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1、ProteinScience(1997).6:2538-2547.CambridgeUniversityPress.PrintedintheUSA.Copyright01997TheProteinSocietyLinkersofsecondarystructuresinproteinsV.GEETHAANDP.J.MUNSONAnalyticalBiostatisticsSection,LaboratoryofStructuralBiology.DivisionofComputerResearch&Technology,Bethesda,Maryland20892-5626(REC
2、EIVEDMarch12,1997;ACCEPTEDAugust8.1997)AbstractLinkersthatconnectrepeatingsecondarystructuresfallintoconformationalclassesbasedondistanceandmain-chaintorsionclustering.Adatasetof300uniqueproteinchainswithlowpainvisesequenceidentitywasclusteredintoonlyafewgroupsrepresentingthepreferredmotifs.Th
3、elinkersoftwotoeightresiduesforthenonredundantdatasetaredesignatedH-Ln-H,H-Ln-E,E-Ln-H,E-Ln-E,wherenisthelength,Hstandsfora-helices,andEforP-strands.Mostoftheclustersidentifiedherecorroborateearlierfindings.However,19newclustersareidentifiedinthispaper,withmanyofthemhavingsevenandeightresiduel
4、inkers.Inourfirstanalysis,thesecondarystructuresflankingthelinkersarebothinteractingandnoninteractingandthereisnopreciseangleoforientationbetweenthem.Asecondanalysiswasperformedonasetofproteinswithrestrictedorientationsfortheflankingelements,namely,mainlyaclassofproteinswithorthogonalarchitect
5、ure.Twodefiniteclustersareidentified,onecorrespondingtolinkersoforthogonalhelicesandtheothertolinkersofantiparallelhelices.Loopsformingbindingsitesorinvolvedincatalyticactivityareimportantdeterminantsofthefunctionofproteins.Althoughthestructuralconservationoftheresiduesaroundthecatalytictriado
6、fserineproteaseshasbeenstudiedwidely,therehasnotbeenasystematicanalysisoftheconformationoftheloopsthatcontainthem.Residuesofthecatalytictriadresideinthelinkersof&strands,withvaryinglengthsofmorethaneightresidues.Here,weanalyzethestructuralconservationofsuchlinkersbysuperposition,andobserveacon
7、servedstructuralfeatureofthelinkersincorporatingeachofthethreeresiduesofthecatalytictriad.Keywords:catalytictriadofserineproteases;clustering;conformationalanalysis;linkers,orthogonalmainlyaproteinsLinkersareloopsconnectingsecondarystru
