Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins.

摘要: Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where problem arises simulation dye-labeled proteins, which are now being widely used design interpretation Forster resonance energy transfer (FRET) experiments. In study, MD simulations characterize motion two commonly FRET dyes attached an immobilized chain polyproline. Even system, exhibit complex behavior that a mixture fast slow motions. Consequently, very long required sufficiently sample entire range dye motion. Here, we compare ability enhanced methods reproduce fluorescent labels on proteins. particular, compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange (REMD), High Temperature (HTMD) equilibrium simulations. We find that, our all these improve motion, but most significant improvement achieved using REMD.