Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
5
pubmed:dateCreated
2010-9-6
pubmed:abstractText
Protein hydration plays an integral role in determining protein function and stability. We develop a simple method with atomic level precision for predicting the solvent density near the surface of a protein. A set of proximal radial distribution functions are defined and calculated for a series of different atom types in proteins using all-atom, explicit solvent molecular dynamic simulations for three globular proteins. A major improvement in predicting the hydration layer is found when the protein is held immobile during the simulations. The distribution functions are used to develop a model for predicting the hydration layer with sub-1-Angstrom resolution without the need for additional simulations. The model and the distribution functions for a given protein are tested in their ability to reproduce the hydration layer from the simulations for that protein, as well as those for other proteins and for simulations in which the protein atoms are mobile. Predictions for the density of water in the hydration shells are then compared with high occupancy sites observed in crystal structures. The accuracy of both tests demonstrates that the solvation model provides a basis for quantitatively understanding protein solvation and thereby predicting the hydration layer without additional simulations.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-10047483, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-10074944, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-10828976, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-11106604, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-11183777, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-11565842, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-12069622, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-12214315, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-12452690, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-16006526, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-16222654, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-16355414, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-17203387, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-3032965, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-3736419, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-3945310, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-4856347, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-7542034, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-7616573, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-7892604, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-7920248, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-7932732, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-8011893, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-8312469, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-8381492, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-8946852, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-8986123, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-9300804, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-9482874, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-9577228, http://linkedlifedata.com/resource/pubmed/commentcorrection/20816074-9631296
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1542-0086
pubmed:author
pubmed:copyrightInfo
Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
pubmed:issnType
Electronic
pubmed:day
8
pubmed:volume
99
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1611-9
pubmed:dateRevised
2011-9-13
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Modeling the hydration layer around proteins: HyPred.
pubmed:affiliation
Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural