GlcNAcβAsn linkage is conserved in the N-glycoproteins of all eukaryotes. l-Glutamine (Gln), which is a one carbon higher homolog of Asn, is never glycosylated. X-ray crystallographic study of several β-1-N-acetamido- and propionamido derivatives of monosaccharides has earlier shown that the N-glycosidic torsion, ΦN, is influenced to a larger extent by the structural variation of the sugar part than that of the aglycon moiety. In order to examine the influence of the carbohydrate pendent groups on the conformational preference of the N-glycosidic linkage with respect to ΦN, several models and analogs with gluco and manno configuration have been studied in the present work by computational chemistry. The crystal structure of XylβNHPr is reported here and its molecular packing compared with related analogs. The conjunction of combining Crystallographic and computational studies allows to demonstrate the strong influence that the group at C2, and environmental factors particularly inter- and intramolecular interactions involving regular hydrogen bonds and the weak C-H···O contacts, have on the energy preference of the ΦN torsion angle. © 2008 Elsevier Ltd. All rights reserved.

Duraikkannu Loganathan

ACETAMIDO

COMPUTATIONAL CHEMISTRIES

Computational studies

Conformational preferences

Crystallographic studies

ENVIRONMENTAL FACTORS

GLYCOSIDIC LINKAGES

GLYCOSIDIC TORSIONS

GLYCOSYLATED

Intra-molecular interactions

MOLECULAR PACKINGS

N-GLYCOPROTEIN

PENDENT GROUPS

Quantum chemical calculations

Structural variations

TORSION ANGLES

Amino acids

Carbohydrates

Crystal Structure

Crystallography

glucose

glycoproteins

Hydrogen

Hydrogen bonds

Mineralogy

Quantum chemistry

quantum theory

Sugar (sucrose)

Sugars

Torsional stress

X ray crystallography

acetamide derivative

monosaccharide

PROPIONAMIDE DERIVATIVE

article

chemical interaction

chemical structure

conformation

GLYCOSIDATION

hydrogen bond

priority journal

Acetamides

Amides

Crystallography, X-Ray

Glycosides

Models, Molecular

Monosaccharides

Eukaryota

IIT Madras is a public technical and research university located in Chennai, Tamil Nadu. Founded in 1959, it is recognised as an Institute of National Importance.

IIT Madras has been ranked as the top engineering institute in India for four years in a row by the National Institutional Ranking Framework of the MHRD

It currently offers undergraduate, postgraduate and research degrees across 16 disciplines in Engineering, Sciences, Humanities and Management. About 596 faculty belonging to science and engineering departments and centres of the Institute are engaged in teaching, research and industrial consultancy.

IIT Madras

Carbohydrate Research

The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, N, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the N value of cellobiosyl analogs deviate ~9 with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ2 value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6 to -109.9). This large span of χ2 value suggests the greater degree of rotational freedom around C1′-C2′ bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions. © 2013 Springer Science+Business Media New York.

Glycoconjugate Journal

Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: Synthesis and X-Ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage

N-Linked glycosylation is not only present in eukaryotes but also occurs in archaea and bacteria and is mainly characterized by the β-glucosylamine linkage to the asparagine (GlcNAcβAsn). Earlier crystallographic studies aimed at understanding the structural significance of the linkage region constituents revealed that N-glycosidic torsion, φN is influenced considerably by variation in the glycan part as compared to the aglycon moiety. The φN value observed for XylβNHAc deviated maximum as compared to that of the model compound, GlcNAcβNHAc. The present work was undertaken to assess the influence of ribose on the N-glycosidic torsions and molecular assembly. Several ribopyranosyl alkanamides have been synthesized and crystal structures of three of them have been solved. A comprehensive crystal structure analysis of ribosyl alkanamides along with xylosyl and arabinosyl alkanamides showed the wide range of deviations in their φN values as compared to the negligible deviation shown by hexopyranosyl alkanamides. This study revealed the importance of C5-hydroxymethyl group and hydroxyl group configurations at C2, C3, and C4 stereocentres in controlling the N-glycosidic torsions. © 2013 Elsevier Ltd. All rights reserved.

Examination of the influence of C5-hydroxymethyl group and configurations of hydroxyl groups at C2, C3, and C4 stereocentres on the N-glycosidic torsion: Synthesis and X-ray crystallographic investigation of N-(d-ribopyranosyl) alkanamides as N-glycoprotein linkage region analogs

The torsion angle around the N-glycoprotein linkage region (GlcNAc-Asn) is an important factor for presenting sugar on the cell surface which is crucial for many biological processes. Earlier studies using model and analogs showed that this important torsion angle is greatly influenced by substitutions in the sugar part. In the present work, uronic acid alkanamides and triazole derivatives have been designed and synthesized as newer analogs of N-glycoprotein linkage region to understand the influence of the carboxylic group on linkage region torsion as well as on molecular packing. Crystal structure of N-(β-d-galacturonopyranosyl)acetamide is solved with the space group of P22121. Comparison of the torsion angle and molecular packing of this compound with N-(β-d-galactopyranosyl)acetamide showed that changing the C6-hydoxymethyl group to the carboxylic acid group has minimum influence on the N-glycosidic torsion angle, ΦN and significant influence on the molecular packing. © 2013 Elsevier Ltd. All rights reserved.

