , Northwest University , Xi'an , Shaanxi 710127 , China.,Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
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6
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Designing the next generation of cryoprotectants - From proteins to small molecules. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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7
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Qadeer S, Khan MA, Ansari MS, Rakha BA, Ejaz R, Iqbal R, Younis M, Ullah N, DeVries AL, Akhter S. Efficiency of antifreeze glycoproteins for cryopreservation of Nili-Ravi (Bubalus bubalis) buffalo bull sperm. Anim Reprod Sci 2015; 157:56-62. [PMID: 25863987 DOI: 10.1016/j.anireprosci.2015.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
Experiments were conducted to evaluate the effect of Antarctic fish antifreeze glycoproteins, (AFGP) size 1-5 (34-10.5 kDa) and 7-8 (3.2 and 2.4 kDa) in extender on buffalo bull sperm at cooling (4 °C) and at post thawing. Semen was collected from three Nili-Ravi buffalo bulls with artificial vagina for 3 weeks. Qualifying ejaculates from each buffalo bull were diluted (at 37 °C having 50×10(6) sperm/mL) in tris-citric acid extender containing AFGP at 0 (control), 0.1, 1 and 10 μg/mL. An aliquot of diluted semen was evaluated for sperm progressive motility and plasma membrane integrity, while the remaining fraction was cooled to 4 °C in 2 h. Further, an aliquot of cooled semen was evaluated for the previously described variables and the remaining fraction was cryopreserved (-196 °C). After 24 h of storage, straws were thawed at 37 °C for 30 s to assess post-thaw sperm quality. Inclusion of AFGP in the extender did not affect (P>0.05) sperm progressive motility and plasma membrane integrity of buffalo bull sperm at cooling stage (4 °C). However, at post thawing, improvement (P<0.05) in sperm progressive motility and plasma membrane integrity was recorded in extender containing AFGP 1-5 and AFGP 7-8 at 1 μg/mL compared to the control. Percentage of live sperm with an intact acrosome remained similar (P>0.05) in extenders containing different amounts of AFGP and control. In conclusion, supplementation of 1 μg/ml of AFGP in extender improved the motility and plasma membrane integrity of Nili-Ravi buffalo sperm after thawing.
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Affiliation(s)
- S Qadeer
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - M A Khan
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - M S Ansari
- Department of Zoology, University of Gujrat, Gujrat, Pakistan
| | - B A Rakha
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - R Ejaz
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - R Iqbal
- Department of Zoology, University of Gujrat, Gujrat, Pakistan
| | - M Younis
- Semen Production Unit Qadirabad, Sahiwal, Pakistan
| | - N Ullah
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - Arthur L DeVries
- Department of Physiology and Biophysics, University of Illinois, Urbana, IL 61801, USA
| | - S Akhter
- Animal Physiology Laboratory, Department of Zoology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan.
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Corcilius L, Santhakumar G, Stone RS, Capicciotti CJ, Joseph S, Matthews JM, Ben RN, Payne RJ. Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules. Bioorg Med Chem 2013; 21:3569-81. [DOI: 10.1016/j.bmc.2013.02.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/01/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
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9
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Reuel NF, Mu B, Zhang J, Hinckley A, Strano MS. Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. Chem Soc Rev 2013; 41:5744-79. [PMID: 22868627 DOI: 10.1039/c2cs35142k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.
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Affiliation(s)
- Nigel F Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Nagel L, Budke C, Dreyer A, Koop T, Sewald N. Antifreeze glycopeptide diastereomers. Beilstein J Org Chem 2012; 8:1657-67. [PMID: 23209499 PMCID: PMC3510999 DOI: 10.3762/bjoc.8.190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 08/28/2012] [Indexed: 01/09/2023] Open
Abstract
Antifreeze glycopeptides (AFGPs) are a special class of biological antifreeze agents, which possess the property to inhibit ice growth in the body fluids of arctic and antarctic fish and, thus, enable life under these harsh conditions. AFGPs are composed of 4-55 tripeptide units -Ala-Ala-Thr- glycosylated at the threonine side chains. Despite the structural homology among all the fish species, divergence regarding the composition of the amino acids occurs in peptides from natural sources. Although AFGPs were discovered in the early 1960s, the adsorption mechanism of these macromolecules to the surface of the ice crystals has not yet been fully elucidated. Two AFGP diastereomers containing different amino acid configurations were synthesized to study the influence of amino acid stereochemistry on conformation and antifreeze activity. For this purpose, peptides containing monosaccharide-substituted allo-L- and D-threonine building blocks were assembled by solid-phase peptide synthesis (SPPS). The retro-inverso AFGP analogue contained all amino acids in D-configuration, while the allo-L-diastereomer was composed of L-amino acids, like native AFGPs, with replacement of L-threonine by its allo-L-diastereomer. Both glycopeptides were analyzed regarding their conformational properties, by circular dichroism (CD), and their ability to inhibit ice recrystallization in microphysical experiments.
