Symbol Nomenclature For Glycans

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Monosaccharide color code in the Symbol Nomenclature For Glycans (SNFG) SNFG.tif
Monosaccharide color code in the Symbol Nomenclature For Glycans (SNFG)

The Symbol Nomenclature For Glycans (SNFG) [1] is a community-curated standard for the depiction of simple monosaccharides and complex carbohydrates (glycans) using various colored-coded, geometric shapes, along with defined text additions. [2] [3] It is hosted by the National Center for Biotechnology Information at the NCBI-Glycans Page. [4] It is curated by an international groups of researchers in the field that are collectively called the SNFG Discussion Group. The overall goal of the SNFG is to:

Contents

  1. Facilitate communications and presentations of monosaccharides and glycans for researchers in the Glycosciences, and for scientists and students less familiar with the field.
  2. Ensure uniform usage of the nomenclature in the literature, thus helping to ensure scientific accuracy in journal and online publications.
  3. Continue to develop the SNFG and its applications to aid wider use by the scientific community.

Description and examples

The SNFG consists of a table that provides color coded symbols for various monosaccharides that are commonly found in nature. It also includes a set of footnotes that describe rules for rendering glycans, including guidelines on how to modify the base set of symbols depicted in the table. These footnotes are organized into 10 themes that provide streamlined recommendations for: i. general usage of the SNFG; ii. CMYK / RGB color codes; iii. symbol colors and shapes; iv. ring configurations; v. bond linkage presentation; vi. sialic acids; vii. glycan modifications; viii. amino substitutions; ix. handling ambiguous or partially defined glycans; and x. depicting non-glycan entities using SNFG renderings. More details are available at the main SNFG webpage, [1] which is periodically updated with additional directions.

Selected examples of SNFG usage SNFG Example1.tif
Selected examples of SNFG usage

The monosaccharides can be linked together to describe complex carbohydrate structures or glycans. More exhaustive cases for mammalian species, other eukaryotes, plants and microbes are considered at the main SNFG page. [1]

Software

Several software tools have been developed to support SNFG implementation by the community including:

  1. GlycoGlyph: An open source glycan drawing and naming tool which enables drawing glycans in SNFG format using either a graphical user interface or from names in CFG linear nomenclature format. When structures are drawn, the application produces both the CFG linear name and the GlycoCT which in turn can be used to get the GlyTouCan ID numbers for the glycan. [5]
  2. 3D-SNFG: For the cartoon representation of the SNFG in atomic models of carbohydrates. Here, the monosaccharides are depicted as large shapes, or icons centered within the rings. [6]
  3. DrawGlycan-SNFG: For the conversion of IUPAC-condensed string inputs to generate glycan and glycopeptide drawings. Bond fragmentation, glycan descriptors and other carbohydrate modifications can be included using string inputs. [7]
  4. GlycanBuilder2: A standalone version of GlycanBuilder that supports the expanded SNFG nomenclature. [8]
  5. Sugarsketcher: An intuitive web-based drag and drop tool for rendering SNFG images. [9]

The SNFG nomenclature has also been adopted as a standard by major databases and journals in the Biomedical Sciences.

History

In 1978, Stuart Kornfeld and colleagues at the Washington University School of Medicine presented a system for symbolic representation of vertebrate glycans. [10] This system gained popularity when it was implemented as a core method for glycan representation in the NCBI text book Essentials of Glycobiology edited by Ajit Varki (University of California, San Diego) and colleagues. [11] While the first edition of this text published in 1999 used black-and-white symbols similar to the Kornfeld system, color was introduced in the second edition of the text (2009). The advantage of color is that different monosaccharide stereoisomers could now be depicted using the same shape, only with different colors. The system of carbohydrate representation was adopted and widely disseminated by many including the NIGMS-funded Consortium for Functional Glycomics, and thus was often referred to as "CFG Nomenclature". This color representation was vastly expanded in the third edition of the text to include 49 new monosaccharides that appear mostly in non-vertebrates, microbes and plants. Inputs and recommendations from a number of scientists beyond the editors of the Essentials textbook was included in this implementation, and the release of the expanded glycan symbol system was coordinated with the IUPAC Carbohydrate Nomenclature committee. For long-term development of this symbol nomenclature and standardization of glycan representation in the Glycosciences, in 2015, the Essentials editors suggested that the representation be formally called SNFG ('Symbol Nomenclature For Glycans'), and future development be entrusted to a global community of scientists. To aid this development, each of the SNFG monosaccharide symbols was linked to PubChem entries at NCBI/NLM and a dedicated website at NCBI was established for future SNFG updates. [1] Thus, the development of the SNFG is currently undertaken by an international community of scientist that are called the SNFG Discussion Group.

Related Research Articles

Glycomics is the comprehensive study of glycomes, including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the omics naming convention established by genomics and proteomics.

Glycome

The glycome is the entire complement of sugars, whether free or present in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature. "Glycomics, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.

