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Hou X, Wang Y, Bu D, Wang Y, Sun S. EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction. Bioinformatics 2023; 39:btad650. [PMID: 37930896 PMCID: PMC10627407 DOI: 10.1093/bioinformatics/btad650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/14/2023] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION N-linked glycosylation is a frequently occurring post-translational protein modification that serves critical functions in protein folding, stability, trafficking, and recognition. Its involvement spans across multiple biological processes and alterations to this process can result in various diseases. Therefore, identifying N-linked glycosylation sites is imperative for comprehending the mechanisms and systems underlying glycosylation. Due to the inherent experimental complexities, machine learning and deep learning have become indispensable tools for predicting these sites. RESULTS In this context, a new approach called EMNGly has been proposed. The EMNGly approach utilizes pretrained protein language model (Evolutionary Scale Modeling) and pretrained protein structure model (Inverse Folding Model) for features extraction and support vector machine for classification. Ten-fold cross-validation and independent tests show that this approach has outperformed existing techniques. And it achieves Matthews Correlation Coefficient, sensitivity, specificity, and accuracy of 0.8282, 0.9343, 0.8934, and 0.9143, respectively on a benchmark independent test set.
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Affiliation(s)
- Xiaoyang Hou
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wang
- Syneron Technology, Guangzhou 510000, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaojun Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Bahadori Z, Shabani AA, Minuchehr Z. Rational design of hyper-glycosylated human follicle-stimulating hormone analogs (a bioinformatics approach). J Biomol Struct Dyn 2021; 40:9114-9125. [PMID: 33998969 DOI: 10.1080/07391102.2021.1924268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-glycosylation is a complex mechanism in which the carbohydrate molecules bind to the Asn amino acid in the N-glycan consensus sequence (AsnXxxThr/Ser sequon, where Xxx is any residue, excluding Pro). Introduction of additional N-linked glycosylation site into proposed location in the protein causes to its hyper-glycosylation and can enhance the protein characteristics to provide promising prospects in treatment. Glycoengineering is a favorably used strategy to design and generate hyper-glycosylated variants. In this research, human follicle-stimulating hormone (HuFSH) was considered to identify appropriate positions for adding novel N-glycan sites. A rational computational strategy was applied to predict functional/structural variations induced through changes in polypeptide chain. We analyzed the amino acid chain of FSH to find out the proper locations to introduce asparagine and/or threonine for creating novel N-glycan positions. This analysis resulted in the recognition of 40 possible N-glycosylation positions, and then the eight adequate ones were chosen for additional investigation. The model validation techniques were used to examine 3-dimensional structures of the chosen mutant proteins. Finally, 2 mutants with a further glycan site were recommended as eligible FSH hyper-glycosylated analogs, which may be regarded for subsequent experimental studies. Our in silico approach may decrease tedious and time-wasting laboratory researches of the mutants.Communicated by Ramaswamy H. Sharma.
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Affiliation(s)
- Zohreh Bahadori
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Students Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Shabani
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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3
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So you want to express your protein in Escherichia coli? Essays Biochem 2021; 65:247-260. [PMID: 33955451 DOI: 10.1042/ebc20200170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Recombinant proteins have been extensively employed as therapeutics for the treatment of various critical and life-threatening diseases and as industrial enzymes in high-value industrial processes. Advances in genetic engineering and synthetic biology have broadened the horizon of heterologous protein production using multiple expression platforms. Selection of a suitable expression system depends on a variety of factors ranging from the physicochemical properties of the target protein to economic considerations. For more than 40 years, Escherichia coli has been an established organism of choice for protein production. This review aims to provide a stepwise approach for any researcher embarking on the journey of recombinant protein production in E. coli. We present an overview of the challenges associated with heterologous protein expression, fundamental considerations connected to the protein of interest (POI) and designing expression constructs, as well as insights into recently developed technologies that have contributed to this ever-growing field.
