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

• Published in: Carbohydrate research 2004-09, Vol.339 (13), p.2275-2280
• Main Authors: Spiwok, Vojtěch, Lipovová, Petra, Skálová, Tereza, Buchtelová, Eva, Hašek, Jindřich, Králová, Blanka
• Format: Article
• Language: English
• Subjects: Ab initio; beta-Galactosidase - metabolism; Binding Sites; Calorimetry; Carbohydrate; Carbon; CH/π interactions; Escherichia coli - enzymology; Escherichia coli Proteins - metabolism; Hexoses - chemistry; Hexoses - metabolism; Hydrogen; Molecular recognition; Substrate Specificity; Thermodynamics; β-Galactosidase
• ISSN: 0008-6215; 1873-426X
• DOI: 10.1016/j.carres.2004.06.016

[Display omitted] Interactions between carbohydrates and aromatic amino-acid residues are often observed in structures of carbohydrate–protein complexes. They are characterized by an orientation of the pyranose or furanose ring parallel with the aromatic ring of amino-acid residues. An important role in the formation of these complexes is supposed to be played by CH/π interactions. This paper presents an ab initio quantum chemistry study of CH/π interactions between β-galactosidase from E. coli and its substrates and products. The energy stabilizing the interaction between Trp999 residue and substrate bound in the shallow binding mode was calculated at the MP2/6-31+G(d) level as 5.2 kcal mol −1 for the glucose moiety of allolactose, 2.4 kcal mol −1 for the galactose moiety of allolactose and 5.0 kcal mol −1 for the glucose moiety of lactose. The energy stabilizing the interaction between Trp568 residue and galactose in the deep binding mode was calculated as 2.7 kcal mol −1. Interaction energies at the HF/6-31+G(d) and B3LYP/6-31+G(d) levels were small or repulsive; therefore, highly correlated ab initio methods were necessary to study these interactions. These unexpectedly strong interactions give a rationale for allolactose formation and illustrate the role of the Trp999 residue. In addition, this illustrates the importance of CH/π interactions for the function of carbohydrate-binding proteins and carbohydrate-processing enzymes.