The molecular and crystal structures of 4-N-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-asparagine trihydrate and 4-N-(beta-D-glucopyranosyl)-L-asparagine monohydrate. The x-ray analysis of a carbohydrate-peptide linkage.
TL;DR: X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn and Glc- asparagine both have the C-1 chair conformation and also that the glucose-asparagine linkage of each molecule is present in the beta-anomeric configuration.
Abstract: X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn [4-N-(2-acetamido-2-deoxy-beta-d-glucopyranosyl)-l-asparagine] and Glc-Asn [4-N-(beta-d-glucopyranosyl)-l-asparagine] both have the C-1 chair conformation and also that the glucose-asparagine linkage of each molecule is present in the beta-anomeric configuration. The dimensions (the estimated standard deviations of the last digit are in parentheses) of the glycosidic bond in GlcNAc-Asn and Glc-Asn are, respectively, C((1))-N((1)) 0.1441(6)nm, 0.146(2)nm; angle O((5))-C((1))-N((1)) 106.8(3) degrees , 105.7(8) degrees ; angle C((2))-C((1))-N((1)) 111.1(4) degrees , 110.4(9) degrees ; angle C((1))-N((1))-C((9)) 121.4(4) degrees , 120.5(9) degrees . The glycosidic torsion angle C((9))-N((1))-C((1))-C((2)) is 141.0 degrees and 157.6 degrees in GlcNAc-Asn and Glc-Asn respectively. Hydrogen-bonding is extensive in these two crystal structures and does affect one torsion angle in particular. Two very different values of chi(1)(N-C(alpha)-C(beta)-C(gamma)) occur for the asparagine residue of the two different molecules; the values of chi(1), -69.0 degrees in GlcNAc-Asn and 61.9 degrees in Glc-Asn, correspond to two different staggered conformations about the C(alpha)-C(beta) bond as the NH(3) (+) group is adjusted to different hydrogen-bonding patterns. The two trans-peptide groups in GlcNAc-Asn show small distortions in planarity whereas that in Glc-Asn is more non-planar. The mean plane through the atoms of the amide group at C((2)) in GlcNAc-Asn is approximately perpendicular (69 degrees ) to the mean plane through the C((2)), C((3)), C((5)) and O((5)) atoms of the glucose ring and that at C((1)) is less perpendicular (65 degrees ). The mean plane through the atoms of the amide group in Glc-Asn makes an angle of only 55 degrees with the mean plane through these same four atoms of the glucose ring. The N((1))-H bond of the amide at C((1)) is trans to the C((1))-H bond in these two compounds; the N((2))-H bond of the amide at C((2)) is trans to the C((2))-H bond in GlcNAc-Asn. The values of the observed and final calculated structure amplitudes have been deposited as Supplementary Publication SUP 50035 (26 pages) at the British Library (Lending Division), (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.
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TL;DR: It is demonstrated that substituent groups, such as hydroxymethyl and acetamido groups, on occasions, should be treated in HSEA calculations as freely rotating about their linkage to a pyranose ring.
74 citations
TL;DR: The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank.
Abstract: Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.
63 citations
Cites background from "The molecular and crystal structure..."
...Therefore, X-ray crystallography (e.g. Delbaere, 1974; Jain et al., 1996; Mølgaard & Larsen, 2002; Stevens et al., 2004; Fry et al., 2005; Smith et al., 2006; Vulliez-Le Normand et al., 2008) and NMR (e.g. Brisson & Carver, 1983; Cumming et al., 1987; Sabesan et al., 1991; Koles et al., 2004;…...
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TL;DR: This review covers conformational analyses of blood group antigens of N-linked and of O-linked oligosaccharide chains, of glycolipids, of oligOSaccharides related to O-specific polysaccharides of bacteria, and of oligosACcharide related to proteoglycans.
Abstract: The three dimensional structure of oligosaccharides determines their interaction with receptors and hence is important for their biological activity. Conformational analysis of oligosaccharides makes the three dimensional structure available. The analysis of the conformation of oligosaccharides is usually determined by a combination of computational methods and experimental techniques. NMR spectroscopy is the most important experimental tool. The calculational techniques cover a wide range with most emphasis put into force field calculations. Conformational flexibility plays an important role in many though not in all oligosaccharide structures. Glycosidic linkages to a side chain of a pyranose ring are more flexible than are linkages to the pyranose ring. The major attempts are described to determine the three dimensional structure of oligosaccharides with the exception of homooligomers. This review covers conformational analyses of blood group antigens of N-linked and of O-linked oligosaccharide chains, of glycolipids, of oligosaccharides related to O-specific polysaccharides of bacteria, and of oligosaccharides related to proteoglycans.
48 citations
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TL;DR: The chemical evidence for the enzymic activity of lysozyme will be discussed in detail by other speakers at this meeting, but in order to describe the crystallographic studies of the interactions between the enzyme and its substrates it is necessary to summarize briefly what was known about them at the beginning of the work.
Abstract: The chemical evidence for the enzymic activity of lysozyme will be discussed in detail by other speakers at this meeting, but in order to describe our crystallographic studies of the interactions between the enzyme and its substrates it is necessary to summarize briefly what was known about them at the beginning of our work. Simultaneously with his discovery of lysozyme Fleming (1922) discovered a Gram-positive species of bacteria, Micrococcus lysodeikticus , which is particularly susceptible to the action of the enzyme. It was not until much later, however, that Salton (1952) demonstrated that the substrate is located entirely within the bacterial cell wall and it is only very recently that its chemical constitution has been established. Valuable early experiments (for example, by Meyer, Palmer, Thomson & Khorazo 1936; Meyer, Hahnel & Steinberg 1946; and by Epstein & Chain 1940) showed that lysozyme releases N -acetyl-amino sugars from M. lysodeikticus , but the first indication of the type of linkage attacked by lysozyme came when Berger & Weiser (1957) showed that lysozyme also degrades chitin, the linear polymer of N -acetylghicosamine.
586 citations
TL;DR: It is concluded that although the equilibrium conformation of the amide group may be planar or close to it, out-of-plane deformation can be made at a very modest energy cost.
319 citations
167 citations
TL;DR: By means of CNDO/2 calculations on N- methyl acetamide, it is shown that the state of minimum energy of the trans-peptide unit is a non-planar conformation, with the NH and NC 2 α bonds being significantly out of the plane formed by the atoms C 1 α, C′, O and N.
75 citations
TL;DR: It is shown that the dihedral angles θ N and Δω are correlated, while θ C, is small and is uncorrelated with Δω, showing that the non-planar distortion at C′ is generally small.
61 citations