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The Poisson‐Boltzmann model for tRNA: Assessment of the calculation set‐up and ionic concentration cutoff
Author(s) -
Gruziel Magdalena,
Grochowski Pawel,
Trylska Joanna
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20953
Subject(s) - poisson–boltzmann equation , ionic bonding , chemistry , cutoff , ion , ionic strength , poisson distribution , statistical physics , molecule , thermodynamics , computational chemistry , physics , mathematics , quantum mechanics , statistics , aqueous solution , organic chemistry
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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008