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Conformations of the type-1 lacto-N-biose I unit in protein complex structures.

ABSTRACT: The lacto-N-biose I (Gal?1-3GlcNAc; LNB) disaccharide is present as a core unit of type-1 blood group antigens of animal glycoconjugates and milk oligosaccharides. Type-1 antigens often serve as cell-surface receptors for infection by pathogens. LNB in human milk oligosaccharides functions as a prebiotic for bifidobacteria and plays a key role in the symbiotic relationship of commensal gut microbes in infants. Protein Data Bank (PDB) entries exhibiting the LNB unit were investigated using the GlycoMapsDB web tool. There are currently 159 ?-LNB and nine ?-LNB moieties represented in ligands in the database. ?-LNB and ?-LNB moieties occur in 74 and six PDB entries, respectively, as NCS copies. The protein and enzyme structures are from various organisms including humans (galectins), viruses (haemagglutinin and capsid proteins), a pathogenic fungus, a parasitic nematode and protist, pathogenic bacteria (adhesins) and a symbiotic bacterium (a solute-binding protein of an ABC transporter). The conformations of LNB-containing glycans in enzymes vary significantly according to their mechanism of substrate recognition and catalysis. Analysis of glycosidic bond conformations indicated that the binding modes are significantly different in proteins adapted for modified or unmodified glycans.

SUBMITTER: Fushinobu S

PROVIDER: S-EPMC6096478 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Conformations of the type-1 lacto-N-biose I unit in protein complex structures.

Fushinobu Shinya S

Acta crystallographica. Section F, Structural biology communications 20180726 Pt 8

The lacto-N-biose I (Galβ1-3GlcNAc; LNB) disaccharide is present as a core unit of type-1 blood group antigens of animal glycoconjugates and milk oligosaccharides. Type-1 antigens often serve as cell-surface receptors for infection by pathogens. LNB in human milk oligosaccharides functions as a prebiotic for bifidobacteria and plays a key role in the symbiotic relationship of commensal gut microbes in infants. Protein Data Bank (PDB) entries exhibiting the LNB unit were investigated using the Gl ...[more]

PMID: 30084396

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Project description:The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a "fingerprint of topological-geometric values" consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains. This allows fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds. Applying GISA to sets of several thousand high resolution structures, we first show how the most basic Gauss integral, the writhe, enables swift identification of pre-defined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, an application of the basic scan method in GISA's tool-box revealed 10 known cases of knots as the top positive writhe cases, while placing at the top of the negative writhe 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed. Possible general applications of GISA are fold classification and structural alignment based on local Gauss integrals. Others include finding errors in protein models and identifying unusual conformations that might be important for protein folding and function. By its broad potential, we believe that GISA will be of general benefit to the structural bioinformatics community. GISA is coded in C and comes as a command line tool. Source and compiled code for GISA plus read-me and examples are publicly available at GitHub (https://github.com).

Dataset Information

Conformations of the type-1 lacto-N-biose I unit in protein complex structures.

Publications

Conformations of the type-1 lacto-N-biose I unit in protein complex structures.

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