Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria 英文参考文献.docVIP

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Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria 英文参考文献.doc

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Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria 英文参考文献

PatternofAminoAcidSubstitutionsinTransmembrane Domainsofb-BarrelMembraneProteinsforDetecting RemoteHomologsinBacteriaandMitochondria DavidJimenez-Morales,JieLiang* DepartmentofBioengineering,UniversityofIllinoisatChicago,Chicago,Illinois,UnitedStatesofAmerica Abstract b-barrelmembraneproteinsplayanimportantroleincontrollingtheexchangeandtransportofionsandorganicmolecules across bacterial and mitochondrial outer membranes. They are also major regulators of apoptosis and are important determinants of bacterial virulence. In contrast to a-helical membrane proteins, their evolutionary pattern of residue substitutionshasnotbeenquantified,andtherearenoscoringmatricesappropriatefortheirdetectionthroughsequence alignment. Using a Bayesian Monte Carlo estimator, we have calculated the instantaneous substitution rates of transmembrane domains of bacterial b-barrel membrane proteins. The scoring matrices constructed from the estimated rates,calledbbTMforb-barrelTransmembraneMatrices,improvesignificantlythesensitivityindetectinghomologsofb- barrelmembraneproteins,whileavoidingerroneousselectionofbothsolubleproteinsandothermembraneproteinsof similar composition. The estimated evolutionary patterns are general and can detect b-barrel membrane proteins very remotefromthoseusedforsubstitutionrateestimation.Furthermore,despitetheseparationof2–3billionyearssincethe proto-mitochondrionenteredtheproto-eukaryoticcell,mitochondriaoutermembraneproteinsineukaryotescanalsobe detectedaccuratelyusingthesescoringmatricesderivedfrombacteria.Thisisconsistentwiththesuggestionthatthereis noeukaryote-specificsignalsfortranslocation.Withthesematrices,remotehomologsofb-barrelmembraneproteinswith knownstructurescanbereliablydetectedatgenomescale,allowingconstructionofhighqualitystructuralmodelsoftheir transmembrane domains, at the rate of 131 structures per template protein. The scoring matrices will be useful for identification, classification, and functional inference of membrane proteins from ge