Investigation of the conformational space of hydrophobic-polar heteropolymers by gyration tensor based parameters

Ozyurt B. T., Arkin H.

Chemical Physics, cilt.552, 2022 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 552
  • Basım Tarihi: 2022
  • Doi Numarası: 10.1016/j.chemphys.2021.111372
  • Dergi Adı: Chemical Physics
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Chemical Abstracts Core, INSPEC
  • Anahtar Kelimeler: Monte Carlo simulations, Molecular modeling, Energy landscape, Polymers, Proteins, Gyration tensor based parameters, PEPTIDES, COOPERATIVITY, MODEL, SHAPE, SIZE
  • Ankara Üniversitesi Adresli: Evet

Özet

© 2021 Elsevier B.V.Multicanonical simulations of hydrophobic-polar heteropolymers were performed with a simple and effective coarse-grained off-lattice model to identify the folding pathways and the topology of the energy landscape with gyration tensor-based parameters. We examined six exemplified sequences of heteropolymers and illustrated three of them which present definitely different folding types such as two-state folding, folding through intermediates, as well as metastability. The major advantage of this study is our chosen ”order” parameter, namely gyration tensor-based analysis, does not require any reference state before the simulation as that is the need for the other order parameters which are chosen in other studies in the same context. Our paper presents the use of very useful parameters to detect conformational phase transitions in polymer chains. Another order parameter that requires a reference conformation is presented in earlier works related to this aspect. This extends the simulation into two steps. With our analysis, there is no need for a global minimum conformation so-called reference state and our simulation will be completed in one step. Furthermore, there is no relative evaluation according to the reference state.