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New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein.

Furanosides have been subjected to extensive studies owing to their inherent flexibility, which is believed to play an important role in the survival and pathogenicity of different disease causing organisms in the human body. This study reports the binding free energy (ΔG) and specificity of arabinofuranose oligosaccharides to a protein, arabinanase (Arb43A) with the use of potential of mean force (PMF) calculations using the umbrella sampling simulations. Long molecular dynamics simulations have been carried out to understand intermolecular interactions in the arabinofuranose-protein complex. The PMF for pulling the α-(1→5)-linked L-arabinohexaose (ligand) from the protein provides a large free energy of binding, -16.8 kcal/mol. The ΔG of the non-reducing arabinotriose end is found -12.6 kcal/mol, while the ΔG of the reducing end is calculated to be -7.7 kcal/mol. In the absence of non-reducing arabinotrioside, the ΔG of the reducing arabinotrioside is -8.5 kcal/mol. Similarly, in the absence of reducing arabinotrioside, the ΔG of the non-reducing arabinotrioside is calculated to be -9.4 kcal/mol. The main contributing factor in the protein-arabinofuranose binding is hydrogen bonding. Acidic amino acid residues, Glu and Asp, with furanosides produce the strongest hydrogen bonding. Araf-A, B and C constructs the reducing arabinotriose, while Araf-D, E and F constructs the non-reducing arabinotriose. Since most of the hydrogen bonding occupancies belong to Araf-D and Araf-E, the non-reducing arabinotriose is bound to protein more strongly than the reducing arabinotriose. This explains why the reducing arabinotriose can detach from the protein in nature.