Journal article
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
The Journal of chemical physics, Vol.126(12), pp.124114-124114-21
03/28/2007
DOI: 10.1063/1.2714528
PMCID: PMC2430168
PMID: 17411115
Abstract
Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager [J. Am. Chem. Soc. 58, 1486 (1936)] used vacuum properties of small molecules, including polarizability, dipole moment, and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors describe the theory underlying a newly developed polarizable multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit AMOEBA water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK(a) prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2 and 13 kcalmole, depending on the formal charge of the protein, but had only a small influence on dipole moments.
Details
- Title: Subtitle
- Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
- Creators
- Michael J Schnieders - Department of Biomedical Engineering, Washington University in St. Louis, Missouri 63130, USANathan A BakerPengyu RenJay W Ponder
- Resource Type
- Journal article
- Publication Details
- The Journal of chemical physics, Vol.126(12), pp.124114-124114-21
- DOI
- 10.1063/1.2714528
- PMID
- 17411115
- PMCID
- PMC2430168
- NLM abbreviation
- J Chem Phys
- ISSN
- 0021-9606
- eISSN
- 1089-7690
- Publisher
- United States
- Grant note
- GM069553 / NIGMS NIH HHS R01 GM069702-01 / NIGMS NIH HHS GM069702 / NIGMS NIH HHS R01 GM069702-03 / NIGMS NIH HHS R01 GM069702-04 / NIGMS NIH HHS R01 GM069702 / NIGMS NIH HHS R01 GM069553 / NIGMS NIH HHS R01 GM069702-02 / NIGMS NIH HHS
- Language
- English
- Date published
- 03/28/2007
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024548002771
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