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Article: Protein flexibility and intrinsic disorder

TitleProtein flexibility and intrinsic disorder
Authors
KeywordsTemperature factor
Natively unfolded
Intrinsically unstructured
Flexibility prediction
Issue Date2004
PublisherCold Spring Harbor Laboratory Press, Publications Department. The Journal's web site is located at http://www.proteinscience.org/
Citation
Protein Science, 2004, v. 13 n. 1, p. 71-80 How to Cite?
AbstractComparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high B-factors. This predictor achieved an accuracy of 70% and a correlation of 0.43 with experimental data, outperforming the 64% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.
Persistent Identifierhttp://hdl.handle.net/10722/48984
ISSN
2015 Impact Factor: 3.039
2015 SCImago Journal Rankings: 2.029
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorRadivojac, Pen_HK
dc.contributor.authorObradovic, Zen_HK
dc.contributor.authorSmith, DKen_HK
dc.contributor.authorZhu, Gen_HK
dc.contributor.authorVucetic, Sen_HK
dc.contributor.authorBrown, CJen_HK
dc.contributor.authorLawson, JDen_HK
dc.contributor.authorDunker, AKen_HK
dc.date.accessioned2008-06-12T06:31:22Z-
dc.date.available2008-06-12T06:31:22Z-
dc.date.issued2004en_HK
dc.identifier.citationProtein Science, 2004, v. 13 n. 1, p. 71-80en_HK
dc.identifier.issn0961-8368en_HK
dc.identifier.urihttp://hdl.handle.net/10722/48984-
dc.description.abstractComparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high B-factors. This predictor achieved an accuracy of 70% and a correlation of 0.43 with experimental data, outperforming the 64% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.en_HK
dc.format.extent388 bytes-
dc.format.mimetypetext/html-
dc.languageengen_HK
dc.publisherCold Spring Harbor Laboratory Press, Publications Department. The Journal's web site is located at http://www.proteinscience.org/en_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectTemperature factoren_HK
dc.subjectNatively unfoldeden_HK
dc.subjectIntrinsically unstructureden_HK
dc.subjectFlexibility predictionen_HK
dc.titleProtein flexibility and intrinsic disorderen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0961-8368&volume=13&issue=1&spage=71&epage=80&date=2004&atitle=Protein+flexibility+and+intrinsic+disorderen_HK
dc.identifier.emailSmith, DK: dsmith@hkucc.hku.hken_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1110/ps.03128904en_HK
dc.identifier.pmid14691223-
dc.identifier.pmcidPMC2286519en_HK
dc.identifier.scopuseid_2-s2.0-0347364621-
dc.identifier.hkuros85334-
dc.identifier.isiWOS:000187587700008-
dc.identifier.citeulike768220-

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