title: The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff.
abstract: Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Poland. magd@icm.edu.pl
authors.forename: Magdalena
authors.initials: M
authors.lastname: Gruziel
authors.forename: Pawel
authors.initials: P
authors.lastname: Grochowski
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D007477:Ions / Q000737:chemistry*; D009994:Osmolar Concentration; D012343:RNA, Transfer / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity; D014867:Water
chemical_list: D007477:Ions; D012997:Solvents; D014867:Water; D012343:RNA, Transfer