Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship 英文参考文献.docVIP
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Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship 英文参考文献
AssignmentofPolyProlineIIConformationandAnalysis
ofSequence–StructureRelationship
YohannMansiaux1,2,3.,AgnelPraveenJoseph1,2,3.,Jean-ChristopheGelly1,2,3,AlexandreG.de
Brevern1,2,3
*
1INSERM,UMR-S665,DynamiquedesStructuresetInteractionsdesMacromole′culesBiologiques(DSIMB),Paris,France,2Universite′ ParisDiderot-Paris7,Paris,France,
3InstitutNationaldelaTransfusionSanguine(INTS),Paris,France
Abstract
Background:Secondarystructuresareelementsofgreatimportanceinstructuralbiology,biochemistryandbioinformatics.
Theyarebroadly composedoftworepetitivestructures namely a-helicesandb-sheets, apartfromturns, andtherestis
associatedtocoil.Theserepetitivesecondarystructureshavespecificandconservedbiophysicalandgeometricproperties.
PolyProlineII(PPII)helixisyetanotherinterestingrepetitivestructurewhichislessfrequentandnotusuallyassociatedwith
stabilizing interactions. Recent studies have shown that PPII frequency is higher thanexpected, andthey could have an
importantroleinprotein–proteininteractions.
Methodology/PrincipalFindings:AmajorfactorthatlimitsthestudyofPPIIisthatitsassignmentcannotbecarriedout
withthemostcommonlyusedsecondarystructureassignmentmethods(SSAMs).Thepurposeofthisworkistoproposea
PPIIassignmentmethodologythatcanbedefinedintheframeofDSSPsecondarystructureassignment.Consideringthe
ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most
consensualruleofPPIIassignment,threeSSAMsthatcanassignPPII,werecomparedandanalyzed.Theassignmentrule
wasdefinedtohaveamaximumcoverageofallassignmentsmadebytheseSSAMs.Notmanyconstraintswereaddedto
theassignmentandonlyPPIIhelicesofatleast2residueslengtharedefined.
Conclusions/Significance: The simple rules designed in this study for characterizing PPII conformation, lead to the
assignment of 5% of all amino as PPII. Sequence – structure relationships associated with PPII, defined by the different
SSAMs, underline few striking differences. A specific study of
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