Molecular Dynamics Simulation of Equine Infectious Anemia Virus Tat Protein in Water and in 40% Trifluoroethanol

Abstract

Abstract Two molecular dynamics (MD) simulations were performed in order to increase the understanding of the dependence of protein conformation on solvent environment. The protein used for these simulations is the transcriptional activator of the equine infectious anemia virus (EIAV-Tat). The structure of this protein has been determined by nuclear magnetic resonance (NMR) in aqueous solution (Willbold et al., Science 264, 1584 (1994)) and in 40% (v/v) trifluoroethanol (TFE) (Sticht et al., Eur. J. Biochem., submitted) showing considerable differences in the stability of the secondary structure elements. In order to investigate the influence of the solvent MD simulations (300 K; 200 ps) were carried out in water and in a solvent containing 40% (v/v) TFE. In both simulations the structure as determined in 40% TFE by NMR, showing three-helices and a tight type II turn, was used as the initial structure. The MD simulations clearly indicate a decreased stability of the secondary structure elements in aqueous environment as made obvious by larger atomic motions and stronger fluctuations in the length of the hydrogen bonds. Complete unfolding of the helices was not observed on a 200 ps timescale. The root mean square deviation (RMSD) values of the backbone atoms after 200 ps simulation compared to the starting structure underline the strong influence of the solvent on the protein stability. This RMSD value is 1.95 Å for the simulation in water and 1.29 Å for the simulation in TFE/water. This result supports the notion that TFE acts as a secondary structure inducing and stabilizing solvent. The differences apparent from the MD simulations are in good agreement with the data derived from NMR measurements, showing the relevance of MD as a method for estimating conformational and dynamical properties of proteins.