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Desikan Sriram

Bio: Desikan Sriram is an academic researcher from Indian Institute of Technology Madras. The author has contributed to research in topics: Primary alcohol & Pyranose. The author has an hindex of 4, co-authored 7 publications receiving 64 citations.

Papers
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Journal ArticleDOI
TL;DR: X-ray diffraction analysis of a hydrated N-glycoprotein linkage region model, N1-(2-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 as mentioned in this paper.

22 citations

Journal ArticleDOI
TL;DR: 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 area.

20 citations

Journal ArticleDOI
TL;DR: In this paper, the pyranose ring adopts the usual 4 C 1 (D) conformation and the N-acetyl group exists in the Z-anti conformation.
Abstract: In the title molecule, C 8 H 15 NO 6 , the pyranose ring adopts the usual 4 C 1 (D) conformation and the N-acetyl group exists in the Z-anti conformation. The orientation of the primary alcohol group is gauche.

11 citations

Journal ArticleDOI
TL;DR: The crystal structure of the title compound, C14H25NO11·2H2O, has been determined as mentioned in this paper, and the glucose and galactose residues are in a 4C1 conformation.
Abstract: The crystal structure of the title compound, C14H25NO11·2H2O, has been determined. The glucose and galactose residues are in a 4C1 conformation. The N-acetyl group has a Z-anti conformation.

9 citations

Journal ArticleDOI
TL;DR: In this paper, the pyranose ring adopts the 4C1(D) conformation and the N-acetyl group exists in the Z-anti conformation, the primary alcohol group is disordered between the two permitted orientations, gg and gt.
Abstract: In the title compound, 1-benzamido-β-d-glucopyranose, C13H17NO6, the pyranose ring adopts the 4C1(D) conformation and the N-acetyl group exists in the Z-anti conformation. The primary alcohol group is disordered between the two permitted orientations, gg and gt.

2 citations


Cited by
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Journal ArticleDOI
TL;DR: This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching.

188 citations

Journal ArticleDOI
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

Journal ArticleDOI
TL;DR: The crystal structure of the 1:1 complex of beta-cyclodextrin (cyclomaltoheptaose) with trans-cinnamic acid was studied by X-ray diffraction and showed strong hydrogen bonds with two water molecules lying in the interdimeric space of the hydrophobic channel.

42 citations

Journal ArticleDOI
27 Nov 2007-Proteins
TL;DR: In this article, the structure of GPb in complex with glucosyltriazolylacetamide at 100 K to 188 A resolution was determined, with and without the crystallographic ordered cavity waters using the GoldScore scoring function.
Abstract: 4-Phenyl-N-(beta-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its potential as a lead for the design of potent antihyperglycaemic agents Docking and molecular dynamics (MD) calculations have been used to monitor more closely the binding modes in operation and compare the results with experiment Kinetic experiments in the direction of glycogen synthesis showed that glucosyltriazolylacetamide is a better inhibitor (K(i) = 018 mM) than the parent compound alpha-D-glucose (K(i) = 17 mM) or beta-D-glucose (K(i) = 74 mM) but less potent inhibitor than the lead compound N-acetyl-beta-D-glucopyranosylamine (K(i) = 32 microM) To elucidate the molecular basis underlying the inhibition of the newly identified compound, we determined the structure of GPb in complex with glucosyltriazolylacetamide at 100 K to 188 A resolution, and the structure of the compound in the free form Glucosyltriazolylacetamide is accommodated in the catalytic site of the enzyme and the glucopyranose interacts in a manner similar to that observed in the GPb-alpha-D-glucose complex, while the substituent group in the beta-position of the C1 atom makes additional hydrogen bonding and van der Waals interactions to the protein A bifurcated donor type hydrogen bonding involving O3H, N3, and N4 is seen as an important structural motif strengthening the binding of glucosyltriazolylacetamide with GP which necessitated change in the torsion about C8-N2 bond by about 62 degrees going from its free to the complex form with GPb On binding to GP, glucosyltriazolylacetamide induces significant conformational changes in the vicinity of this site Specifically, the 280s loop (residues 282-288) shifts 07 to 31 A (CA atoms) to accommodate glucosyltriazolylacetamide These conformational changes do not lead to increased contacts between the inhibitor and the protein that would improve ligand binding compared with the lead compound In the molecular modeling calculations, the GOLD docking runs with and without the crystallographic ordered cavity waters using the GoldScore scoring function, and without cavity waters using the ChemScore scoring function successfully reproduced the crystallographic binding conformation However, the GLIDE docking calculations both with (GLIDE XP) and without (GLIDE SP and XP) the cavity water molecules were, impressively, further able to accurately reproduce the finer details of the GPb-glucosyltriazolylacetamide complex structure The importance of cavity waters in flexible receptor MD calculations compared to "rigid" (docking) is analyzed and highlighted, while in the MD itself very little conformational flexibility of the glucosyltriazolylacetamide ligand was observed over the time scale of the simulations

31 citations