2001/06/27 by Anne Voegler Smith, Carol K. Hall
paper · doi:10.1002/prot.1100
Abstract 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 Φ–Ψ conformational space. Model polyalanine chains undergo a locally cooperative transition to form α‐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 α‐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. Proteins 2001;44:344–360. © 2001 Wiley‐Liss, Inc.