Simulation of the hydration structure of glycyl-alanine

Abstract

Molecular dynamics (MD) simulations studies have been performed on the aqueous solvation of the dipeptide glycyl-alanine (GA) using classical force-fields AMBER (J. Wang, P. Cieplak, P. A. Kollman, J. Comp. Chem. 21, 1049 (2000)) and CHARMM (N. Foloppe, A. D. MacKerell, J. Comp. Chem. 21, 86 (2000)), and the polarizable force-field AMOEBAPRO (P. Ren, J. W. Ponder, J. Comp. Chem. 23, 1497 (2002), P. Ren, J. W. Ponder, J. Phys. Chem. B. 107, 5933 (2003)). Radial distribution functions and hydration numbers are calculated and compared with the data from Car-Parrinello molecular dynamics (CPMD) and experiments. Our results show all three force-fields can reproduce most of the features of the hydration structure of dipeptide GA. It is also found that AMBER and CHARMM force-fields can describe an averaged chemical environment, while AMOEBAPRO force-field has the capability of capturing the changes in the local environment caused by conformational transitions.

Keywords:

• Molecular dynamics
• Polarizable force-field
• Hydration structure

Acknowledgements

The authors gratefully acknowledge the computing facilities of the Centre for Scientific Computing, University of Warwick. This project is funded by the EPSRC Materials Modelling Consortium “Modelling the Biological Interface with Materials”, GR/S80127/01.