Direct computation of long time processes in peptides and proteins: reaction path study of the coil-to-helix transition in polyalanine.
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 alpha-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) 310-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. Proteins 1999;36:249-261.
Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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D000465:Algorithms; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012997:Solvents; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry / Q000378:metabolism
D010455:Peptides; D011506:Proteins; D012997:Solvents; D014867:Water; C019529:polyalanine