Synthesis of N-(β-d-glycuronopyranosyl)alkanamides and 1-(β-d-glycuronopyranosyl)-4-phenyl-[1,2,3]-triazoles as N-glycoprotein linkage region analogs: Examination of the effect of C5 substituent on the N-glycosidic torsion (ΦN) based on X-ray crystallography

N-Glycoprotein linkage region constituents namely 2-deoxy-2-acetamido- β-d-glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all eukaryotes. Earlier crystallographic studies on the linkage region conformation revealed that among all the models and analogs of the N-glycoprotein linkage region, XylβNHAc showed maximum deviation in the φN value as compared to the value reported for the model compound, GlcNAcβNHAc. In order to understand the effect of another pentopyranose, viz., arabinose, on the N-glycosidic torsion angles and molecular assembly, three arabinopyranosyl alkanamides were synthesized and their X-ray crystal structures elucidated. A comparative analysis of the N-glycosidic torsion, φN of the three analogs revealed the greater rotational freedom around the C1-N1 bond as compared to the GlcNAc derivatives. Molecular assembly of propionamido and chloroacetamido derivatives is characterized by the presence of anti-parallel bilayers of the molecules. This unique molecular assembly is hitherto unknown in all other models and analogs of N-glycoprotein linkage region. This study reveals that N-glycosidic torsions are influenced by the glycan as well as molecular packing. © 2013 Elsevier Ltd. All rights reserved.

Synthesis and X-ray crystallographic investigation of N-(α-d- arabinopyranosyl)alkanamides as N-glycoprotein linkage region analogs

N-Glycoprotein linkage region constituents, 2-acetamido-2-deoxy-β-D- glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all the eukaryotes. To gain a better understanding for nature's choice of GlcNAcβAsn as linkage region constituents and inter- and intramolecular carbohydrate-protein interactions, a detailed systemic structural study of the linkage region conformation is essential. Earlier crystallographic studies of several N-(β-glycopyranosyl)alkanamides showed that N-glycosidic torsion, φN, is influenced to a larger extent by structural variation in the sugar part than that of the aglycon moiety. To explore the effect of the bioisosteric replacement of a carboxamide group by a sulfonamide moiety on the N-glycosidic torsions as well as on molecular assembly, several glycosyl methanesulfonamides and glycosyl chloromethanesulfonamides were synthesized as analogues of the N-glycoprotein linkage region, and crystal structures of seven of these compounds have been solved. A comparative analysis of this series of crystal structures as well as with those of the corresponding alkanamido derivatives revealed that N-glycosidic torsion, φN, does not alter significantly. Methanesulfonamido and chloromethanesulfonamido derivatives of GlcNAc display a different aglycon conformation compared to other sulfonamido analogues. This may be due to the cumulative effect of the direct hydrogen bonding between N1 and O1′ and C-H×××O interactions of the aglycon chain, revealing the uniqueness of the GlcNAc as the linkage sugar. Unique molecular assembly motif of GlcNAc: The different aglycon conformations of methanesulfonamido and chloromethanesulfonamido derivatives of GlcNAc as compared to other sulfonamido analogues is a unique feature of their molecular assembly. This could be due to the cumulative effect of the direct hydrogen bonding between N1 and O1′ and C-H×××O interactions of the aglycon chain. Copyright © 2013 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.

Chemistry - A European Journal

Exploring the effect of bioisosteric replacement of carboxamide by a sulfonamide moiety on N-glycosidic torsions and molecular assembly: Synthesis and x-ray crystallographic investigation of n-(β- D -glycosyl)sulfonamides as n-glycoprotein linkage region analogues

The biological addition of oligosaccharide structures to asparagine residues of N-glycoproteins influences the properties and bioactivities of these macromolecules. The linkage region constituents, 2-acetamino-2-deoxy-β-D- glucopyranose monosaccharide (GlcNAc) and L-asparagine amino acid (Asn), are conserved in the N-glycoproteins of all eukaryotes. In order to gain information about the structure and dynamics of glycosylated proteins, two chloroacetamido sugars, GlcβNAcNHCOCH2Cl and ManβNHCOCH2Cl, have been synthesized, and their crystal structures have been solved. Structural comparison with a series of other models and analogs gives insight about the influence of the N-acetyl group at position C2 on the conformation of the glycan-peptide linkage at C1. Interestingly, this N-acetyl group also influences the packing and network of hydrogen bonds with involvement in weak hydrogen bonds C-H⋯X that are of biological importance. DFT ab initio calculations performed on a series of models and analogs also confirm that the GlcNAc derivatives present different preferred conformation about the N-CO-CH 2-X (χ2) torsion angle of the glycan-peptide linkage, when compared to other monosaccharide derivatives. The energy profiles that have been obtained will be useful for parametrization of molecular mechanics force-field. The conjunction of crystallographic and computational chemistry studies provides arguments for the structural effect of the N-acetyl group at C2 in establishing an extended conformation that presents the oligosaccharide away from the protein surface. © 2008 American Chemical Society.

