Combining 3D structure with glycan array data provides insight into the origin of glycan specificity

Abstract

Defining how a glycan-binding protein (GBP) specifically selects its cognate glycan from among the ensemble of glycans within the cellular glycome is an area of intense study. Powerful insight into recognition mechanisms can be gained from 3D structures of GBPs complexed to glycans; however, such structures remain difficult to obtain experimentally. Here an automated 3D structure generation technique, called computational carbohydrate grafting, is combined with the wealth of specificity information available from glycan array screening. Integration of the array data with modeling and crystallography allows generation of putative co-complex structures that can be objectively assessed and iteratively altered until a high level of agreement with experiment is achieved. Given an accurate model of the co-complexes, grafting is also able to discern which binding determinants are active when multiple potential determinants are present within a glycan. In some cases, induced fit in the protein or glycan was necessary to explain the observed specificity, while in other examples a revised definition of the minimal binding determinants was required. When applied to a collection of 10 GBP-glycan complexes, for which crystallographic and array data have been reported, grafting provided a structural rationalization for the binding specificity of >90% of 1223 arrayed glycans. A webtool that enables researchers to perform computational carbohydrate grafting is available at www.glycam.org/gr (accessed 03 March 2016).

Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Avidity

“…Since this specificity does not appear to be sensitive to the presence of HA N-glycans, we considered that the extended, branched glycans could adopt a unique geometry that permits simultaneous bidentate binding to receptor sites on two protomers within the same HA trimer, which are ~45 Å apart (Figure 7A & B). To assess this possibility, 3D structures for biantennary glycans were generated and grafted (Nivedha et al, 2014) onto the bound receptor oligosaccharide in a crystal structure of HA (CA/04/09; PDB code 3UBE) such that the NeuAcα2-6Gal receptor fragment was constrained to bind in the same conformation in the reported structure (Grant et al, 2016; Xu et al, 2012). NeuAcα2-6Gal on the other arm of the glycan was then brought towards the binding site of an adjacent protomer by varying the intervening glycosidic linkages within normal angular bounds (Nivedha et al, 2014).…”

New insights into influenza A specificity: an evolution of paradigms

“…This limitation has obvious consequences for ligand discovery [45 •• ], and for the elucidation of structure-specificity relationships. Although at present, data from glycan array screening need generally to be treated qualitatively, community-wide standards are being developed [117], which together with more quantitative approaches to data processing [64 •• ] and computational analysis [118 • ,119 • ], will enhance the interpretability of such data. A powerful example of the generation and use of quantitative surface K D values from glycan array screening was reported by Wong et al [120 •• ].…”

Induction of Antibodies Directed Against Branched Core O‐Mannosyl Glycopeptides—Selectivity Complimentary to the ConA Lectin

“…This latter observation is notable since studies based on N -linked glycans binding to ConA lead to the conclusion that interactions within the 3-arm site are weaker than those within the 6-arm. [36] The binding observed for the glycopeptide array elements 4 and 17 could be a combination of weak binding through the 3-arm site and the consistently observed enhancing effect of the YAT*AVA peptide sequence.…”