Relative Effects of Ionic and Neutral Substituents on the Binding of an Oligosaccharide by a Protein

Lemieux, R. U.; Du, Ming-Hui; Spohr, Ulrike

doi:10.1021/ja00100a077

Cited by 32 publications

(24 citation statements)

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“…The slight changes in AAG* within each group indicate that the substituents at C-1 are also exposed to bulk water, a conclusion in accord with the X-ray structure of the glucoamylase-acarbose complex (12). The small effects caused by the structural changes can be attributed to a change in the water structure about the C-l substituents (26).…”

Section: Glusupporting

confidence: 61%

Chemical mapping of the active site of the glucoamylase ofAspergillus niger

et al. 1996

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Abstract:A recently developed technique for the probing of the combining sites of lectins and antibodies, to establish the structure of the epitope that is involved in the binding of an oligosaccharide, is used to study the binding of methyl aisomaltoside by the enzyme glucoamylase. The procedure involved the determination of the effects on the kinetics of hydrolysis of both monodeoxygenation and mono-0-methylation at each of the seven hydroxyl groups in order to gain an estimate of the differential changes in the free energies of activation, AAG' . As expected, from previous publications, both deoxygenation and 0-methylation of OH-4 (reducing unit), OH-4', or OH-6' strongly hindered hydrolysis, whereas the kinetics were virtually unaffected by either the substitutions at OH-2 or structural changes at C-I. The substitutions at OH-3 caused increases of 2.1 and 1.9 kcallmol in the AAG'. In contrast, whereas deoxygenation of either OH-2' or OH-3' caused much smaller (0.96 and 0.52 kcallmol) increases in AAG', the mono-0-methylations resulted in severe steric hindrance to the formation of the activated complex. The relatively weak effects of deoxygenation suggest that the hydroxyl groups are replaced by water molecules and thereby participate in the binding by contributing effective complementarity. Methyl a-isomaltoside was docked into the combining site of the X-ray crystal structure at 2.4 A resolution of the complex with the inhibitor acarbose. A fit free of steric interactions with the protein was found that has the methyl a-glucopyranoside unit in the normal "C, conformation and the other glucose unit approachin a half-chair conformation with the interunit fragment defined by the torsion angles +IIJJ/W = 74°/1340/ % 166' (0-5'-C-l'h-64-6%-5-0-5).The model provides a network of hydrogen bonds that appears to well represent the activated complex formed by the glucoamylase with both maltose and isomaltose since the structures appear to provide a sound rationale for both the specificity and catalysis provided by the enzyme.Key war-ds: monodeoxy and mono-0-methyl derivatives of methyl a-isomaltoside, enzyme binding domain, functioning of glucoamylase, differential changes in free energy of activation, characteristics of hydrogen bonding networks. Resum6: Dans le but d'Ctudier la fixation de l'a-isomaltoside de mCthyle par l'enzyme glucoamylase, on a fait appel B une technique, dCveloppCe rCcemment pour I'examen des sites de fixation des lectines et des anticorps, pour Ctablir la structure de I'Cpitope impliqui dans la fixation d'un oligosaccharide. I,a procCdure implique la dktermination des effets, provoquCs sur la cinCtique d'hydrolyse, par la monodCsoxygCnation ainsi que la mono-0-methylation de chacun des sept groupes hydroxyles; on espitre ainsi obtenir une evaluation des changements diffkrentiels dans les Cnergies libres d'activation, AAG'. Tel qu'on peut s'y attendre sur la base des publications antkrieures, tant la dCsoxygCnation que la 0-mtthylation des groupes OH-4 (unit6 rkductrice), OH-4' ou OH-6' empsc...

