Fast coarse-grained model for RNA titration

J Chem Phys. 2017 Jan 21;146(3):035101. doi: 10.1063/1.4972986.


A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

MeSH terms

  • Azotobacter vinelandii / enzymology
  • Introns
  • Models, Chemical
  • Molecular Dynamics Simulation
  • Monte Carlo Method
  • Protein Structure, Secondary
  • Protons
  • RNA / chemistry*
  • RNA, Catalytic / chemistry
  • Titrimetry


  • Protons
  • RNA, Catalytic
  • RNA