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Lan R, Xin M, Hao Z, You S, Xu Y, Wu J, Dang L, Zhang X, Sun S. Biological Functions and Large-Scale Profiling of Protein Glycosylation in Human Semen. J Proteome Res 2020; 19:3877-3889. [DOI: 10.1021/acs.jproteome.9b00795] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rongxia Lan
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Miaomiao Xin
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
- Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Vodnany 38925, Czech Republic
| | - Zhifang Hao
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Shanshan You
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Yintai Xu
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Jingyu Wu
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Liuyi Dang
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Xinwen Zhang
- The Medical Genetics Centre, Xi 'an People's Hospital (Xi 'an Fourth Hospital), Xi’an Obstetrics and Gynecology Hospital, Xi’an, Shaanxi Province 710004, P. R. China
| | - Shisheng Sun
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
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5
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Nabizadeh Z, Minuchehr Z, Shabani AA. Rational Design of Hyper-glycosylated Human Chorionic Gonadotropin Analogs (A Bioinformatics Approach). LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817666200225101938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Protein pharmaceuticals routinely display a series of intrinsic physicochemical instabilities during their production and administration that can unfavorably affect their therapeutic effectiveness. Glycoengineering is one of the most desirable techniques to improve the attributes of therapeutic proteins. One aspect of glycoengineering is the rational manipulation of the peptide backbone to introduce new N-glycosylation consensus sequences (Asn-X-Ser/Thr, where X is any amino acid except proline).Methods:In this work, the amino acid sequence of human chorionic gonadotropin (hCG) was analyzed to identify suitable positions in order to create new N-glycosylation sites. This survey led to the detection of 46 potential N-glycosylation sites. The N-glycosylation probability of all the potential positions was measured with the NetNGlyc 1.0 server. After theoretical reviews and the removal of unsuitable positions, the five acceptable ones were selected for more analyses. Then, threedimensional (3D) structures of the selected analogs were generated and evaluated by SPDBV software. The molecular stability and flexibility profile of five designed analogs were examined using Molecular Dynamics (MD) simulations.Results:Finally, three analogs with one additional N-glycosylation site (V68T, V79N and R67N) were proposed as the qualified analogs that could be glycosylated at the new sites.Conclusion:According to the results of this study, further experimental investigations could be guided on the three analogs. Therefore, our computational strategy can be a valuable method due to the reduction in the number of the expensive, tiresome and time-consuming experimental studies of hCG analogs.
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Affiliation(s)
- Zahra Nabizadeh
- Dept. and Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology (IIEB), National Institute for Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran
| | - Ali Akbar Shabani
- Dept. and Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran
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Besançon C, Guillot A, Blaise S, Dauchez M, Belloy N, Prévoteau-Jonquet J, Baud S. Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol. Methods 2020; 173:94-104. [PMID: 31302178 PMCID: PMC7128144 DOI: 10.1016/j.ymeth.2019.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 07/09/2019] [Indexed: 01/17/2023] Open
Abstract
N-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of N-glycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions.
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Affiliation(s)
- Camille Besançon
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France.
| | - Alexandre Guillot
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Sébastien Blaise
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - Nicolas Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | | | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
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7
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Maciel VL, Tamashiro LK, Bertolla RP. Post-translational modifications of seminal proteins and their importance in male fertility potential. Expert Rev Proteomics 2019; 16:941-950. [PMID: 31726898 DOI: 10.1080/14789450.2019.1693895] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: The seminal proteome has been shown to directly influence the male fertile potential. Post-translational modifications (PTMs) are significant changes that play a role in the biological regulation of proteins. Sperm cells are transcriptionally and translationally inactive and these modifications are essential to control protein function.Areas covered: Here we reviewed seven PTMs which importance for male reproductive function investigated in the past decade, namely S-nitrosylation and tyrosine nitration (both occurring by the action of NO), glycosylation, ubiquitination, acetylation, methylation, and SUMOylation. Since they were previously identified in human semen, we focus on their role in sperm function, as well as in physiological and pathophysiological processes which could contribute to the fertility potential. The following keywords were applied: 'post-translational modification', 'sperm', 'semen', 'seminal plasma', 'male infertility', 'nitrosylation', 'nitration', 'histone methylation', 'SUMOylation', 'ubiquitination', 'ubiquitilation', 'glycosylation', and 'acetylation'.Expert opinion: Most biological processes orchestrated by proteins require PTMs for their activation or inhibition. Most of them are dynamic and occur in mature sperm, modulating protein function, thus exerting a significant role in sperm function and fertility. Finally, the study of PTMs should be also addressed in pathophysiological processes, as different clinical conditions are known to alter the proteome.