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Affiliation(s)
- Lilly Nagel
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Carsten Budke
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Axel Dreyer
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Thomas Koop
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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Nagel L, Budke C, Erdmann RS, Dreyer A, Wennemers H, Koop T, Sewald N. Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity. Chemistry 2012; 18:12783-93. [DOI: 10.1002/chem.201202119] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 11/08/2022]
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12
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Nagel L, Plattner C, Budke C, Majer Z, DeVries AL, Berkemeier T, Koop T, Sewald N. Synthesis and characterization of natural and modified antifreeze glycopeptides: glycosylated foldamers. Amino Acids 2011; 41:719-32. [DOI: 10.1007/s00726-011-0937-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 04/18/2011] [Indexed: 11/29/2022]
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13
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Tissot B, North SJ, Ceroni A, Pang PC, Panico M, Rosati F, Capone A, Haslam SM, Dell A, Morris HR. Glycoproteomics: past, present and future. FEBS Lett 2009; 583:1728-35. [PMID: 19328791 DOI: 10.1016/j.febslet.2009.03.049] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 03/20/2009] [Accepted: 03/20/2009] [Indexed: 11/28/2022]
Abstract
This invited paper reviews the study of protein glycosylation, commonly known as glycoproteomics, beginning with the origins of the subject area in the early 1970s shortly after mass spectrometry was first applied to protein sequencing. We go on to describe current analytical approaches to glycoproteomic analyses, with exemplar projects presented in the form of the complex story of human glycodelin and the characterisation of blood group H eptitopes on the O-glycans of gp273 from Unio elongatulus. Finally, we present an update on the latest progress in the field of automated and semi-automated interpretation and annotation of these data in the form of GlycoWorkBench, a powerful informatics tool that provides valuable assistance in unravelling the complexities of glycoproteomic studies.
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Affiliation(s)
- Bérangère Tissot
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Koller A, Khandurina J, Li J, Kreps J, Schieltz D, Guttman A. Analysis of high-mannose-type oligosaccharides by microliquid chromatography-mass spectrometry and capillary electrophoresis. Electrophoresis 2004; 25:2003-2009. [PMID: 15237400 DOI: 10.1002/elps.200305837] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report on microbore liquid chromatography (microLC) and capillary electrophoresis (CE) separation of glycopeptides and high-mannose-type oligosaccharides, digested from recombinant phospholipase C, expressed in Pichia pastoris. The glycopeptides were subject to microLC/electrospray ionization/mass spectrometry (ESI-MS) and microLC/ESI-tandem MS (MS/MS) analysis that revealed high-mannose structure size variation between Man(7)GlcNAc(2) and Man(14)GlcNAc(2). Then, high-performance CE was applied to identify possible positional isomers of the high-mannose structures. For the CE experiments, the oligosaccharides were released from the glycoproteins by peptide-N-glycosidase F and labeled with 1-aminopyrene-3,6,8-trisulfonic acid (APTS). Excellent separation of the possible positional isomers was attained, suggesting one for Man(9)GlcNAc(2), two for Man(10)GlcNAc(2), three for Man(11)GlcNAc(2), Man(12)GlcNAc(2), and Man(13)GlcNAc(2), and two for Man(14)GlcNAc(2). The CE results provided complementary information to the microLC/ESI-MS and MS/MS data with respect to the possible number of positional isomers.
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Affiliation(s)
| | | | - Jincai Li
- Diversa Corporation, San Diego, CA, USA
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15
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Eniade A, Ben RN. Fully convergent solid phase synthesis of antifreeze glycoprotein analogues. Biomacromolecules 2003; 2:557-61. [PMID: 11749220 DOI: 10.1021/bm0155120] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The convergent solid phase synthesis of C-linked analogues of antifreeze glycoprotein (AFGP) has been achieved. In this approach, three to six carbohydrate residues are simultaneously coupled to a resin-bound polypeptide. Glycopeptides ranging from 1.6 to 3.0 kDa are easily prepared in 26-44% yield demonstrating the utility of this approach.
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Affiliation(s)
- A Eniade
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, USA
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16
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Eniade A, Murphy AV, Landreau G, Ben RN. A general synthesis of structurally diverse building blocks for preparing analogues of C-linked antifreeze glycoproteins. Bioconjug Chem 2001; 12:817-23. [PMID: 11562200 DOI: 10.1021/bc0155059] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A synthetic methodology to afford unusual glycoconjugate building blocks useful for the solid-phase synthesis of C-linked antifreeze glycoprotein (AFGP) analogues is described. Such compounds are urgently required in order to elucidate the molecular mechanism by which AFGPs function. All reactions are general in nature and accommodate structural variation in the carbohydrate moiety, polypeptide backbone, and amino acid side chain.
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Affiliation(s)
- A Eniade
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, USA
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17
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Abstract
The human genome encodes 30,000 to 40,000 proteins, and a major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. Glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces where their oligosaccharide moieties are implicated in a wide range of cell-cell and cell-matrix recognition events. The power of ultrahigh-sensitivity mass spectrometric strategies for defining the primary structures of highly complex mixtures of glycoprotein glycoforms is set to revolutionize structural glycobiology in the coming postgenomic era.
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Affiliation(s)
- A Dell
- Department of Biochemistry, Imperial College of Science, Technology and Medicine, London SW7 2AY, UK.
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18
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Ben RN, Eniade AA, Hauer L. Synthesis of a C-linked Antifreeze Glycoprotein (AFGP) Mimic: Probes for Investigating the Mechanism of Action. Org Lett 1999. [DOI: 10.1021/ol991025+] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Chen L, DeVries AL, Cheng CH. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc Natl Acad Sci U S A 1997; 94:3817-22. [PMID: 9108061 PMCID: PMC20524 DOI: 10.1073/pnas.94.8.3817] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Antarctic notothenioid fishes and several northern cods are phylogenetically distant (in different orders and superorders), yet produce near-identical antifreeze glycoproteins (AFGPs) to survive in their respective freezing environments. AFGPs in both fishes are made as a family of discretely sized polymers composed of a simple glycotripeptide monomeric repeat. Characterizations of the AFGP genes from notothenioids and the Arctic cod show that their AFGPs are both encoded by a family of polyprotein genes, with each gene encoding multiple AFGP molecules linked in tandem by small cleavable spacers. Despite these apparent similarities, detailed analyses of the AFGP gene sequences and substructures provide strong evidence that AFGPs in these two polar fishes in fact evolved independently. First, although Antarctic notothenioid AFGP genes have been shown to originate from a pancreatic trypsinogen, Arctic cod AFGP genes share no sequence identity with the trypsinogen gene, indicating trypsinogen is not the progenitor. Second, the AFGP genes of the two fish have different intron-exon organizations and different spacer sequences and, thus, different processing of the polyprotein precursors, consistent with separate genomic origins. Third, the repetitive AFGP tripeptide (Thr-Ala/Pro-Ala) coding sequences are drastically different in the two groups of genes, suggesting that they arose from duplications of two distinct, short ancestral sequences with a different permutation of three codons for the same tripeptide. The molecular evidence for separate ancestry is supported by morphological, paleontological, and paleoclimatic evidence, which collectively indicate that these two polar fishes evolved their respective AFGPs separately and thus arrived at the same AFGPs through convergent evolution.
