An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations 英文参考文献.docVIP

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An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations 英文参考文献.doc

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An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations 英文参考文献

AnAtlasoftheThioredoxinFoldClassRevealsthe ComplexityofFunction-EnablingAdaptations HollyJ.Atkinson1,2,PatriciaC.Babbitt2,3,4 * 1Graduate Program in Biological and Medical Informatics, University of California, San Francisco, California, United States of America, 2Institute for Quantitative Biosciences,UniversityofCalifornia,SanFrancisco,California,UnitedStatesofAmerica,3DepartmentofBioengineeringandTherapeuticSciences,UniversityofCalifornia, SanFrancisco,California,UnitedStatesofAmerica,4DepartmentofPharmaceuticalChemistry,UniversityofCalifornia,SanFrancisco,California,UnitedStatesofAmerica Abstract The group of proteins that contain a thioredoxin (Trx) fold is huge and diverse. Assessment of the variation in catalytic machinery of Trx fold proteins is essential in providing a foundation for understanding their functional diversity and predictingthefunctionofthemanyuncharacterizedmembersoftheclass.TheproteinsoftheTrxfoldclassretaincommon features—includingvariationsonadithiolCxxCactivesitemotif—thatleadtodeliveryoffunction.Weuseproteinsimilarity networkstoguideananalysisofhowstructuralandsequencemotifstrackwithcatalyticfunctionandtaxonomiccategories for4,082representativesequencesspanningtheknownsuperfamiliesoftheTrxfold.Domainstructureinthefoldclassis varied and modular, with 2.8% of sequences containing more than one Trx fold domain. Most member proteins are bacterial. The fold class exhibits many modifications to the CxxC active site motif—only 56.8% of proteins have both cysteines,andnofunctionalgroupingshaveabsoluteconservationoftheexpectedcatalyticmotif.Onlyasmallfractionof Trxfoldsequenceshavebeenfunctionallycharacterized.Thisworkprovidesaglobalviewofthecomplexdistributionof domainsandcatalyticmachinerythroughoutthefoldclass,showingthateachsuperfamilycontainsremnantsoftheCxxC active site. The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relation