New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein.
Shahidul M IslamBrandon HavranekZahin IbnatPierre-Nicholas RoyPublished in: The journal of physical chemistry. B (2020)
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 nonreducing arabinotriose end is found to be -12.6 kcal/mol, while the ΔG of the reducing end is calculated to be -7.7 kcal/mol. In the absence of nonreducing arabinotrioside, the ΔG of the reducing arabinotrioside is -8.5 kcal/mol. Similarly, in the absence of reducing arabinotrioside, the ΔG of the nonreducing 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 construct the reducing arabinotriose, while Araf-D, E, and F construct the nonreducing arabinotriose. Since most of the hydrogen-bonding occupancies belong to Araf-D and Araf-E, the nonreducing arabinotriose is bound to protein more strongly than the reducing arabinotriose. This explains why the reducing arabinotriose can detach from the protein in nature.
Keyphrases
- amino acid
- molecular dynamics simulations
- binding protein
- protein protein
- small molecule
- pseudomonas aeruginosa
- risk assessment
- emergency department
- randomized controlled trial
- systematic review
- escherichia coli
- transcription factor
- biofilm formation
- staphylococcus aureus
- molecular docking
- electronic health record
- drug induced
- candida albicans
- free survival