Journal of Computer-Aided Molecular Design

, Volume 19, Issue 12, pp 887–901 | Cite as

Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance

  • Vojtěch Spiwok
  • Petra Lipovová
  • Tereza Skálová
  • Eva Vondráčková
  • Jan Dohnálek
  • Jindřich Hašek
  • Blanka Králová
Article
First Online:
Received:
Accepted:

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 lectins 

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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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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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Vojtěch Spiwok
    • 1
  • Petra Lipovová
    • 1
  • Tereza Skálová
    • 2
  • Eva Vondráčková
    • 2
  • Jan Dohnálek
    • 2
  • Jindřich Hašek
    • 2
  • Blanka Králová
    • 1
  1. 1.Department of BiochemistryInstitute of Chemical Technology in PraguePrague 6Czech Republic
  2. 2.Institute of Macromolecular ChemistryAcademy of Sciences of the Czech RepublicPraha 6Czech Republic

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