Molecular dynamics study of the conformational stability of esterase 2 from Alicyclobacillus acidocaldarius

Circular dichroism and differential scanning calorimetry measurements showed that esterase 2 from the thermophilic microorganism Alicyclobacillus acidocaldarius, EST2, and its variant in which the first 35 residues have been deleted. EST2-36del, unfold reversibly on increasing temperature, and possess two cooperative and coupled domains [12]. Structural features of the alpha/beta hydrolase fold of EST2, with nine alpha-helices packed against the central twisted beta-sheet, do not allow a straightforward identification of these two cooperative and coupled domains. Molecular dynamics simulations, each one 20 ns long, have been performed at 300, 400 and 500 K. on both proteins in explicit water. Suitable analysis of MD trajectories has allowed a reliable identification of the two cooperative domains (i.e., the less stable one corresponds to external alpha-helices, whereas the more stable one corresponds to the central twisted beta-sheet) and the attribution of the key coupling role to the last and long a-helix of EST2. (C) 2011 Elsevier B.V. All rights reserved.