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Affiliation(s)
- L Chen
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana 61801, USA
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20
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Affiliation(s)
- Yin Yeh
- Departments of Applied Science and Food Science and Technology, University of California, Davis, California 95616
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21
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Dell A, Morris HR, Easton RL, Panico M, Patankar M, Oehniger S, Koistinen R, Koistinen H, Seppala M, Clark GF. Structural analysis of the oligosaccharides derived from glycodelin, a human glycoprotein with potent immunosuppressive and contraceptive activities. J Biol Chem 1995; 270:24116-26. [PMID: 7592613 DOI: 10.1074/jbc.270.41.24116] [Citation(s) in RCA: 171] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Glycodelin, also known as placental protein 14 (PP14) or progesterone-associated endometrial protein (PAEP), is a human glycoprotein with potent immunosuppressive and contraceptive activities. In this paper we report the first characterization of glycodelin-derived oligosaccharides. Using strategies based upon fast atom bombardment and electrospray mass spectrometry we have established that glycodelin is glycosylated at Asn-28 and Asn-63. The Asn-28 site carries high mannose, hybrid and complex-type structures, whereas the second site is exclusively occupied by complex-type glycans. The major non-reducing epitopes in the complex-type glycans are: Gal beta 1-4GlcNAc (lacNAc), GalNAc beta 1-4GlcNAc (lacdiNAc), NeuAc alpha 2-6Gal beta 1-4GlcNAc (sialylated lacNAc), NeuAc alpha 2-6Gal beta 1-4GlcNAc (sialylated lacdiNAc), Gal beta 1-4(Fuc alpha 1-3)GlcNAc (Lewisx), and GalNAc beta 1-4(Fuc alpha 1-3)GlcNAc (lacdiNAc analogue of Lewisx). It is possible that the oligosaccharides bearing sialylated lacNAc or lacdiNAc antennae may manifest immunosuppressive effects by specifically blocking adhesive and activation-related events mediated by CD22, the human B cell associated receptor. Oligosaccharides with fucosylated lacdiNAc antennae have previously been shown to potently block selectin-mediated adhesions and may perform the same function in glycodelin. The potent inhibitory effect of glycodelin on initial human sperm-zona pellucida binding is consistent with our previous suggestion that this cell adhesion event requires a selectin-like adhesion process. This result also raises the possibility that a convergence between immune and gamete recognition processes may have occurred in the types of carbohydrate ligands recognized in the human.
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Affiliation(s)
- A Dell
- Department of Biochemistry, Imperial College of Science, Technology and Medicine, London, United Kingdom
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22
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Dell A, Reason AJ, Khoo KH, Panico M, McDowell RA, Morris HR. Mass spectrometry of carbohydrate-containing biopolymers. Methods Enzymol 1994; 230:108-32. [PMID: 8139492 DOI: 10.1016/0076-6879(94)30010-0] [Citation(s) in RCA: 208] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A Dell
- Department of Biochemistry, Imperial College of Science, Technology, and Medicine, London, United Kingdom
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23
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Rademaker GJ, Haverkamp J, Thomas-Oates J. Determination of glycosylation sites inO-linked glycopeptides: A sensitive mass spectrometric protocol. ACTA ACUST UNITED AC 1993. [DOI: 10.1002/oms.1210281228] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Khoo KH, Morris HR, McDowell RA, Dell A, Maccarana M, Lindahl U. FABMS/derivatisation strategies for the analysis of heparin-derived oligosaccharides. Carbohydr Res 1993; 244:205-23. [PMID: 8348550 DOI: 10.1016/0008-6215(83)85002-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Derivatisation/FABMS strategies applicable to the structure analysis of low microgram quantities of heparin-derived oligosaccharides are described. Negative and positive FAB data from permethyl derivatives and positive FAB data from the products of subsequent methanolysis are reported for sulfated tetrasaccharides prepared by nitrous acid degradation of heparin. The preparation and FAB behaviour of acetylated derivatives of sulfated oligosaccharides are described for the first time, and the stability of the sulfate groups to base-catalysed acetylation is demonstrated. The acetylation/FABMS methodology, which yields high quality data, shows promise for the characterisation of a wide range of sulfated glycoconjugates.
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Affiliation(s)
- K H Khoo
- Department of Biochemistry, Imperial College, London, United Kingdom
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25
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Reason A, Morris H, Panico M, Marais R, Treisman R, Haltiwanger R, Hart G, Kelly W, Dell A. Localization of O-GlcNAc modification on the serum response transcription factor. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41871-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Dell A, Morris HR, Greer F, Redfern JM, Rogers ME, Weisshaar G, Hiyama J, Renwick AG. Fast-atom-bombardment mass spectrometry of sulphated oligosaccharides from ovine lutropin. Carbohydr Res 1991; 209:33-50. [PMID: 2036654 DOI: 10.1016/0008-6215(91)80143-b] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The positive- and negative-ion f.a.b.-mass spectra and the fragmentation of sulphated oligosaccharides derived from ovine lutropin are described. Negative-ion f.a.b.-m.s. of methylated derivatives offers a sensitive and rapid method for screening glycans for sulphation, for defining the location of sulphated residues, and for sequencing sulphated branches. Positive-ion f.a.b.-m.s. gives complementary data on non-sulphated branches in both complex and hybrid-type sulphated structures.
