Oligomeric Interfaces Under the Lens Gemini 英文参考文献.docVIP

OligomericInterfacesUndertheLens:Gemini GiovanniFeverati,ClaireLesieur* Laboratoiredephysiquethe′oriqueLAPTH,CNRS,UMR5108associe′ a` l’Universite′ deSavoie,BP110,AnnecyleVieux,France Abstract Theassemblyofsubunitsinproteinoligomersisanimportanttopictostudyasavastnumberofproteinsexistsasstableor transientoligomerandbecauseitisamechanismusedbysomeproteinoligomersforkillingcells(e.g.,perforinfromthe humanimmunesystem,pore-formingtoxinsfrombacteria,phage,amoeba,proteinmisfoldingdiseases,etc.).Onlyafewof the amino acids that constitute a protein oligomer seem to regulate the capacity of the protein to assemble (to form interfaces),andsomeoftheseaminoacidsarelocalizedattheinterfacesthatlinkthedifferentchains.Theidentificationof theresiduesoftheseinterfacesisratherdifficult.Wehavedevelopedaseriesofprograms,underthecommonnameof Gemini,thatcanselectthesubsetoftheresiduesthatisinvolvedintheinterfacesofaproteinoligomerofknownatomic structure, and generate a 2D interaction network (or graph) of the subset. The graphs generated for several oligomers demonstratetheaccuracyoftheselectionofsubsetsthatareinvolvedinthegeometricalandthechemicalpropertiesof interfaces.TheresultsoftheGeminiprogramsareingoodagreementwiththoseofsimilarprogramswithanadvantage thatGeminiprogramscanperformtheresidueselectionmuchmorerapidly.Moreover,Geminiprogramscanalsoperform onasingleproteinoligomerwithouttheneedofcomparisonpartners.Thegraphsareextremelyusefulforcomparative studiesthatwouldhelpinaddressingquestionsnotonlyonthesequencespecificityofproteininterfacesbutalsoonthe mechanismoftheassemblyofunrelatedproteinoligomers. Citation:FeveratiG,LesieurC(2010)OligomericInterfacesUndertheLens:Gemini.PLoSONE5(3):e9897.doi:10.1371/journal.pone.0009897 Editor:MarkusJ.Buehler,MassachusettsInstituteofTechnology,UnitedStatesofAmerica ReceivedAugust11,2009;AcceptedMarch2,2010;PublishedMarch25,2010 Copyright: ?2010 Feverati, Lesieur. Thisisanopen-access article distributedunder theterms oftheCreativeCommons