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Affiliation(s)
- Valter Luiz Maciel
- Departamento de Cirurgia, Disciplina de Urologia, Centro de pesquisa em Urologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Letícia Kaory Tamashiro
- Departamento de Cirurgia, Disciplina de Urologia, Centro de pesquisa em Urologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ricardo Pimenta Bertolla
- Departamento de Cirurgia, Disciplina de Urologia, Centro de pesquisa em Urologia, Universidade Federal de São Paulo, São Paulo, Brazil
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8
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Shafaghi M, Shabani AA, Minuchehr Z. Rational design of hyper-glycosylated human luteinizing hormone analogs (a bioinformatics approach). Comput Biol Chem 2019; 79:16-23. [PMID: 30708139 DOI: 10.1016/j.compbiolchem.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/29/2018] [Accepted: 01/02/2019] [Indexed: 01/09/2023]
Abstract
Glycoengineering is a recently used approach to extend serum half-life of valuable protein therapeutics. One aspect of glycoengineering is to introduce new N-glycosylation site (Asn-X-Thr/Ser, where X ≠ Pro) into desirable positions in the peptide backbone, resulting in the generation of hyper-glycosylated protein. In this study, human luteinizing hormone (LH) was considered for identification of the suitable positions for the addition of new N-linked glycosylation sites. A rational in silico approach was applied for prediction of structural and functional alterations caused by changes in amino acid sequence. As the first step, we explored the amino acid sequence of LH to find out desirable positions for introducing Asn or/and Thr to create new N-glycosylation sites. This exploration led to the identification of 38 potential N-glycan sites, and then the four acceptable ones were selected for further analysis. Three-dimensional (3D) structures of the selected analogs were generated and examined by the model evaluation methods. Finally, two analogs with one additional glycosylation site were suggested as the qualified analogs for hyper-glycosylation of the LH, which can be considered for further experimental investigations. Our computational strategy can reduce laborious and time-consuming experimental analyses of the analogs.
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Affiliation(s)
- Mona Shafaghi
- Dept. & Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran; Students Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Shabani
- Dept. & Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran.
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Moenes EM, Al-Ghobashy MA, Mohamed AA, Salem MY. Comparative Assessment of the Effect of Hyper-glycosylation on the Pattern and Kinetics of Degradation of Darbepoetin Alfa using a Stability-Indicating Orthogonal Testing Protocol. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1072:405-414. [DOI: 10.1016/j.jchromb.2017.10.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/21/2017] [Accepted: 10/29/2017] [Indexed: 10/18/2022]
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10
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Dolinska MB, Sergeev YV. The consequences of deglycosylation of recombinant intra-melanosomal domain of human tyrosinase. Biol Chem 2017; 399:73-77. [PMID: 28858842 PMCID: PMC6108172 DOI: 10.1515/hsz-2017-0178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/25/2017] [Indexed: 11/15/2022]
Abstract
Tyrosinase, a melanosomal glycoenzyme, catalyzes initial steps of the melanin biosynthesis. While glycosylation was previously studied in vivo, we present three recombinant mutant variants of human tyrosinase, which were obtained using multiple site-directed mutagenesis, expressed in insect larvae, purified and characterized biochemically. The mutagenesis demonstrated the reduced protein expression and enzymatic activity due to possible loss of protein stability and protein degradation. However, the complete deglycosylation of asparagine residues in vitro, including the residue in position 371, interrupts tyrosinase function, which is consistent with a melanin loss in oculocutaneous albinism type 1 (OCA1) patients.
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Affiliation(s)
- Monika B. Dolinska
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 31 Center Drive MSC 2510, Bethesda, MD 20892, USA
| | - Yuri V. Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10 Center Dr., 31 Center Drive MSC 2510, Bethesda, MD 20892, USA
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11
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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12
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Song Q, Wu Z, Fan Y, Song W, Zhang P, Wang L, Wang F, Xu Y, Wang PG, Cheng J. Production of homogeneous glycoprotein with multisite modifications by an engineered N-glycosyltransferase mutant. J Biol Chem 2017; 292:8856-8863. [PMID: 28381551 DOI: 10.1074/jbc.m117.777383] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/04/2017] [Indexed: 12/26/2022] Open
Abstract
Naturally occurring N-glycoproteins exhibit glycoform heterogeneity with respect to N-glycan sequon occupancy (macroheterogeneity) and glycan structure (microheterogeneity). However, access to well-defined glycoproteins is always important for both basic research and therapeutic purposes. As a result, there has been a substantial effort to identify and understand the catalytic properties of N-glycosyltransferases, enzymes that install the first glycan on the protein chain. In this study we found that ApNGT, a newly discovered cytoplasmic N-glycosyltransferase from Actinobacillus pleuropneumoniae, has strict selectivity toward the residues around the Asn of N-glycosylation sequon by screening a small library of synthetic peptides. The inherent stringency was subsequently demonstrated to be closely associated with a critical residue (Gln-469) of ApNGT which we propose hinders the access of bulky residues surrounding the occupied Asn into the active site. Site-saturated mutagenesis revealed that the introduction of small hydrophobic residues at the site cannot only weaken the stringency of ApNGT but can also contribute to enormous improvement of glycosylation efficiency against both short peptides and proteins. We then employed the most efficient mutant (Q469A) other than the wild-type ApNGT to produce a homogeneous glycoprotein carrying multiple (up to 10) N-glycans, demonstrating that this construct is a promising biocatalyst for potentially addressing the issue of macroheterogeneity in glycoprotein preparation.
