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1、ProteinScience(1997).6:2538-2547.CambridgeUniversityPress.PrintedintheUSA.Copyright01997TheProteinSocietyLinkersofsecondarystructuresinproteinsV.GEETHAANDP.J.MUNSONAnalyticalBiostatisticsSection,LaboratoryofStructuralBiology.DivisionofComputerResearch&Technology,Bethesda,Maryla
2、nd20892-5626(RECEIVEDMarch12,1997;ACCEPTEDAugust8.1997)AbstractLinkersthatconnectrepeatingsecondarystructuresfallintoconformationalclassesbasedondistanceandmain-chaintorsionclustering.Adatasetof300uniqueproteinchainswithlowpainvisesequenceidentitywasclusteredintoonlyafewgroupsr
3、epresentingthepreferredmotifs.ThelinkersoftwotoeightresiduesforthenonredundantdatasetaredesignatedH-Ln-H,H-Ln-E,E-Ln-H,E-Ln-E,wherenisthelength,Hstandsfora-helices,andEforP-strands.Mostoftheclustersidentifiedherecorroborateearlierfindings.However,19newclustersareidentifiedinthi
4、spaper,withmanyofthemhavingsevenandeightresiduelinkers.Inourfirstanalysis,thesecondarystructuresflankingthelinkersarebothinteractingandnoninteractingandthereisnopreciseangleoforientationbetweenthem.Asecondanalysiswasperformedonasetofproteinswithrestrictedorientationsfortheflank
5、ingelements,namely,mainlyaclassofproteinswithorthogonalarchitecture.Twodefiniteclustersareidentified,onecorrespondingtolinkersoforthogonalhelicesandtheothertolinkersofantiparallelhelices.Loopsformingbindingsitesorinvolvedincatalyticactivityareimportantdeterminantsofthefunctiono
6、fproteins.Althoughthestructuralconservationoftheresiduesaroundthecatalytictriadofserineproteaseshasbeenstudiedwidely,therehasnotbeenasystematicanalysisoftheconformationoftheloopsthatcontainthem.Residuesofthecatalytictriadresideinthelinkersof&strands,withvaryinglengthsofmorethan
7、eightresidues.Here,weanalyzethestructuralconservationofsuchlinkersbysuperposition,andobserveaconservedstructuralfeatureofthelinkersincorporatingeachofthethreeresiduesofthecatalytictriad.Keywords:catalytictriadofserineproteases;clustering;conformationalanalysis;linkers,orthogona
8、lmainlyaproteinsLinkersareloopsconnectingsecondarystru
