On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1 英文参考文献.docVIP
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On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1 英文参考文献
OntheOriginsoftheWeakFoldingCooperativityofa
DesignedbbaUltrafastProteinFSD-1
ChunWu1,Joan-EmmaShea1,2*
1Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California, United States of America, 2Department of Physics,
UniversityofCalifornia,SantaBarbara,SantaBarbara,California,UnitedStatesofAmerica
Abstract
FSD-1,adesignedsmallultrafastfolderwithabbafold,hasbeenactivelystudiedinthelastfewyearsasamodelsystemfor
studyingproteinfoldingmechanismsandfortestingoftheaccuracyofcomputationalmodels.Thesuitabilityofthisprotein
todescribethefoldingofnaturallyoccurringa/bproteinshasrecentlybeenchallengedbasedontheobservationthatthe
meltingtransitionisverybroad,withill-resolvedbaselines.UsingmoleculardynamicssimulationswiththeAMBERprotein
forcefield(ff96)coupledwiththeimplicitsolventmodel(IGB=5),weshednewlightintothenatureofthistransitionand
resolvetheexperimentalcontroversies.Weshowthatthemeltingtransitioncorrespondstothemeltingoftheproteinasa
whole,andnotsolelytothehelix-coiltransition.Thebreadthofthefoldingtransitionarisesfromthespreadinthemelting
temperatures (from ,325K to ,302K) of the individual transitions: formation of the hydrophobic core, b-hairpin and
tertiaryfold,withthehelixformedearlier.Oursimulationsinitiatedfromanextendedchainaccuratelypredictthenative
structure,provideareasonableestimateofthetransitionbarrierheight,andexplicitlydemonstratetheexistenceofmultiple
pathwaysandmultipletransitionstatesforfolding.OurexhaustivesamplingenablesustoassessthequalityoftheAmber
ff96/igb5combinationandrevealsthatwhilethisforcefieldcanpredictthecorrectnativefold,itnonethelessoverstabilizes
thea-helixportionoftheprotein(Tm=,387K)aswellasthedenaturedstructures.
Citation:WuC,SheaJ-E(2010)OntheOriginsoftheWeakFoldingCooperativityofaDesignedbbaUltrafastProteinFSD-1.PLoSComputBiol6(11):e1000998.
doi:10.1371/journal.pcbi.1000998
Editor:VictorMun?oz,CentrodeInvestigacionesBiolo′gicas,Spain
ReceivedJune11,2010;AcceptedOctober14,2010;Publi
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