Analysis of the dynamics of Rhizomucor miehei lipase at different temperatures

The dynamics of Rhizomucor miehei lipase has been studied by molecular dynamics simulations at temperatures ranging from 200-500K. Simulations carried out in periodic boundary conditions and using explicit water molecules were performed for 400 ps at each temperature. Our results indicate that conformational changes and internal motions in the protein are significantly influenced by the temperature increase. With increasing temperature, the number of internal hydrogen bonds decreases, while surface accessibility, radius of gyration and the number of residues in random coil conformation increase. In the temperature range studied, the motions can be described in a low dimensional subspace, whose dimensionality decreases with increasing temperature. Approximately 80% of the total motion is described by the first (i) 80 eigenvectors at T=200K, (ii) 30 eigenvectors at T=300K and (iii) 10 eigenvectors at T=400K. At high temperature, the alpha-helix covering the active site in the native Rhizomucor miehei lipase, the helix at which end the active site is located, and in particular, the loop (Gly35-Lys50) show extensive flexibility.