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Affiliation(s)
- A Dell
- Department of Biochemistry, Imperial College, London, Great Britain
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27
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Dell A. Preparation and desorption mass spectrometry of permethyl and peracetyl derivatives of oligosaccharides. Methods Enzymol 1990; 193:647-60. [PMID: 2074840 DOI: 10.1016/0076-6879(90)93443-o] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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D'Avino R, Caruso C, Romano M, Camardella L, Rutigliano B, Di Prisco G. Hemoglobin from the Antarctic fish Notothenia coriiceps neglecta. 2. Amino acid sequence of the alpha chain of Hb1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 179:707-13. [PMID: 2920735 DOI: 10.1111/j.1432-1033.1989.tb14604.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The complete amino acid sequence of the alpha chain of the main hemoglobin of the Antarctic fish Notothenia coriiceps neglecta (family Nototheniidae) has been determined. It consists of 142 residues; an acetylated seryl residue is at the amino terminal. The molecular mass is 15,519 Da. In comparison with alpha-chain sequences of non-Antarctic poikilothermic fish hemoglobins, the homology appears to be significantly lower than that existing among the latter species. A higher homology has been found with the alpha-chain sequence of the non-poikilothermic bluefin tuna.
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Affiliation(s)
- R D'Avino
- Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, Naples, Italy
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29
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Feeney RE, Osuga DT. Egg-white and blood-serum proteins functioning by noncovalent interactions: studies by chemical modification and comparative biochemistry. JOURNAL OF PROTEIN CHEMISTRY 1988; 7:667-87. [PMID: 3252892 DOI: 10.1007/bf01025577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Some of the more interesting and important proteins are those that function by forming associations or complexes with other substances. The structure-function relationships of three of these with very different substances are transferrins, which chelate metal ions; avian ovomucoids, which form complexes with proteolytic enzymes; and antifreeze glycoproteins, which interact at the ice-solution interface. Interrelating studies on the comparative biochemistry with studies using chemical modification have helped identify the side-chain groups of the proteins involved in function as well as to be useful for studies on general protein chemistry. The most strongly associated interaction is the chelation of iron by transferrin, with an association constant of approximately 10(21); tyrosines, histidines, and sometimes aspartate are involved. For ovomucoids, individual substratelike residues such as lysine are involved in a Michaelis-like complex, and association constants are as high as 10(10). By contrast, the antifreeze glycoproteins appear to function by a polymeric interaction at the surface of ice, with a much weaker association.
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Affiliation(s)
- R E Feeney
- Department of Food Science and Technology, University of California, Davis 95616
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30
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Chatterjee BP, Ahmed H, Chowdhury S. Further characterization of Artocarpus lakoocha lectin (artocarpin) purified using rivanol. Carbohydr Res 1988. [DOI: 10.1016/0008-6215(88)80067-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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DeVries AL. The role of antifreeze glycopeptides and peptides in the freezing avoidance of antarctic fishes. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0305-0491(88)90302-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Schrag JD, Cheng CH, Panico M, Morris HR, DeVries AL. Primary and secondary structure of antifreeze peptides from arctic and antarctic zoarcid fishes. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 915:357-70. [PMID: 3477289 DOI: 10.1016/0167-4838(87)90021-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Antifreeze peptides were isolated from Rhigophila dearborni, an antarctic eel pout, and Lycodes polaris, an arctic eel pout (both from the family Zoarcidae). The primary structures of two peptides, one from each species, were determined using a combination of Edman degradation and mass spectrometric techniques. The two sequences show a high degree of homology with nearly 80% of the residues being identical. These peptides are also homologous to antifreeze peptides from a third eel pout which inhabits the north Atlantic Ocean. The CD spectra of all of these peptides are also very similar. Unlike the antifreeze peptides of cottid fishes, the structures of antifreeze peptides from zoarcid fishes appear to be highly conserved, despite the large geographic distances which separate the different species. The zoarcid peptides also appear to have structures very different from other fish antifreezes.
