Sucrose: X-ray refinement and comparison with neutron refinement

“…Osmolyte probe radii were calculated assuming a spherical geometry from the molecular volumes determined from the osmolyte crystal coordinates45–53 in the Cambridge Structure Database54 using the program STERIC 55. The used probe radii in Å were 1.4 (water), 2.33 (urea), 2.66 (TMAO), 2.69 (sarcosine), 2.74 (glycerol), 2.94 (proline), 2.98 (glycine betaine), 3.32 (sorbitol), 3.98 (sucrose), and 4.01 (trehalose).…”

Section: Methodsmentioning

confidence: 99%

Structural thermodynamics of protein preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides

2008

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Protein stability and solubility depend strongly on the presence of osmolytes, because of the protein preference to be solvated by either water or osmolyte. It has traditionally been assumed that only this relative preference can be measured, and that the individual solvation contributions of water and osmolyte are inaccessible. However, it is possible to determine hydration and osmolyte solvation (osmolation) separately using Kirkwood-Buff theory, and this fact has recently been utilized by several researchers. Here, we provide a thermodynamic assessment of how each surface group on proteins contributes to the overall hydration and osmolation. Our analysis is based on transfer free energy measurements with model-compounds that were previously demonstrated to allow for a very successful prediction of osmolyte-dependent protein stability. When combined with Kirkwood-Buff theory, the Transfer Model provides a space-resolved solvation pattern of the peptide unit, amino acids, and the folding/unfolding equilibrium of proteins in the presence of osmolytes. We find that the major solvation effects on protein side-chains originate from the osmolytes, and that the hydration mostly depends on the size of the side-chain. The peptide backbone unit displays a much more variable hydration in the different osmolyte solutions. Interestingly, the presence of sucrose leads to simultaneous accumulation of both the sugar and water in the vicinity of peptide groups, resulting from a saccharide accumulation that is less than the accumulation of water, a net preferential exclusion. Only the denaturing osmolyte, urea, obeys the classical solvent exchange mechanism in which the preferential interaction with the peptide unit excludes water.

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“…CHARMM (22,23), with a force field particularly adapted for the treatment of carbohydrates (24,25), with the explicit incorporation of water as the solvent. The starting structures used were derived either from the corresponding x-ray-based solid-state geometries of sucrose (26,27), ␤-p-turanose (28), ␤-p-leucrose (29), ␤-f-palatinose (30), ␣, ␣-trehalose (31), ␤-p-maltose (32, 33), and maltitol (34,35) or from compounds of similar backbone structure found in the Cambridge Crystallographic Database (www.ccdc.com.ac.uk) (36,37). Any water molecules present in the crystal structures were removed.…”

Section: Methodsmentioning

confidence: 99%

Metabolism of Sucrose and Its Five Linkage-isomeric α-d-Glucosyl-d-fructoses by Klebsiella pneumoniae

Thompson¹,

Robrish²,

Immel³

et al. 2001

Journal of Biological Chemistry

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Klebsiella pneumoniae is presently unique among bacterial species in its ability to metabolize not only sucrose but also its five linkage-isomeric ␣-D-glucosyl-D-fructoses: trehalulose, turanose, maltulose, leucrose, and palatinose. Growth on the isomeric compounds induced a protein of molecular mass ϳ 50 kDa that was not present in sucrose-grown cells and which we have identified as an NAD ؉ and metal ion-dependent 6-phospho-␣-glucosidase (AglB). The aglB gene has been cloned and sequenced, and AglB (M r ‫؍‬ 49,256) has been purified from a high expression system using the chromogenic p-nitrophenyl ␣-glucopyranoside 6-phosphate as substrate. Phospho-␣-glucosidase catalyzed the hydrolysis of a wide variety of 6-phospho-␣-glucosides including maltose-6-phosphate, maltitol-6-phosphate, isomaltose-6-phosphate, and all five 6-phosphorylated isomers of sucrose (K m ϳ 1-5 mM) yet did not hydrolyze sucrose-6-phosphate. By contrast, purified sucrose-6-phosphate hydrolase (M r ϳ 53,000) hydrolyzed only sucrose-6-phosphate (K m ϳ 80 M). Differences in molecular shape and lipophilicity potential between sucrose and its isomers may be important determinants for substrate discrimination by the two phosphoglucosyl hydrolases. Phospho-␣-glucosidase and sucrose-6-phosphate hydrolase exhibit no significant homology, and by sequence-based alignment, the two enzymes are assigned to Families 4 and 32, respectively, of the glycosyl hydrolase superfamily. The phospho-␣-glucosidase gene (aglB) lies adjacent to a second gene (aglA), which encodes an EII(CB) component of the phosphoenolpyruvate-dependent sugar: phosphotransferase system. We suggest that the products of the two genes facilitate the phosphorylative translocation and subsequent hydrolysis of the five ␣-Dglucosyl-D-fructoses by K. pneumoniae.The discovery in 1964 of the phosphoenolpyruvate-dependent sugar:phosphotransferase system (PEP:PTS) 1 by Roseman and colleagues (1) is a landmark in our understanding of carbohydrate dissimilation by microorganisms. Since the initial description of this multi-component system in Escherichia coli, the PEP:PTS has been established as the primary route for the transport and concomitant phosphorylation of a wide variety of sugars by bacteria from both Gram-negative (2, 3) and Grampositive genera (4, 5). In many species, including Bacillus subtilis, Lactococcus lactis, Streptococcus mutans, Escherichia coli, and Klebsiella pneumoniae (6, 7), sucrose is accumulated via the PTS simultaneously with phosphorylation at C-6 of the glucopyranosyl moiety of the disaccharide. Intracellularly, sucrose-6-phosphate (sucrose-6-P) is hydrolyzed by sucrose-6-phosphate hydrolase (8, 9) to glucose-6-phosphate and fructose, which are then fermented via the glycolytic pathway to yield primarily lactic acid.The structures of sucrose, its five isomeric ␣-D-glucosyl-Dfructoses (trivially designated trehalulose, turanose, maltulose, leucrose, and palatinose), and some related ␣-linked disaccharides are depicted in Fig. 1. In contrast to the many reports of sucros...

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Sucrose: X-ray refinement and comparison with neutron refinement

Cited by 122 publications

References 20 publications

Three-Dimensional Magnetically-Oriented Microcrystal Array: A Large Sample for Neutron Diffraction Analysis

Three-Dimensional Magnetically-Oriented Microcrystal Array: A Large Sample for Neutron Diffraction Analysis

Structural thermodynamics of protein preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides

Metabolism of Sucrose and Its Five Linkage-isomeric α-d-Glucosyl-d-fructoses by Klebsiella pneumoniae

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