Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

UNAN H., Yildirim A., Tekpinar M.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, cilt.29, sa.7, ss.655-665, 2015 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 29 Sayı: 7
  • Basım Tarihi: 2015
  • Doi Numarası: 10.1007/s10822-015-9849-0
  • Dergi Adı: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.655-665
  • Van Yüzüncü Yıl Üniversitesi Adresli: Evet

Özet

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.