Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
| Authors | |
|---|---|
| Year of publication | 2012 |
| Type | Article in Periodical |
| Magazine / Source | Plos One |
| MU Faculty or unit | |
| Citation | |
| Web | http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046032 |
| Doi | http://dx.doi.org/10.1371/journal.pone.0046032 |
| Field | Biochemistry |
| Keywords | 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 |
| Attached files | |
| Description | 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. |
| Related projects: |
|