Journal of the American Chemical Society

Conformational preferences of the aglycon moiety in models and analogs of GlcNAc-Asn linkage: Crystal structures and ab initio quantum chemical calculations of N-(β-D-glycopyranosyl)haloacetamides

Elucidation of the intra- and intermolecular carbohydrate-protein interactions would greatly contribute toward obtaining a better understanding of the structure-function correlations of the protein-linked glycans. The weak interactions involving C-H...O have recently been attracting immense attention in the domain of biomolecular recognition. However, there has been no report so far on the occurrence of C-H...O hydrogen bonds in the crystal structures of models and analogs of N-glycoproteins. We present herein an analysis of C-H...O interactions in the crystal structures of all N-glycoprotein linkage region models and analogs. The study reveals a cooperative network of bifurcated hydrogen bonds consisting of N-H...O and C-H...O interactions seen uniquely for the models. The cooperative network consists of two antiparallel chains of bifurcated hydrogen bonds, one involving N1-H, C2′-H and O1′ of the aglycon moiety and the other involving N2-H, C1-H and O1″ of the sugar. Such bifurcated hydrogen bonds between the core glycan and protein are likely to play an important role in the folding and stabilization of proteins. © 2006 Oxford University Press.

Fulltext

Glycobiology

Observation of a unique pattern of bifurcated hydrogen bonds in the crystal structures of the N-glycoprotein linkage region models

The linkage region constituents, namely, 2-acetamido-2-deoxy-β-D- glucopyranose and asparagine are conserved in the N-glycoproteins of all the eukaryotes. The present work is aimed at understanding the reasons for the occurrence of GlcNAc and Asn as the linkage region constituents. A total of six sugar amides have been designed as models and analogs of the linkage region and their crystal structures have been solved. This is the first report on the X-ray crystallographic investigation of the effect of systematic changes in the linkage sugar as well as its aglycon moiety on the N-glycosidic torsion, ψN (O5-C1-N1-C1′). This also forms the first report on the crystal structure of a model of L-RhaβAsn, a variant linkage found in the surface layer glycoprotein of Bacillus stearothermophillus. Among the models and analogs examined, the acetamido derivatives of Man and Xyl, the linkage sugars of O-glycoproteins, show a ψN value of -114. 5° and -121.2°, respectively, deviating maximum from the value of -89.8° reported for the model compound GlcNAcβNHAc. The L-Rha and Gal derivatives also show noticeable deviations. The ψN values, -89.5° and -91.0°, of the propionamide derivatives of Glc and GlcNAc (analogs of GlcβGln and GlcNAcβGln, respectively) agree well with those (-93.8° and -89.8°) reported for their corresponding acetamide derivatives suggesting Gln could serve as well as Asn as the linkage region amino acid. However, the rotational freedom about the additional C-C bond would lead to altered rigidity of the linkage region. An analysis of packing reveals that the molecular assembly of these compounds is driven by different infinite and finite chains of hydrogen bonds. The double pillaring of hydrogen bonds involving the amide groups at C1 and C2 is seen as a unique packing feature characteristic of β-1-N-acyl derivatives of GlcNAc. Based on the findings of the present study, it is speculated that the linkage region constituents of the eukaryotic N-glycoproteins appear to fulfill three essential structural requirements: rigidity, planarity, and linearity and these are met by the trisaccharide core and Asn at the linkage region. © 2003 Elsevier Inc. All rights reserved.

Biochemical and Biophysical Research Communications

On the structural significance of the linkage region constituents of N-glycoproteins: An X-ray crystallographic investigation using models and analogs

X-Ray diffraction analysis of a hydrated N-glycoprotein linkage region model, N1-(2-acetamido-2-deoxy-β-D-glucopyranosyl)acetamido- 2-deoxy-β-D-glucopyranosyl)acetamide (1) and its N1-benzamido analogue 2 reveals very interesting molecular architecture involving seven hydrogen bonds in both compounds and further stabilization of packing in 2 due to π-π stacking. The crystal structure has a two dimensional network of hydrogen bonds formed by infinite chains running along the b-axis and homodromic cycles, intersecting at the water oxygens.

Crystal structure of a hydrated N-glycoprotein linkage region model and its analogue: Hydrogen bonding and π-π stacking driven molecular assembly

In the title molecule, C8H15NO6, the pyranose ring adopts the usual 4C1(D) conformation and the N-acetyl group exists in the Z-anti conformation. The orientation of the primary alcohol group is gauche.

Acta Crystallographica Section C: Crystal Structure Communications

β-1-N-acetamido-D-glucopyranose

Examination of the effect of structural variation on the N-glycosidic torsion (ΦN) among N-(β-d-glycopyranosyl)acetamido and propionamido derivatives of monosaccharides based on crystallography and quantum chemical calculations

Journal	Carbohydrate Research
ISSN	00086215
Open Access	No