Linked Life Data

16877712

Source:http://linkedlifedata.com/resource/pubmed/id/16877712

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
8
pubmed:dateCreated
2006-7-31
pubmed:abstractText
Hydrophobicity analyses applied to databases of soluble and transmembrane (TM) proteins of known structure were used to resolve total genomic hydrophobicity profiles into (helical) TM sequences and mainly "subhydrophobic" soluble components. This information was used to define a refined "hydrophobicity"-type TM sequence prediction scale that should approach the theoretical limit of accuracy. The refinement procedure involved adjusting scale values to eliminate differences between the average amino acid composition of populations TM and soluble sequences of equal hydrophobicity, a required property of a scale having maximum accuracy. Application of this procedure to different hydrophobicity scales caused them to collapse to essentially a single TM tendency scale. As expected, when different scales were compared, the TM tendency scale was the most accurate at predicting TM sequences. It was especially highly correlated (r = 0.95) to the biological hydrophobicity scale, derived experimentally from the percent TM conformation formed by artificial sequences passing though the translocon. It was also found that resolution of total genomic sequence data into TM and soluble components could be used to define the percent probability that a sequence with a specific hydrophobicity value forms a TM segment. Application of the TM tendency scale to whole genomic data revealed an overlap of TM and soluble sequences in the "semihydrophobic" range. This raises the possibility that a significant number of proteins have sequences that can switch between TM and non-TM states. Such proteins may exist in moonlighting forms having properties very different from those of the predominant conformation.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-10231543, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-10592235, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-10865957, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-10933779, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-11053137, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-11266608, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-11580239, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-11808871, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-11859081, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-12441377, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-12490439, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-12520035, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-12641459, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-14681391, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15111065, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15130854, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15131699, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15236588, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15248770, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-15674282, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-1593632, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-2134053, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-2430611, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-3521657, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-4023714, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-4032478, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-6502707, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-7108955, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-7704669, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-7723011, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-7795533, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-8130217, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-8844859, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-8868045, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-8947574, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9141356, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9169866, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9246628, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9254619, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9278280, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9278503, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9514275, http://linkedlifedata.com/resource/pubmed/commentcorrection/16877712-9769220
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0961-8368
pubmed:author
pubmed:issnType
Print
pubmed:volume
15
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1987-2001
pubmed:dateRevised
2010-11-18
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity.
pubmed:affiliation
Department of Biochemistry and Cell Biology, Stony Brook University, New York 11794-5215, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural