Analysis of Domain-Swapped Oligomers Reveals Local Sequence Preferences and Structural Imprints at the Linker Regions and Swapped Interfaces 英文参考文献.docVIP

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Analysis of Domain-Swapped Oligomers Reveals Local Sequence Preferences and Structural Imprints at the Linker Regions and Swapped Interfaces 英文参考文献.doc

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Analysis of Domain-Swapped Oligomers Reveals Local Sequence Preferences and Structural Imprints at the Linker Regions and Swapped Interfaces 英文参考文献

AnalysisofDomain-SwappedOligomersRevealsLocal SequencePreferencesandStructuralImprintsatthe LinkerRegionsandSwappedInterfaces PrashantShingate,R.Sowdhamini* NationalCentreforBiologicalSciences,UAS-GKVKCampus,Bangalore,India Abstract Background: 3D domain swapping is an oligomerization process in which structural elements get exchanged between subunits.Thismechanismgraspedinterestofmanyresearchersduetoitsassociationwithneurodegenerativediseaseslike Alzheimer’s disease, spongiform encephalopathy etc. Despite the biomedical relevance, very little is known about understanding this mechanism. The quest for rulingprinciples behindthis curious phenomenonthat could enable early predictionprovidedanimpetusforourbioinformaticsstudies. Methodology:Anovelmethod,HIDE,hasbeendevelopedtofindnon-domain-swappedhomologuesandtoidentifyhinge fromdomain-swappedoligomers.Non-domain-swappedhomologueswereidentifiedfromtheproteinstructuraldatabank for majority of the domain-swapped entries and hinge boundaries could be recognised automatically by means of successivesuperpositiontechniques.Differentsequenceandstructuralfeaturesindomain-swappedproteinsandrelated proteinshavealsobeenanalysed. Conclusions:TheHIDEalgorithmwasabletoidentifyhingeregionin83%cases.Sequenceandstructuralanalysesofhinge andinterfacesrevealaminoacidpreferencesandspecificconformationsofresiduesathingeregions,whilecomparingthe domain-swappedandnon-domain-swappedstates.Interactionsdiffersignificantlybetweenregulardimericinterfacesand interfaceformedatthesite ofdomain-swappedexamples. Suchpreferences ofresidues, conformationsandinteractions couldbeofpredictivevalue. Citation:ShingateP,SowdhaminiR(2012)AnalysisofDomain-SwappedOligomersRevealsLocalSequencePreferencesandStructuralImprintsattheLinker RegionsandSwappedInterfaces.PLoSONE7(7):e39305.doi:10.1371/journal.pone.0039305 Editor:BinXue,Uni.ofSouthFlorida,UnitedStatesofAmerica ReceivedFebruary2,2012;AcceptedMay17,2012;PublishedJuly27,2012 Copyright: ? 2012 Shingate, So