alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model

An intermediate-resolution model of small, homogeneous peptides is introduced, and discontinuous molecular dynamics simulation is applied to study secondary structure formation. Physically, each model residue consists of a detailed three-bead backbone and a simplified single-bead side-chain. Excluded volume and hydrogen bond interactions are constructed with discontinuous (i.e., hard-sphere and square-well) potentials. Simulation results show that the backbone motion of the model is limited to realistic regions of Phi-Psi conformational space. Model polyalanine chains undergo a locally cooperative transition to form alpha-helices that are stabilized by backbone hydrogen bonding, while model polyglycine chains tend to adopt nonhelical structures. When side-chain size is increased beyond a critical diameter, steric interactions prevent formation of long alpha-helices. These trends in helicity as a function of residue type have been well documented by experimental, theoretical, and simulation studies and demonstrate the ability of the intermediate-resolution model developed in this work to accurately mimic realistic peptide behavior. The efficient algorithm used permits observation of the complete helix-coil transition within 15 min on a single-processor workstation, suggesting that simulations of very long times are possible with this model.