Consortium for Functional Glycomics

The Consortium for Functional Glycomics (CFG) is a large research initiative funded in 2001 by a glue grant from the National Institute of General Medical Sciences (NIGMS) to “define paradigms by which protein-carbohydrate interactions mediate cell communication”. To achieve this goal, the CFG studies the functions of:

Defined in the narrowest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides that are widely distributed in nature. Sugars or saccharides are essential components of all living things and aspects of the various roles they play in biology are researched in various medical, biochemical and biotechnological fields.

The terms glycan and polysaccharide are defined by IUPAC as synonyms meaning "compounds consisting of a large number of monosaccharides linked glycosidically". However, in practice the term glycan may also be used to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, or a proteoglycan, even if the carbohydrate is only an oligosaccharide. Glycans usually consist solely of O-glycosidic linkages of monosaccharides. For example, cellulose is a glycan composed of β-1,4-linked D-glucose, and chitin is a glycan composed of β-1,4-linked N-acetyl-D-glucosamine. Glycans can be homo- or heteropolymers of monosaccharide residues, and can be linear or branched.

KEGG

KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.

Siglecs(Sialic acid-binding immunoglobulin-type lectins) are cell surface proteins that bind sialic acid. They are found primarily on the surface of immune cells and are a subset of the I-type lectins. There are 14 different mammalian Siglecs, providing an array of different functions based on cell surface receptor-ligand interactions.

Glycoinformatics is a field of bioinformatics that pertains to the study of carbohydrates involved in protein post-translational modification. It broadly includes database, software, and algorithm development for the study of carbohydrate structures, glycoconjugates, enzymatic carbohydrate synthesis and degradation, as well as carbohydrate interactions. Conventional usage of the term does not currently include the treatment of carbohydrates from the better-known nutritive aspect.

Ajit Varki is a physician-scientist who is distinguished professor of medicine and cellular and molecular medicine, co-director of the Glycobiology Research and Training Center at the University of California, San Diego (UCSD), and co-director of the UCSD/Salk Center for Academic Research and Training in Anthropogeny (CARTA). He is also executive editor of the textbook Essentials of Glycobiology and Distinguished Visiting Professor at the Indian Institute of Technology in Madras and the National Center for Biological Sciences in Bangalore. He is a specialist advisor to the Human Gene Nomenclature Committee.

Anne Dell is an Australian biochemist specialising in the study of glycomics and the carbohydrate structures that modify proteins. Anne's work could be used to figure out how pathogens such as HIV are able to evade termination by the immune system which could be applied toward understanding how this occurs in fetuses. Her research has also led to the development of higher sensitivity mass spectroscopy techniques which have allowed for the better studying of the structure of carbohydrates. Anne also established GlycoTRIC at Imperial College London, a research center that allows for glycobiology to be better understood in biomedical applications. She is currently Professor of Carbohydrate Biochemistry and Head of the Department of Life Sciences at Imperial College London. Dell's other contributions to the study of Glycobiology are the additions she has made to the textbook "Essentials of Glycobiology" Dell was appointed Commander of the Order of the British Empire (CBE) in the 2009 Birthday Honours.

Glycopeptides are peptides that contain carbohydrate moieties (glycans) covalently attached to the side chains of the amino acid residues that constitute the peptide.

Structure validation

Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.

Translational glycobiology or applied glycobiology is the branch of glycobiology and glycochemistry that focuses on developing new pharmaceuticals through glycomics and glycoengineering. Research in the field aims to use therapeutic glycoconjugates for preventing transplant rejection, treating various bone diseases, and developing therapeutic cancer vaccines and other targeted therapies.

Carbohydrate Structure Database

Carbohydrate Structure Database (CSDB) is a free curated database and service platform in glycoinformatics, launched in 2005 by a group of Russian scientists from N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic data on natural carbohydrates and carbohydrate-related molecules.

National Center for Functional Glycomics

The National Center for Functional Glycomics is an organization that is focused on the development of technology development in glycosciences. They are specifically focused on glycan analysis and molecular mechanisms of glycan recognition by proteins important in human biology and disease. The center was established at Emory University in 2013 with $5.5 million funding by National Institutes of Health under the leadership of Richard D. Cummings. The center moved to Harvard University in September 2015 and is currently located at Beth Israel Deaconess Medical Center in Boston Massachusetts. The center is affiliated with the Consortium for Functional Glycomics.

The Minimum Information Required About a Glycomics Experiment (MIRAGE) initiative is part of the Minimum Information Standards and specifically applies to guidelines for reporting on a glycomics experiment. The initiative is supported by the Beilstein Institute for the Advancement of Chemical Sciences. The MIRAGE project focuses on the development of publication guidelines for interaction and structural glycomics data as well as the development of data exchange formats. The project was launched in 2011 in Seattle and set off with the description of the aims of the MIRAGE project.

Glycan arrays, like that offered by the Consortium for Functional Glycomics (CFG), National Center for Functional Glycomics (NCFG) and Z Biotech, LLC, contain carbohydrate compounds that can be screened with lectins, antibodies or cell receptors to define carbohydrate specificity and identify ligands. Glycan array screening works in much the same way as other microarray that is used for instance to study gene expression DNA microarrays or protein interaction Protein microarrays.

