A perspective on the PDB’s impact on the field of glycobiology

Abstract

Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function. Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function. Glycobiology is the study of how glycans, also called carbohydrates or oligosaccharides, result from, or have an impact on, a wide array of biological processes (1Varki A. Kornfeld S. Historical background and overview.in: Varki A. Cummings R. Esko J. Stanley P. Hart G. Aebi M. Darvill A. Kinoshita T. Packer N. Prestegard J. Schnaar R. Seeberger P. Essentials of Glycobiology. 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY2017: 387-400Google Scholar). Their impact is broad, with glycans occurring on the surfaces of most cells in addition to being excreted into the environment and incorporated into structural materials that constitute most of the biomass on earth (2Williams C.L. Westover T.L. Emerson R.M. Tumuluru J.S. Li C.L. Sources of biomass feedstock variability and the potential impact on biofuels production.Bioenerg. Res. 2016; 9: 1-14Crossref Scopus (173) Google Scholar). Many glycans are covalently attached to proteins, making them glycoproteins. It is estimated that, among all proteins in the Swiss-Prot database, between 20% and 50%, are glycosylated (3Apweiler R. Hermjakob H. Sharon N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.Biochim. Biophys. Acta. 1999; 1473: 4-8Crossref PubMed Scopus (1456) Google Scholar, 4Spiro R.G. Protein glycosylation: Nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds.Glycobiology. 2002; 12: 43R-56RCrossref PubMed Scopus (1028) Google Scholar); among eukaryotes (about one-third of the proteins in the database), the percentage is likely to be much higher (5Cummings R.D. Pierce J.M. The challenge and promise of glycomics.Chem. Biol. 2014; 21: 1-15Abstract Full Text Full Text PDF PubMed Scopus (270) Google Scholar, 6Steentoft C. Vakhrushev S.Y. Joshi H.J. Kong Y. Vester-Christensen M.B. Schjoldager K. Lavrsen K. Dabelsteen S. Pedersen N.B. Marcos-Silva L. Gupta R. Bennett E.P. Mandel U. Brunak S. Wandall H.H. et al.Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.EMBO J. 2013; 32: 1478-1488Crossref PubMed Scopus (846) Google Scholar). In addition to glycoproteins, numerous other proteins bind glycans in the process of transforming them for a source of energy or for substrates needed to build other biological macromolecules, including the structural carbohydrates of plants and microbes. Some proteins also bind to glycans on cell surfaces to initiate various signaling and adhesion events, and pathogens, both bacterial and viral, have proteins that bind to cell surface glycans as a step in the infection process. This adds to the biomedical importance of glycans and has raised the interest of the pharmaceutical industry in both glycoproteins and glycomimetic glycans (7Valverde P. Arda A. Reichardt N.C. Jimenez-Barbero J. Gimeno A. Glycans in drug discovery.MedChemComm. 2019; 10: 1678-1691Crossref PubMed Google Scholar). Glycans are structurally very diverse, more so than polypeptides and nucleic acids of comparable size. Although the number of residue types (sugars) making up glycans is similar to the number of amino acid types making up proteins, residues can be linked in multiple ways and they can exist as branched and linear oligomers. Differences between some glycan residues seem subtle. For example, glucose (Glc), mannose (Man), and galactose (Gal) are all composed of six-membered pyranose rings with exactly the same composition, C6H12O6, from which the name carbohydrate is derived. However, structural consequences associated with differences in chirality are significant. Also, unlike proteins and nucleic acids, glycan synthesis is not template driven but occurs via the combined action of hundreds of enzymes that add or remove individual residues. As a result, glycoproteins seldom carry a single type of glycan, making them heterogeneous even at the single site level. These properties have certainly impeded characterization of glycans and perhaps the interest of the broader scientific community in studying of how glycans influence biological processes. Recently, some steps have been taken to make glycobiology more accessible to a broad audience and to attract a new generation of scientists who will tackle challenging glycobiology problems. One step is a text, now in its third edition, Essentials of Glycobiology, that begins with a useful historical review of the field (1Varki A. Kornfeld S. Historical background and overview.in: Varki A. Cummings R. Esko J. Stanley P. Hart G. Aebi M. Darvill A. Kinoshita T. Packer N. Prestegard J. Schnaar R. Seeberger P. Essentials of Glycobiology. 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY2017: 387-400Google Scholar). The authors and editors receive no financial benefit from sales of this book, and they have arranged to have electronic versions freely available through the NCBI Bookshelf (https://www.ncbi.nlm.nih.gov/books/NBK310274/). Another step is the adoption of a set of symbols for residues that make up glycans. Chemical structures are, of course, important to understanding glycan interactions with proteins and other glycoconjugates, but in many cases replacing atomic depictions of sugar residues with simple symbols is sufficient to show differences in glycan structures and place glycans in the larger biological contest where they function. Symbol Nomenclature for Glycans (SNFG) provides different symbols for each type of sugar (8Neelamegham S. Aoki-Kinoshita K. Bolton E. Frank M. Lisacek F. Lutteke T. O'Boyle N. Packer N.H. Stanley P. Toukach P. Varki A. Woods R.J. Darvill A. Dell A. Henrissat B. et al.Updates to the symbol nomenclature for glycans 2019; PubMed Scopus Google Scholar). the of symbols in has also been K. Woods R.J. of the symbol nomenclature for of 2016; PubMed Scopus Google Scholar). the of the symbols to a of glycans in a glycosylated the of human cell adhesion For the same is in the atomic of glycans. The has in which glycans are linked to the of an in a amino acid of the glycans on this are glycan composed of residues and residues and glycans that have residues residues and a type of acid acid These glycans have been the of a of the protein Data Bank computational R.J. the structures of glycans, glycoproteins, and PubMed Scopus Google Scholar). As with other in this this has been with available A. K. Scopus Google Scholar, a for and PubMed Scopus Google Scholar). 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