Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

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Publikace nespadá pod Filozofickou fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.
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WIMMEROVÁ Michaela KOZMON Stanislav NEČASOVÁ Ivona MISHRA Sushil Kumar KOMÁREK Jan KOČA Jaroslav

Rok publikování 2012
Druh Článek v odborném periodiku
Časopis / Zdroj Plos One
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046032
Doi http://dx.doi.org/10.1371/journal.pone.0046032
Obor Biochemie
Klíčová slova SMALL MOLECULAR-INTERACTIONS; DENSITY-FUNCTIONAL THEORY; SEPARATE TOTAL ENERGIES; INTERACTIONS AB-INITIO; DOT-PI-INTERACTIONS; O HYDROGEN-BONDS; AROMATIC INTERACTIONS; RALSTONIA-SOLANACEARUM; STRUCTURAL BASIS; EXCHANGE-ENERGY
Přiložené soubory
Popis Carbohydrate - receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/pi interaction. In the study presented here, we attempted for the first time to quantify how the CH/pi interaction contributes to a more general carbohydrate - protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with alpha-L-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were -8.5, -7.1 and -4.1 kcal.mol(-1), respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values -8.8, -7.9 kcal.mol(-1), excluding the alanine mutant where the interaction energy was -0.9 kcal.mol(-1). Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the alpha-L-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.
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