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

Michaela Wimmerová,Jaroslav Koča,Sushil Kumar Mishra,Jan Komárek,Stanislav Kozmon,Ivona Nečasová,Narayanaswamy Srinivasan

doi:10.1371/journal.pone.0046032

Abstract

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/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π 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 α-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 α-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.

Highlights

Carbohydrate - protein interactions are incorporated into a wide range of biologically relevant processes [1]
The ultracentrifugation was done for the wild type Ralstonia solanacearum (RSL) and W31A mutant only because the residue 31 is in the binding site on the edge between the monomers
In the study presented here, we have attempted to quantify the contribution of the dispersion CH/p interaction to the binding of the a-L-Me-fucoside to the RSL lectin

Summary

Introduction

Carbohydrate - protein interactions are incorporated into a wide range of biologically relevant processes [1]. The mutual positions of carbohydrate apolar faces and aromatic amino acid residues found in crystallographic structures of protein - carbohydrate complexes quite often indicate another type of contact classified as a van der Waals or hydrophobic interaction. It was proven, in the last few years that this is a specific type of interaction where London dispersion forces [11,12] are mainly contributing. Inspection of protein-carbohydrate complexes in the PDB database reveals that this interaction occurs in many different carbohydrate processing enzymes, ranging from glycosidases through to transglycosidases or glycosyltransferases to carbohydrate-recognizing proteins, including lectins, immunoglobulins, glycosaminoglycans and many others [13]

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Results

Conclusion