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.
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Abbreviations
- 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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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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Spiwok, V., Lipovová, P., Skálová, T. et al. Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance. J Comput Aided Mol Des 19, 887–901 (2005). https://doi.org/10.1007/s10822-005-9033-z
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DOI: https://doi.org/10.1007/s10822-005-9033-z