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Affiliation(s)
- J D Schrag
- Department of Physiology and Biophysics, University of Illinois, Urbana
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33
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Burcham TS, Osuga DT, Rao BN, Bush CA, Feeney RE. Purification and primary sequences of the major arginine-containing antifreeze glycopeptides from the fish Eleginus gracilis. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)84573-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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34
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Driessen HP, de Jong WW, Tesser GI, Bloemendal H. The mechanism of N-terminal acetylation of proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1985; 18:281-325. [PMID: 3902358 DOI: 10.3109/10409238509086784] [Citation(s) in RCA: 192] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
N alpha-acetylation is almost exclusively restricted to eukaryotic structural proteins. As a rule it is a post-initiational process, requiring the presence of the enzyme N alpha-acetyltransferase and the acetyl donor acetylcoenzyme A. N alpha-acetyltransferases appear to have a narrow substrate specificity, which is very similar for enzymes from different tissues and species. Amino acids predominantly present at the N terminus of N alpha-acetylated proteins are alanine, serine, and methionine. The occurrence of these residues is apparently a prerequisite for acetylation. The region following these amino acids is also important. If methionine is at the N terminus, the second position is always occupied by a strongly hydrophilic amino acid. Two- and three-dimensional structural characteristics of the protein do not seem to play a major role in N alpha-acetylation. Up to now the exact function for N alpha-acetylation is not known.
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35
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Burcham TS, Knauf MJ, Osuga DT, Feeney RE, Yeh Y. Antifreeze glycoproteins: influence of polymer length and ice crystal habit on activity. Biopolymers 1984; 23:1379-95. [PMID: 6466773 DOI: 10.1002/bip.360230720] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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36
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37
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Carr SA, Biemann K. Identification of posttranslationally modified amino acids in proteins by mass spectrometry. Methods Enzymol 1984; 106:29-58. [PMID: 6493059 DOI: 10.1016/0076-6879(84)06006-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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38
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Hew CL, Slaughter D, Joshi SB, Fletcher GL, Ananthanarayanan VS. Antifreeze polypeptides from the Newfoundland ocean pout,Macrozoarces americanus: presence of multiple and compositionally diverse components. J Comp Physiol B 1984. [DOI: 10.1007/bf00688795] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Biosynthesis of the O-glycosidically linked oligosaccharide chains of fetuin. Indications for an alpha-N-acetylgalactosaminide alpha 2 leads to 6 sialyltransferase with a narrow acceptor specificity in fetal calf liver. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32197-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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40
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Van den Eijnden DH, Schiphorst WE, Berger EG. Specific detection of N-acetylglucosamine-containing oligosaccharide chains on ovine submaxillary asialomucin. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 755:32-9. [PMID: 6402035 DOI: 10.1016/0304-4165(83)90269-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human milk beta-N-acetylglucosaminide beta 1 leads to 4-galactosyltransferase (EC 2.4.1.38) was used to galactosylate ovine submaxillary asialomucin to saturation. The major [14C]galactosylated product chain was obtained as a reduced oligosaccharide by beta-elimination under reducing conditions. Analysis by Bio-Gel filtration and gas-liquid chromatography indicated that this compound was a tetrasaccharide composed of galactose, N-acetylglucosamine and reduced N-acetylgalactosamine in a molar ratio of 2:0.9:0.8. Periodate oxidation studies before and after mild acid hydrolysis in addition to thin-layer chromatography revealed that the most probable structure of the tetrasaccharide is Gal beta 1 leads to 3([14C]Gal beta 1 leads to 4GlcNAc beta 1 leads to 6)GalNAcol. Thus it appears that Gal beta 1 leads to 3(GlcNAc beta 1 leads to 6)GalNAc units occur as minor chains on the asialomucin. The potential interference of these chains in the assay of alpha-N-acetylgalactosaminylprotein beta 1 leads to 3-galactosyltransferase activity using ovine submaxillary asialomucin as an acceptor can be counteracted by the addition of N-acetylglucosamine.
