Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance
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Summary
Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate–aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from −2.8 to −12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree–Fock method (interaction energies from +1.0 to −6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.
Keywords
ab initio carbohydrate recognition C–H/π interactions force field glycobiology glycosidases lectinsAbbreviations
- AMBER
assisted model building with energy refinement
- B3LYP
Becke–Slater-HF 3-term exchange and Lee–Yang–Parr correlation hybrid functional
- BSSE
basis set superposition error
- CBM
carbohydrate-binding module
- CBS
complete basis set
- CCSD(T)
coupled cluster with single, double and perturbative triple excitation
- CHARMM
chemistry at Harvard molecular mechanics
- CHEAT
carbohydrate hydroxyl groups represented by extended atoms
- CSFF
carbohydrate solution force field
- DFT
density functional theory
- GROMOS
Groningen molecular simulation
- HF
Hartree–Fock␣method
- MM2
molecular mechanics version 2
- MM3
molecular mechanics version 3
- MP2
Møller–Plesset perturbation theory; second order
- OPLS
optimized potentials for liquid simulations
- PDB
protein data bank
- RMSD
root mean square deviation
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Notes
Acknowledgements
Authors would like to gratefully acknowledge the Czech Science Foundation (GACR 204/02/0843) and the Academy of Sciences of the Czech Republic (projects B500500512 and AVOZ 40500505) for financial support.
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