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Section: Glusupporting

confidence: 61%

Chemical mapping of the active site of the glucoamylase ofAspergillus niger

et al. 1996

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“…This was mainly interpreted to be due to solvent reorganization (19). This and other results led to the conclusion that release of solvent molecules from polyamphiphilic surfaces can drive binding reactions not only by an increase in entropy (hydrophobic effect) but also by a decrease in enthalpy (20)(21)(22)(23). Structural and solution data for binding of monosaccharides and small oligosaccharides to lectins and transport proteins indicate a somewhat higher number of hydrogen bonds and a higher binding enthalpy per contact surface than in protein folding and protein-protein complexes (15).…”

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confidence: 89%

“…Thus, direct hydrogen bonds might not be that important. Instead, as stated by Lemieux and co-workers, the solvent release from polyamphiphilic surfaces could supply a large part of the enthalpy (20,21,23). It seems plausible therefore that different parameter sets have to be established whenever different polyamphiphilic surfaces are involved in binding reactions as in protein-protein and protein-carbohydrate interactions.…”

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confidence: 99%

Enthalpic Barriers to the Hydrophobic Binding of Oligosaccharides to Phage P22 Tailspike Protein

et al. 2001

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The structural thermodynamics of the recognition of complex carbohydrates by proteins are not well understood. The recognition of O-antigen polysaccharide by phage P22 tailspike protein is a highly suitable model for advancing knowledge in this field. The binding to octa-and dodecasaccharides derived from Salmonella enteritidis O-antigen was studied by isothermal titration calorimetry and stoppedflow spectrofluorimetry. At room temperature, the binding reaction is enthalpically driven with an unfavorable change in entropy. A large change of -1.8 ( 0.2 kJ mol -1 K -1 in heat capacity suggests that the hydrophobic effect and water reorganization contribute substantially to complex formation. As expected from the large heat-capacity change, we found enthalpy-entropy compensation. The calorimetrically measured binding enthalpies were identical within error to van't Hoff enthalpies determined from fluorescence titrations. Binding kinetics were determined at temperatures ranging from 10 to 30°C. The second-order association rate constant varied from 1 × 10 5 M -1 s -1 for dodecasaccharide at 10°C to 7 × 10 5 M -1 s -1 for octasaccharide at 30°C. The first-order dissociation rate constants ranged from 0.2 to 3.8 s -1 . The Arrhenius activation energies were close to 50 and 100 kJ mol -1 for the association and dissociation reactions, respectively, indicating mainly enthalpic barriers. Despite the fact that this system is quite complex due to the flexibility of the saccharide, both the thermodynamic and kinetic data are compatible with a simple one-step binding model. Carbohydrate-protein interactions play an important role in many biological recognition processes. Compared to protein-protein interactions (1-4), the relation between structure and thermodynamics of carbohydrate binding is much less well understood, although there are some very well studied systems (5-14) and although the concept of empirical parameters for calculating thermodynamic data from the change in accessible surface area has been applied here, too (14-16). Generally, most carbohydrate-protein interactions are enthalpically driven and opposed by an unfavorable change in entropy (17,18). Most of the determined changes in heat capacity for these binding reactions with small oligosaccharides were small (<0.5 kJ mol -1 K -1 ) and negative. Enthalpy-entropy compensation for different ligands to the same protein and even for totally different systems was described (17). This was mainly interpreted to be due to solvent reorganization (19). This and other results led to the conclusion that release of solvent molecules from polyamphiphilic surfaces can drive binding reactions not only by an increase in entropy (hydrophobic effect) but also by a decrease in enthalpy (20-23). Structural and solution data for binding of monosaccharides and small oligosaccharides to lectins and transport proteins indicate a somewhat higher number of hydrogen bonds and a higher binding enthalpy per contact surface than in protein folding and protein-protein complexes ...

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“…The ability of proteins to fulfill these various biological functions is encoded in their amino acid sequences. Although for a very long time it has been believed that the specific functionality of a given protein is predetermined by its unique three-dimensional (3-D) structure, 1,2 it is recognized now that a large portion of any given proteome is occupied by so-called intrinsically disordered proteins (IDPs). 3–67 These proteins and others with disordered regions (IDPRs) possess a very wide range of biological functions, but are characterized by the lack of a well-defined 3-D structure under physiological conditions.…”

Section: Introductionmentioning

confidence: 99%