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An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson–Boltzmann equation
Author(s) -
Augspurger Joseph D.,
Scheraga Harold A.
Publication year - 1997
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/(sici)1096-987x(199706)18:8<1072::aid-jcc11>3.0.co;2-f
Subject(s) - electrostatics , chemistry , solvation , implicit solvation , poisson–boltzmann equation , solvent models , dielectric , electric potential energy , computational chemistry , range (aeronautics) , chemical physics , thermodynamics , solvent , physics , materials science , quantum mechanics , organic chemistry , ion , power (physics) , composite material
A rapid, pairwise hydration potential, the reduced radiusindependent Gaussian sphere (RRIGS) approximation, has been presentedrecently. Because experimental values of the conformational dependence ofthe hydration free energy are unavailable, this hydration potential istestable by comparison to a presumably more accurate (yet morecomputationally intensive) model. One such method is the electrostatichydration approach, which models the protein as a collection of pointcharges in a low‐dielectric medium and the solvent as a high‐dielectriccontinuum. The electrostatic free energy can be determined by solving thePoisson–Boltzmann equation, which is carried out with the programDelPhi. The total free energy of hydration is calculated by adding a freeenergy of cavity formation term to this electrostatic term. Comparison ismade for many conformations of two proteins, bovine pancreatic trypsininhibitor (BPTI) and the carboxy‐terminal fragment of the L7/L12 ribosomalprotein (CTF). Thirty‐nine near‐native structures of BPTI, previouslygenerated by Ripoll and coworkers, and 150 conformations of CTF, generatedby a threading algorithm to cover a wide range of conformational space,were used in these comparisons. It is shown that, for the neutral forms ofthese proteins, the RRIGS hydration potential correlates very well with theelectrostatic model hydration free energy, although the correlation isbetter for the CTF conformations than for the near‐native BPTIconformations. For charged forms, the correlation is much poorer. Theseresults serve as evidence that solvent‐exposure models of hydration, whichleave out cooperative effects between different groups, may be appropriatefor modeling neutral or slightly charged species, because these cooperativeeffects are likely to be small. However, for highly charged species wherecooperative effects are surely large, such an approach will be lessaccurate. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :1072–1078, 1997