| Abstract | Molecular dynamics simulations on DNA hairpin stems containing A. . |
| Methods | Subsequently, the models are subjected to a total of 1.5us molecular dynamics simulations (MD) using Sander module of AMBER 12 package [40]. |
| Molecular dynamics simulation protocol | Molecular dynamics simulation protocol |
| Author Summary | However, commonly employed molecular dynamics simulations suffer from a limitation in accessible time scale, making it difficult to model large-scale unfolding events in a realistic amount of simulation time without employing unrealistically high temperatures. |
| Introduction | Tm is obtainable by experiment and, in theory, from simulation, although current molecular dynamics simulations are limited in their ability to capture full folding or unfolding trajectories of most proteins (except very small fast folding domains [15]) in a tractable amount of simulation time [16]. |
| Predicting the effects of mutations on protein stability from non-equilibrium unfolding simulations | Although the idea of obtaining equilibrium free energy differences from non-equilibrium measurements is not new [35], and protein stabilities have been calculated from molecular dynamics simulations using the Iarzynski equality, e.g., [36—38] , such simulations require application of an external steering force; in the present paper we report the use of multi-temperature Monte-Carlo unfolding simulations in obtaining protein stabilities. |