All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

We report the results of protein folding (2I9M, C34, N36, 2KES, 2KHK) by the method of accelerated molecular dynamics (aMD) at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a 100-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 ?, 0.63 ?, 0.52 ?, 1.1 ? and 0.78 ?. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.