A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains 英文参考文献.docVIP

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A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains 英文参考文献.doc

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A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains 英文参考文献

AGeneralizedAllostericMechanismforcis-Regulated CyclicNucleotideBindingDomains AlexandrP.Kornev1,SusanS.Taylor2,3*,LynnF.TenEyck1,2 1San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America, 2Department of Chemistry and Biochemistry, UniversityofCaliforniaSanDiego,LaJolla,California,UnitedStatesofAmerica,3HowardHughesMedicalInstitute,UniversityofCaliforniaSanDiego,LaJolla,California, UnitedStatesofAmerica Abstract Cyclic nucleotides (cAMP and cGMP) regulate multiple intracellular processes and are thus of a great general interest for molecularandstructuralbiologists.Tostudytheallostericmechanismofdifferentcyclicnucleotidebinding(CNB)domains,we comparedcAMP-boundandcAMP-freestructures(PKA,Epac,andtwoionicchannels)usinganewbioinformaticsmethod:local spatialpatternalignment.Ouranalysishighlightsfourmajorconservedstructuralmotifs:1)thephosphatebindingcassette (PBC),whichbindsthecAMPribose-phosphate,2)the‘‘hinge,’’aflexiblehelix,whichcontactsthePBC,3)theb2,3loop,which providesprecisepositioningofaninvariantargininefromthePBC,and4)aconservedstructuralelementconsistingofanN- terminal helix, aneight residue loop and the A-helix (N3A-motif). The PBC and the hinge were included in the previously reportedallostericmodel,whereasthedefinitionoftheb2,3loopandtheN3A-motifasconservedelementsisnovel.TheN3A- motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolitegeneactivatorprotein(CAP)representsatrans-regulatedCNBdomainfamily:itdoesnotcontaintheN3A-motif,and itslongrangeallostericinteractionsaresubstantiallydifferentfromthecis-regulatedCNBdomains. Citation: Kornev AP, Taylor SS, Ten Eyck LF (2008) A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains. PLoS Comput Biol4(4):e1000056.doi:10.1371/journal.pcbi.1000056 Editor:RamaRanganathan,HHMI/UTSouthwesternMedicalCenter,UnitedStatesofAmerica ReceivedAugust22,2007;Accepte