Harry Schachter

Harry Schachter FRSC is a Canadian biochemist and glycobiologist, and professor emeritus at the University of Toronto and the Hospital For Sick Children in Toronto, Canada.

Ten Feizi is a British molecular biologist who is Professor and Director of the Glycosciences Laboratory at Imperial College London. Her research considers the structure and function of glycans. She was awarded the Society for Glycobiology Rosalind Kornfeld award in 2014.

Glycan-protein interactions A class of biological intermolecular interactions

Glycan-Protein interactions represent a class of biomolecular interactions that occur between free or protein-bound glycans and their cognate binding partners. Intramolecular glycan-protein (protein-glycan) interactions occur between glycans and proteins that they are covalently attached to. Together with protein-protein interactions, they form a mechanistic basis for many essential cell processes, especially for cell-cell interactions and host-cell interactions. For instance, SARS-CoV-2, the causative agent of COVID-19, employs its extensively glycosylated spike (S) protein to bind to the ACE2 receptor, allowing it to enter host cells. The spike protein is a trimeric structure, with each subunit containing 22 N-glycosylation sites, making it an attractive target for vaccine search.

References

  1. 1 2 3 4 "Symbol Nomenclature for Glycans (SNFG) - NCBI". www.ncbi.nlm.nih.gov. Retrieved 19 August 2019.
  2. ↑ Varki, A; Cummings, RD; Aebi, M; Packer, NH; Seeberger, PH; Esko, JD; Stanley, P; Hart, G; Darvill, A; Kinoshita, T; Prestegard, JJ; Schnaar, RL; Freeze, HH; Marth, JD; Bertozzi, CR; Etzler, ME; Frank, M; Vliegenthart, JF; Lütteke, T; Perez, S; Bolton, E; Rudd, P; Paulson, J; Kanehisa, M; Toukach, P; Aoki-Kinoshita, KF; Dell, A; Narimatsu, H; York, W; Taniguchi, N; Kornfeld, S (December 2015). "Symbol Nomenclature for Graphical Representations of Glycans". Glycobiology. 25 (12): 1323–4. doi:10.1093/glycob/cwv091. PMC   4643639 . PMID   26543186.
  3. ↑ Neelamegham, S; Aoki-Kinoshita, K; Bolton, E; Frank, M; Lisacek, F; Lütteke, T; O'Boyle, N; Packer, N; Stanley, P; Toukach, P; Varki, A; Woods, RJ; SNFG Discussion, group. (11 June 2019). "Updates to the Symbol Nomenclature For Glycans (SNFG) Guidelines". Glycobiology. 29 (9): 620–624. doi:10.1093/glycob/cwz045. PMC   7335484 . PMID   31184695.
  4. ↑ "NCBI-Glycans". ncbi.nlm.nih.gov. Retrieved 19 August 2019.
  5. ↑ Mehta, AY; Cummings, RD (14 March 2020). "GlycoGlyph: A glycan visualizing, drawing and naming application". Bioinformatics. 36 (11): 3613–3614. doi:10.1093/bioinformatics/btaa190. PMC  7267839. PMID   32170934.
  6. ↑ Thieker, DF; Hadden, JA; Schulten, K; Woods, RJ (August 2016). "3D implementation of the symbol nomenclature for graphical representation of glycans". Glycobiology. 26 (8): 786–7. doi:10.1093/glycob/cww076. PMC   5018049 . PMID   27514939.
  7. ↑ Cheng, K; Zhou, Y; Neelamegham, S (15 March 2017). "DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information". Glycobiology. 27 (3): 200–205. doi:10.1093/glycob/cww115. PMC   6410959 . PMID   28177454.
  8. ↑ Tsuchiya, S; Aoki, NP; Shinmachi, D; Matsubara, M; Yamada, I; Aoki-Kinoshita, KF; Narimatsu, H (5 June 2017). "Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans". Carbohydrate Research. 445: 104–116. doi: 10.1016/j.carres.2017.04.015 . PMID   28525772.
  9. ↑ Alocci, D; Suchánková, P; Costa, R; Hory, N; Mariethoz, J; Vařeková, RS; Toukach, P; Lisacek, F (5 December 2018). "SugarSketcher: Quick and Intuitive Online Glycan Drawing". Molecules (Basel, Switzerland). 23 (12): 3206. doi:10.3390/molecules23123206. PMC   6320881 . PMID   30563078.
  10. ↑ Kornfeld, S; Li, E; Tabas, I (10 November 1978). "The synthesis of complex-type oligosaccharides. II. Characterization of the processing intermediates in the synthesis of the complex oligosaccharide units of the vesicular stomatitis virus G protein". The Journal of Biological Chemistry. 253 (21): 7771–8. doi: 10.1016/S0021-9258(17)34436-8 . PMID   212435.
  11. ↑ "Essentials of Glycobiology, 3rd Ed". Cold Spring Harbor Laboratory Press. 2015. Retrieved 19 August 2019.
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