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Classication of α-Helical Membrane Proteins Using Predicted Helix Architectures.doc

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Classication of α-Helical Membrane Proteins Using Predicted Helix Architectures

Classificationofa-HelicalMembraneProteinsUsing PredictedHelixArchitectures SindyNeumann1,AngelikaFuchs2,BarbaraHummel3,DmitrijFrishman1,4* 1DepartmentofGenomeOrientedBioinformatics,TechnischeUniversita¨tMu¨nchen,WissenschaftszentrumWeihenstephan,Freising,Germany,2pRED,PharmaResearch andEarlyDevelopment,pREDInformatics,RocheDiagnosticsGmbH,Penzberg,Germany,3DepartmentofUrology/Women’sHospitalandCenterforClinicalResearch, University of Freiburg Medical Center, Freiburg, Germany, 4Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of BioinformaticsandSystemsBiology,Neuherberg,Germany Abstract Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural classification approach for a-helical membrane proteins is introduced based on the similarity of predicted helix interaction patterns. Its application to proteins with known 3D structureshowedthatitisabletoreliablydetectstructurallysimilarproteinsevenintheabsenceofanysequencesimilarity, reproducing the SCOP and CATH classifications with a sensitivity of 65% at a specificity of 90%. We applied the new approach to enhance our comprehensive structural classification of a-helical membrane proteins (CAMPS), which is primarilybasedonsequenceandtopologysimilarity,inordertofindproteinclustersthatdescribethesamefoldinthe absence of sequence similarity. The total of 151 helix architectures were delineated for proteins with more than four transmembranesegments.Interestingly,weobservedthatproteinswith8andmoretransmembranehelicescorrespondto fewer different architectures than proteins with up to 7 helices, suggesting that in large membrane proteins the evolutionarytendencytore-usealreadyavailablefoldsismorepronounced. Citation:NeumannS,FuchsA,HummelB,Frishman