Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics

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Jiang P., YAŞAR F., Hansmann U. H. E.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, cilt.9, sa.8, ss.3816-3825, 2013 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 9 Sayı: 8
  • Basım Tarihi: 2013
  • Doi Numarası: 10.1021/ct400312d
  • Dergi Adı: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.3816-3825
  • Hacettepe Üniversitesi Adresli: Evet

Özet

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end beta-sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel beta-sheet formed by the two chain ends.