Molecular Dynamics of the Ha-ras Protein: Nucleotide Atom-Centred Charges within the AMBER Force Field

Abstract

Molecular dynamics simulations have become an essential tool for the study of biological systems. The Ha-ras protein, is a system suitable for such studies. Despite much recent progress, it is still not known exactly how the protein functions in the cell growth cycle.

In this work atom-centred point charges for the guanosine nucleotide ligands are calculated and tested. To be compatible with the other AMBER force field parameters these are fitted to a molecular electrostatic potential derived from an ab initio wavefunction. The smallest basis set able to produce a stable wavefunction for the negatively charged GDP and GTP molecule ions was 3-21G* with diffuse functions added on the phosphate groups. To maintain force field integrity these charges were scaled to be equivalent to STO-3G derived values. This procedure is seen to produce a good magnesium-phosphate interaction potential when compared to 6-31++G* ab initio calculations.

With the nucleotides fixed in the binding site conformation, it was found essential to include the electrostatics of the binding site in the calculation of the charges. It was also found to be inappropriate to divide the nucleotide into constituent parts for the calculations. From the calculated charges and experimental data, the nucleotide protonation states in the protein are deduced. It is unlikely that GDP is protonated, GTP probably binds one proton. The charges were tested in MD simulations of a protein modelled on the crystal structure of Tong et al., during which the dynamics of the nucleotide and binding site residues were in good agreement with the crystal structure data.

The model is seen to be sensitive, not only to the inclusion of explicit solvent, but to the number of waters ligating the magnesium ion and the conformation of the loop between residues 60 and 66; both pieces of information are lacking in the crystal structure data.