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Affiliation(s)
- Qitao Song
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Zhigang Wu
- the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yueyuan Fan
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Woran Song
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Peiru Zhang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Li Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Faxing Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Yangyang Xu
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Peng G Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Jiansong Cheng
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
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Bednarska NG, Wren BW, Willcocks SJ. The importance of the glycosylation of antimicrobial peptides: natural and synthetic approaches. Drug Discov Today 2017; 22:919-926. [PMID: 28212948 DOI: 10.1016/j.drudis.2017.02.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/24/2017] [Accepted: 02/02/2017] [Indexed: 12/16/2022]
Abstract
Glycosylation is one of the most prevalent post-translational modifications of a protein, with a defining impact on its structure and function. Many of the proteins involved in the innate or adaptive immune response, including cytokines, chemokines, and antimicrobial peptides (AMPs), are glycosylated, contributing to their myriad activities. The current availability of synthetic coupling and glycoengineering technology makes it possible to customise the most beneficial glycan modifications for improved AMP stability, microbicidal potency, pathogen specificity, tissue or cell targeting, and immunomodulation.
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Affiliation(s)
| | - Brendan W Wren
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Sam J Willcocks
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
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14
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Barnett CB, Aoki-Kinoshita KF, Naidoo KJ. The Glycome Analytics Platform: an integrative framework for glycobioinformatics. Bioinformatics 2016; 32:3005-11. [PMID: 27288496 DOI: 10.1093/bioinformatics/btw341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/26/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Complex carbohydrates play a central role in cellular communication and in disease development. O- and N-glycans, which are post-translationally attached to proteins and lipids, are sugar chains that are rooted, tree structures. Independent efforts to develop computational tools for analyzing complex carbohydrate structures have been designed to exploit specific databases requiring unique formatting and limited transferability. Attempts have been made at integrating these resources, yet it remains difficult to communicate and share data across several online resources. A disadvantage of the lack of coordination between development efforts is the inability of the user community to create reproducible analyses (workflows). The latter results in the more serious unreliability of glycomics metadata. RESULTS In this paper, we realize the significance of connecting multiple online glycan resources that can be used to design reproducible experiments for obtaining, generating and analyzing cell glycomes. To address this, a suite of tools and utilities, have been integrated into the analytic functionality of the Galaxy bioinformatics platform to provide a Glycome Analytics Platform (GAP).Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services. We illustrate the central functionality and features of the GAP by way of example; we analyze and compare the features of the N-glycan glycome of monocytic cells sourced from two separate data depositions.This paper highlights the use of reproducible research methods for glycomics analysis and the GAP presents an opportunity for integrating tools in glycobioinformatics. AVAILABILITY AND IMPLEMENTATION This software is open-source and available online at https://bitbucket.org/scientificomputing/glycome-analytics-platform CONTACTS chris.barnett@uct.ac.za or kevin.naidoo@uct.ac.za SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christopher B Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Kevin J Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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15
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Ghasemi F, Zomorodipour A, Karkhane AA, Khorramizadeh MR. In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. J Mol Graph Model 2016; 68:39-47. [PMID: 27356208 DOI: 10.1016/j.jmgm.2016.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 11/17/2022]
Abstract
N-glycosylation is a process during which a glycan moiety attaches to the asparagine residue in the N-glycosylation consensus sequence (Asn-Xxx-Ser/Thr), where Xxx can be any amino acid except proline. Introduction of a new N-glycosylation site into a protein backbone leads to its hyper-glycosylation, and may improve the protein properties such as solubility, folding, stability, and secretion. Glyco-engineering is an approach to facilitate the hyper-glycosylation of recombinant proteins by application of the site-directed mutagenesis methods. In this regard, selection of a suitable location on the surface of a protein for introduction of a new N-glycosylation site is a main concern. In this work, a computational approach was conducted to select suitable location(s) for introducing new N-glycosylation sites into the human coagulation factor IX (hFIX). With this aim, the first 45 residues of mature hFIX were explored to find out suitable positions for introducing either Asn or Ser/Thr residues, to create new N-glycosylation site(s). Our exploration lead to detection of five potential positions, for hyper-glycosylation. For each suggested position, an analog was defined and subjected for N-glycosylation efficiency prediction. After generation of three-dimensional structures, by homology-based modeling, the five designed analogs were examined by molecular dynamic (MD) simulations, to predict their stability levels and probable structural distortions caused by amino acid substitutions, relative to the native counterpart. Three out of five suggested analogs, namely; E15T, K22N, and R37N, reached equilibration state with relatively constant Root Mean Square Deviation values. Additional analysis on the data obtained during MD simulations, lead us to conclude that, R37N is the only qualified analog with the most similar structure and dynamic behavior to that of the native counterpart, to be considered for further experimental investigations.
