Linked Life Data

17411115

Source:http://linkedlifedata.com/resource/pubmed/id/17411115

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2007-4-6
pubmed:abstractText
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.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-10592235, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-11913378, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-12395419, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-15267263, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-15268373, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-15377512, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-15481091, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-16257567, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-16898764, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-16942269, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-17030302, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-17744720, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-3449851, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-6288964, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-7761829, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-8161530, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-9164455, http://linkedlifedata.com/resource/pubmed/commentcorrection/17411115-9311930
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
0021-9606
pubmed:author
pubmed:issnType
Print
pubmed:day
28
pubmed:volume
126
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
124114
pubmed:dateRevised
2011-9-26
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
pubmed:affiliation
Department of Biomedical Engineering, Washington University in St. Louis, Missouri 63130, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Review, Research Support, N.I.H., Extramural, Validation Studies