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
Section snippets
Results and discussion
Among the various sugar amides (Fig. 2) designed in the present work, GlcβNHPr (1) and GlcNAcβNHPr (2) are analogs of the respective sugar conjugates of glutamine. l-RhaβNHAc (3) is the model of l-RhaβAsn, the unusual N-glycosidic linkage found in the crystalline surface layer glycoproteins of the eubacterium B. stearothermophillus[6d]. Man, Gal, and Xyl are the common linkage region sugars attached to Ser in O-glycoproteins. In an effort to evaluate the conformational preferences of these
Linkage region conformation
The value, 172.3°(3), of χ1 (N1–C1′–C2′–C3′) for the propionamide derivative (1) reveals the anti conformation about C1′–C2′ bond and compares well with that of 166.5° reported for GlcβAsn · H2O [12b]. The corresponding value observed for 2 turns out to be 114.7°(7) differing by about 73.2° from the value of 187.9° observed for GlcNAcβAsn · 3H2O. This large difference in the χ1value is noteworthy. The Z conformation about the amide linkage (N1–C1′) in all the compounds is evident from the torsion ψN
Molecular packing and hydrogen bonding
Hydrogen bonding plays a major role in the structural and hence the functional attributes of all the three major classes of biomolecules—proteins, nucleic acids, and carbohydrates. Not surprisingly, these classes of compounds are found in aqueous environments resulting in further modifications owing to the formation of an intense network of intermolecular hydrogen bonding. In proteins, the number of intramolecular hydrogen bonding components namely the amide groups is about one for every four
Conclusions
Glycosylation occurs without exception in the entire phylogenetic spectrum, ranging from archaea and eubacteria to eukaryotes. Formation of the sugar–amino acid linkage is a vital event in the biosynthesis of glycoproteins. The linkage region, GlcNAcβAsn, is conserved in all the eukaryotic N-glycoproteins. The present work is aimed at understanding the structural significance of GlcNAc and Asn as the linkage region constituents. The study is focused on the glycosidic torsion, ψN (O5–C1–N1–C1′),
Experimental
All the sugars used in the study are d-sugars unless mentioned otherwise. Synthesis of the sugar amides 1 and 2 was accomplished from the glycosylamines by selective N-acylation [21a] while the remaining amides were prepared by peracylation followed by de-O-acylation [21b]. Crystallization was done in aqueous methanol at room temperature. X-ray diffraction data were collected at room temperature in the ω−2θ scan mode on an Enfra-Nonius CAD4 diffractometer and the relevant details of data
Acknowledgements
This work was supported by the Department of Science and Technology, New Delhi. T.L. thanks the CSIR, New Delhi, for the Junior and Senior Research Fellowships during the course of this work. We acknowledge Dr. Babu Varghese for his valuable technical help and Mr. M.V. Chandrasekar for his assistance in preparing a few of the compounds. We thank Professor S. Srinivasan, Professor V.S.R. Rao, and Professor P.K. Qasba for their valuable suggestions and the RSIC, IIT Madras for data collection.
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