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Affiliation(s)
- Fahimeh Ghasemi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Alireza Zomorodipour
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box: 14965/161, Tehran, Iran.
| | - Ali Asghar Karkhane
- Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - M Reza Khorramizadeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences, 5th Fl., Dr. Shariati Hospital, North Karegar Ave., Tehran 1411413137, Iran.
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Cheon YP, Kim CH. Impact of glycosylation on the unimpaired functions of the sperm. Clin Exp Reprod Med 2015; 42:77-85. [PMID: 26473106 PMCID: PMC4604297 DOI: 10.5653/cerm.2015.42.3.77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 09/20/2015] [Accepted: 09/20/2015] [Indexed: 12/24/2022] Open
Abstract
One of the key factors of early development is the specification of competence between the oocyte and the sperm, which occurs during gametogenesis. However, the starting point, growth, and maturation for acquiring competence during spermatogenesis and oogenesis in mammals are very different. Spermatogenesis includes spermiogenesis, but such a metamorphosis is not observed during oogenesis. Glycosylation, a ubiquitous modification, is a preliminary requisite for distribution of the structural and functional components of spermatids for metamorphosis. In addition, glycosylation using epididymal or female genital secretory glycans is an important process for the sperm maturation, the acquisition of the potential for fertilization, and the acceleration of early embryo development. However, nonemzymatic unexpected covalent bonding of a carbohydrate and malglycosylation can result in falling fertility rates as shown in the diabetic male. So far, glycosylation during spermatogenesis and the dynamics of the plasma membrane in the process of capacitation and fertilization have been evaluated, and a powerful role of glycosylation in spermatogenesis and early development is also suggested by structural bioinformatics, functional genomics, and functional proteomics. Further understanding of glycosylation is needed to provide a better understanding of fertilization and embryo development and for the development of new diagnostic and therapeutic tools for infertility.
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Affiliation(s)
- Yong-Pil Cheon
- Division of Developmental Biology and Physiology, School of Biosciences and Chemistry, Sungshin Women's University, Seoul, Korea
| | - Chung-Hoon Kim
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
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Assessment of the Effects of Glycosylation on the Pattern and Kinetics of Degradation of Lenograstim in Comparison to Filgrastim Using a Stability-Indicating Orthogonal Testing Protocol. Chromatographia 2015. [DOI: 10.1007/s10337-015-2910-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J. GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinformatics 2015; 31:1411-9. [DOI: 10.1093/bioinformatics/btu852] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/23/2014] [Indexed: 12/31/2022] Open
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Ruiz-May E, Hucko S, Howe KJ, Zhang S, Sherwood RW, Thannhauser TW, Rose JKC. A comparative study of lectin affinity based plant N-glycoproteome profiling using tomato fruit as a model. Mol Cell Proteomics 2014; 13:566-79. [PMID: 24198434 PMCID: PMC3916654 DOI: 10.1074/mcp.m113.028969] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 10/20/2013] [Indexed: 12/22/2022] Open
Abstract
Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be determined whether certain lectins, or combinations of lectins are optimal for plant N-glycoproteome profiling; or whether specific lectins show preferential association with particular N-glycosylation sites or N-glycan structures. We describe here a comparative study of three mannose-binding lectins, concanavalin A, snowdrop lectin, and lentil lectin, to profile the N-glycoproteome of mature green stage tomato (Solanum lycopersicum) fruit pericarp. Through coupling lectin affinity chromatography with a shotgun proteomics strategy, we identified 448 putative N-glycoproteins, whereas a parallel lectin affinity chromatography plus hydrophilic interaction chromatography analysis revealed 318 putative N-glycosylation sites on 230 N-glycoproteins, of which 100 overlapped with the shotgun analysis, as well as 17 N-glycan structures. The use of multiple lectins substantially increased N-glycoproteome coverage and although there were no discernible differences in the structures of N-glycans, or the charge, isoelectric point (pI) or hydrophobicity of the glycopeptides that differentially bound to each lectin, differences were observed in the amino acid frequency at the -1 and +1 subsites of the N-glycosylation sites. We also demonstrated an alternative and complementary in planta recombinant expression strategy, followed by affinity MS analysis, to identify the putative N-glycan structures of glycoproteins whose abundance is too low to be readily determined by a shotgun approach, and/or combined with deglycosylation for predicted deamidated sites, using a xyloglucan-specific endoglucanase inhibitor protein as an example.
