Role of CH/π interactions in substrate binding by Escherichia coli β-galactosidase

Spiwok, Vojtěch; Lipovová, Petra; Skálová, Tereza; Buchtelova, Eva; Hašek, Jindřich; Králová, Blanka

doi:10.1016/j.carres.2004.06.016

Cited by 97 publications

(81 citation statements)

References 18 publications

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“…[14,[19][20][21][22] An extensive study of protein-carbohydrate complexes obtained from six high-resolution (1.3 or better) X-ray structures has been undertaken by Spiwok et al [14] The estimated interaction energies fall between À11.7 and À26.8 kJ mol…”

Section: Introductionmentioning

confidence: 99%

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Vandenbussche

Díaz

Fernández‐Alonso

et al. 2008

Chemistry A European J

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The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.

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Section: Introductionmentioning

confidence: 99%

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Vandenbussche

Díaz

Fernández‐Alonso

et al. 2008

Chemistry A European J

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“…Not surprisingly, therefore, carbohydrate-p interactions are widely utilized by glycoside hydrolases (e.g. [6,7]), glycosyltransferases (e.g. [8][9][10]) and carbohydrate-binding modules [11,12] to achieve recognition and specificity for their natural substrates.…”

Section: Introductionmentioning

confidence: 99%

Aromatic interactions at the catalytic subsite of sucrose phosphorylase: Their roles in enzymatic glucosyl transfer probed with Phe⁵² → Ala and Phe⁵² → Asn mutants

2011

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a b s t r a c tMutants of Leuconostoc mesenteroides sucrose phosphorylase having active-site Phe 52 replaced by Ala (F52A) or Asn (F52N) were characterized by free energy profile analysis for catalytic glucosyl transfer from sucrose to phosphate. Despite large destabilization (P3.5 kcal/mol) of the transition states for enzyme glucosylation and deglucosylation in both mutants as compared to wild-type, the relative stability of the glucosyl enzyme intermediate was weakly affected by substitution of Phe 52 . In reverse reaction where fructose becomes glucocylated, ''error hydrolysis'' was the preponderant path of breakdown of the covalent intermediate of F52A and F52N. It is proposed, therefore, that Phe 52 facilitates reaction of the phosphorylase through (1) positioning of the transferred glucosyl moiety at the catalytic subsite and (2) strong cation-p stabilization of the oxocarbenium ion-like transition states flanking the covalent enzyme intermediate.

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“…The later method evaluates interfragment van der Waals type stabilization in the protein-ligand complex. Stabilizations of CH-π interaction between tryptophan and carbohydrate in the β-galactosidase-substrates or products complex were calculated at the MP2/6-31+G(d) level as 2.4-5.2 kcal/mol [52]. Stabilizing interaction energy of the fucose-benzene complex was estimated 3.0 kcal/mol at the MP2/6-31G(d,p) level of theory [53].…”

Section: Methodsmentioning

confidence: 99%

Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination

et al. 2008

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If we predict the host range of new or mutant influenza virus in advance, we are able to measure against pandemic human influenza immediately after the new virus emerges somewhere. Influenza viral hemagglutinin(HA)-sialoside receptor interaction is a target event for in silico chemical prediction studies about the virus host range determination. We theoretically studied avian and human influenza A virus HA H3 subtype complexed with avian or human type receptor Neu5Acα(2-3 or 2-6)Gal analogues by ab initio fragment molecular orbital (FMO) method at the second order Møller-Plesset (MP2)/6-31G level, which can evaluate correctly not only electrostatic interactions but also lipophilic interactions based on van der Waals dispersion force. Avian H3 bound to avian α2-3 11.4 kcal/mol stronger than to human α2-6 in the model complexes with taking account of intermolecular lipophilic interaction. A substitution at the position 226 between Gln (avian) and Leu(human) on influenza H3 HA1 has altered Glycoconj J (2008) its virus host range between avian and human. In the ab initio FMO studies, binding energy of avian Gln226Leu H3-human α2-6 was quite similar to that in the human H3-human α2-6 complex with amino acid sequence differences at nine positions in the models. This similarity indicates that avian Gln226Leu H3 virus can infect human with the same level as human H3 virus. Opposite mutation Leu226Gln in the human H3 gave the moderate binding energies to avian α2-3 with similarity to avian H3-α2-3 complex that supported our previous virus-sialoside binding assay. Ab initio FMO studies have revealed the relationship between influenza H3 virus host range and H3-α(2-3 or 2-6) receptors binding. Our theoretical approach may predict the infectious level of new viruses and point out some unknown dangerous mutation positions on HA in advance.

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Role of CH/π interactions in substrate binding by Escherichia coli β-galactosidase

Cited by 97 publications

References 18 publications

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Aromatic interactions at the catalytic subsite of sucrose phosphorylase: Their roles in enzymatic glucosyl transfer probed with Phe⁵² → Ala and Phe⁵² → Asn mutants

Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination

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Role of CH/π interactions in substrate binding by Escherichia coli β-galactosidase

Cited by 97 publications

References 18 publications

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

Aromatic interactions at the catalytic subsite of sucrose phosphorylase: Their roles in enzymatic glucosyl transfer probed with Phe52 → Ala and Phe52 → Asn mutants

Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination

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Aromatic interactions at the catalytic subsite of sucrose phosphorylase: Their roles in enzymatic glucosyl transfer probed with Phe⁵² → Ala and Phe⁵² → Asn mutants