Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 44, Issue 3, Pages 344-360Publisher
WILEY
DOI: 10.1002/prot.1100
Keywords
helix-coil transition; computer simulation; four-bead protein model
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Funding
- NIGMS NIH HHS [GM-56766] Funding Source: Medline
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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 a-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 a-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. (C) 2001 Wiley-Liss, Inc.
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