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Affiliation(s)
- Eliel Ruiz-May
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Simon Hucko
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Kevin J. Howe
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Sheng Zhang
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | - Robert W. Sherwood
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | | | - Jocelyn K. C. Rose
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
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Muta K, Fukami T, Nakajima M, Yokoi T. N-Glycosylation during translation is essential for human arylacetamide deacetylase enzyme activity. Biochem Pharmacol 2014; 87:352-9. [DOI: 10.1016/j.bcp.2013.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/01/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
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Woodin CL, Maxon M, Desaire H. Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. Analyst 2013; 138:2793-803. [PMID: 23293784 DOI: 10.1039/c2an36042j] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.
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Affiliation(s)
- Carrie L Woodin
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
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Vandermarliere E, Martens L. Protein structure as a means to triage proposed PTM sites. Proteomics 2013; 13:1028-35. [PMID: 23172737 DOI: 10.1002/pmic.201200232] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/13/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
Abstract
PTMs such as phosphorylation are often important actors in protein regulation and recognition. These functions require both visibility and accessibility to other proteins; that the modification is located at the surface of the protein. Currently, many repositories provide information on PTMs but structural information is often lacking. This study, which focuses on phosphorylation sites available in UniProtKB/Swiss-Prot, illustrates that most phosphorylation sites are indeed found at the surface of the protein, but that some sites are found buried in the core of the protein. Several of these identified buried phosphorylation sites can easily become accessible upon small conformational changes while others would require the whole protein to unfold and are hence most unlikely modification sites. Subsequent analysis of phosphorylation sites available in PRIDE demonstrates that taking the structure of the protein into account would be a good guide in the identification of the actual phosphorylated positions in phophoproteomics experiments. This analysis illustrates that care must be taken when simply accepting the position of a PTM without first analyzing its position within the protein structure if the latter is available.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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Lazar IM, Lee W, Lazar AC. Glycoproteomics on the rise: established methods, advanced techniques, sophisticated biological applications. Electrophoresis 2012; 34:113-25. [PMID: 23161435 DOI: 10.1002/elps.201200445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/07/2012] [Accepted: 10/07/2012] [Indexed: 02/05/2023]
Abstract
Glycosylation is the most complex form of protein PTMs. Affected proteins may carry dozens of glycosylation sites with tens to hundreds of glycan residues attached to every site. Glycosylated proteins have many important functions in biology, from cellular to organismal levels, being involved in cell-cell signaling, cell adhesion, immune response, host-pathogen interactions, and development and growth. Glycosylation, however, expands the biological functional diversity of proteins at the expense of a tremendous increase in structural heterogeneity. Aberrant glycosylation of cell surface proteins, as well as their detectable fingerprint in plasma samples, has been associated with cancer, inflammatory and degenerative diseases, and congenital disorders of glycosylation. Therefore, there are on-going efforts directed toward developing new technologies and approaches for glycan sequencing and high-throughput analysis of glycosylated proteins in complex samples with simultaneous characterization of both the protein and glycan moieties. This work is aimed primarily at pinpointing the challenges associated with the large-scale analysis of glycoproteins and the latest developments in glycoproteomic research, with focus on recent advancements (2011-2012) in microcolumn separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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