Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

John S. Perkyns, Gillian C. Lynch, Jesse J. Howard, Bernard Pettitt

Research output: Contribution to journalArticle

58 Citations (Scopus)

Abstract

Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko-Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.

Original languageEnglish (US)
Article number064106
JournalJournal of Chemical Physics
Volume132
Issue number6
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Solvation
Coulomb interactions
closures
Integral equations
solvation
solutes
proteins
integral equations
Molecular dynamics
approximation
Proteins
Aprotinin
simulation
interactions
molecular dynamics
trypsin
Molecular Dynamics Simulation
Distribution functions
Thermodynamics
inhibitors

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Protein solvation from theory and simulation : Exact treatment of Coulomb interactions in three-dimensional theories. / Perkyns, John S.; Lynch, Gillian C.; Howard, Jesse J.; Pettitt, Bernard.

In: Journal of Chemical Physics, Vol. 132, No. 6, 064106, 2010.

Research output: Contribution to journalArticle

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