Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase


Tekpinar M. , Yildirim A., WASSENAAR T. A.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, cilt.44, ss.685-696, 2015 (SCI İndekslerine Giren Dergi) identifier identifier identifier

  • Cilt numarası: 44 Konu: 8
  • Basım Tarihi: 2015
  • Doi Numarası: 10.1007/s00249-015-1067-0
  • Dergi Adı: EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
  • Sayfa Sayıları: ss.685-696

Özet

The protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is involved in the quorum sensing of several bacterial species, including Helicobacter pylori. In particular, these bacteria depend on MTAN for synthesis of vitamin K-2 homologs. The residue D198 in the active site of MTAN seems to be of crucial importance, by acting as a hydrogen-bond acceptor for the ligand. In this study, we investigated the conformation and dynamics of apo and holo H. pylori MTAN (HpMTAN), and assessed the effect of protonation of D198 by use of molecular dynamics simulations. Our results show that protonation of the active site of HpMTAN can cause a conformational transition from a closed state to an open state even in the absence of substrate, via inter-chain mechanical coupling.