Direct computation of long time processes in peptides and proteins: Reaction path study of the coil-to-helix transition in polyalanine
✍ Scribed by Shuanghong Huo; John E. Straub
- Publisher
- John Wiley and Sons
- Year
- 1999
- Tongue
- English
- Weight
- 414 KB
- Volume
- 36
- Category
- Article
- ISSN
- 0887-3585
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✦ Synopsis
The MaxFlux reaction path algorithm was used to isolate optimal transition pathways for the coil-to-helix transition in polyalanine. Eighteen transition pathways, each connecting one random coil configuration with an ideal ␣-helical configuration, were computed and analyzed. The transition pathway energetics and mechanism were analyzed in terms of the progression of the peptide nonbonded contact formation, helicity, end-to-end distance and energetics. It was found that (1) localized turns characterized by i, i ؉ 3 hydrogen bonds form in the early stages of the coil-to-helix transition, (2) the peptide first collapses and then becomes somewhat more extended in the final stage of helix formation, and (3) 3 10 -helix formation does not appear to be a necessary step in the transition from coil to helix. These conclusions are in agreement with the results of more computationally intensive direct molecular dynamics simulations.