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41
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Schrag JD, Devries AL. The effect of freezing rate on the cooperativity of antifreeze glycopeptides. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0300-9629(83)90619-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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O'Grady SM, Schrag JD, Raymond JA, Devries AL. Comparison of antifreeze glycopeptides from arctic and antarctic fishes. ACTA ACUST UNITED AC 1982. [DOI: 10.1002/jez.1402240207] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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44
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Schrag JD, O'Grady SM, DeVries AL. Relationship of amino acid composition and molecular weight of antifreeze glycopeptides to non-colligative freezing point depression. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 717:322-6. [PMID: 7115772 DOI: 10.1016/0304-4165(82)90186-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Many polar fishes synthesize a group of eight glycopeptides that exhibit a non-colligative lowering of the freezing point of water. These glycopeptides range in molecular weight between 2600 and 33 700. The largest glycopeptides [1-5] lower the freezing point more than the small ones on a weight basis and contain only two amino acids, alanine and threonine, with the disaccharide galactose-N-acetyl-galactosamine attached to threonine. The small glycopeptides, 6, 7, and 8, also lower the freezing point and contain proline, which periodically substitutes for alanine. Glycopeptides with similar antifreeze properties isolated from the saffron cod and the Atlantic tomcod contain an additional amino acid, arginine, which substitutes for threonine in glycopeptide 6. In this study we address the question of whether differences in amino acid composition or molecular weight between large and small glycopeptides are responsible for the reduced freezing point depressing capability of the low molecular weight glycopeptides. The results indicate that the degree of amino acid substitutions that occur in glycopeptides 6-8 do not have a significant effect on the unusual freezing point lowering and that the observed decrease in freezing point depression with smaller glycopeptides can be accounted for on the basis of molecular weight.
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45
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Feeney RE. Penguin egg-white and polar fish blood-serum proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1982; 19:215-32. [PMID: 6749729 DOI: 10.1111/j.1399-3011.1982.tb03030.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of, and findings in, a long-term research program on penguin proteins and polar fish blood proteins are described. Two of the egg-white proteins from the Adelie penguin (Pygoscelis adeliae) have unique properties: a glycoprotein named penalbumin that is a major constituent with some characteristics similar to ovalbumin, and an ovomucoid with strong inhibitory capacity for subtilisin as well as for bovine trypsin and alpha-chymotrypsin. The antifreeze glycoproteins from Antarctic fish (Trematomus borchgrevinki and Dissostichus mawsoni) and an Arctic fish (Boreogadus saida) appear to function noncolligatively by lowering the freezing temperature without affecting the melting point. Current evidence indicates that the antifreeze glycoprotein functions at the ice-solution interface, either on the ice surface or in a transition layer between the solution and the ice.
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46
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47
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Driessen HP, Herbrink P, Bloemendal H, de Jong WW. Primary structure of the bovine beta-crystallin Bp chain. Internal duplication and homology with gamma-crystallin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 121:83-91. [PMID: 7035168 DOI: 10.1111/j.1432-1033.1981.tb06433.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The major polypeptide chain of bovine beta-crystallin, beta Bp, was fragmented by means of cyanogen bromide treatment and by enzymatic digestions. Manual and automated Edman degradation of the resulting peptides provided the complete amino acid sequence of the beta Bp chain. The N-terminal alanine residue was shown to be N-alpha-acetylated by mass spectrometry. The chain has a length of 204 residues and a calculated molecular weight of 23210. There is a considerable degree of homology between the N-terminal and C-terminal halves of the chain, presumably reflecting a tandem duplication of a shorter ancestral gene. The sequence of beta Bp is sufficiently related to that of gamma-crystallin II to place these proteins in the same superfamily. No sequence relationship was found with the alpha-crystallin chains.
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48
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Hunt DF, Buko AM, Ballard JM, Shabanowitz J, Giordani AB. Sequence analysis of polypeptides by collision activated dissociation on a triple quadrupole mass spectrometer. BIOMEDICAL MASS SPECTROMETRY 1981; 8:397-408. [PMID: 7306675 DOI: 10.1002/bms.1200080909] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new approach to the direct sequencing of oligopeptides in complex mixtures is described. Mixtures of [2Ho]/[2H3]-N-acetylated and N,O-permethylated peptides are analyzed by collision activate dissociation on a triple quadrupole mass spectrometer using isobutane chemical ionization. Analysis of the collision activated dissociation spectra enables peptide sequences to be deduced. Use of electron capture negative chemical ionization for the sequence analysis of neuropeptides at the picomole level is also described.
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49
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Abstract
Mass spectometry, conventionally used with smallish molecules (less than 1,000 daltons), has suprisingly emerged as a powerful technique for the determination of the amino acid sequences of proteins and the structure of glycopeptides as well as for the characterization of biologically active materials of unusual structure such as the peptidolipids. Further applications to biomedical problems are foreseen.
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50
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Berman E, Allerhand A, DeVries A. Natural abundance carbon 13 nuclear magnetic resonance spectroscopy of antifreeze glycoproteins. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85503-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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