Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments 英文参考文献.docVIP

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Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments 英文参考文献.doc

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Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments 英文参考文献

AccurateSimulationandDetectionofCoevolution SignalsinMultipleSequenceAlignments SharonH.Ackerman1,ElisabethR.Tillier3,DomenicoL.Gatti1,2* 1DepartmentofBiochemistryandMolecularBiology,WayneStateUniversitySchoolofMedicine,Detroit,Michigan,UnitedStatesofAmerica,2CardiovascularResearch Institute,WayneStateUniversitySchoolofMedicine,Detroit,Michigan,UnitedStatesofAmerica,3DepartmentofMedicalBiophysics,UniversityofToronto,Campbell FamilyInstituteforCancerResearch,OntarioCancerInstitute,UniversityHealthNetwork,Toronto,Ontario,Canada Abstract Background:Whiletheconservedpositionsofamultiplesequencealignment(MSA)areclearlyofinterest,non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizingeffectsatanotherposition.Differentmethodshavebeendevelopedtorecognizetheevolutionaryrelationship betweenaminoacidsites,andtodisentanglefunctional/structuraldependenciesfromhistorical/phylogeneticones. Methodology/PrincipalFindings:Wehaveusedtwocomplementaryapproachestotesttheefficacyofthesemethods.In thefirstapproach,wehaveusedanewprogram,MSAvolve,fortheinsilicoevolutionofMSAs,whichrecordsadetailed historyofallcovaryingpositions,andbuildsaglobalcoevolutionmatrixastheaccumulatedsumofindividualmatricesfor thepositionsforcedtoco-vary,therecombinantcoevolution,andthestochasticcoevolution.Wehavesimulatedover1600 MSAs for 8 protein families, which reflect sequences of different sizes and proteins with widely different functions. The calculatedcoevolutionmatriceswerecomparedwiththecoevolutionmatricesobtainedforthesameevolvedMSAswith differentcoevolutiondetectionmethods.Inasecondapproachwehaveevaluatedthecapacityofthedifferentmethodsto predictclosecontactsintherepresentativeX-raystructuresofanadditional150proteinfamiliesusingonlyexperimental MSAs. Conclusions/Significance: Methods based on the identification of global correlations between pairs were found to be generallysuperiortomethodsbasedonlyonlocalcorrelationsint