Optimized Null Model for Protein Structure Networks 英文参考文献.docVIP

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Optimized Null Model for Protein Structure Networks 英文参考文献.doc

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Optimized Null Model for Protein Structure Networks 英文参考文献

OptimizedNullModelforProteinStructureNetworks TijanaMilenkovic′1.,IoannisFilippis2.,MichaelLappe2,Natasˇa Przˇulj1* 1Department of Computer Science, University of California Irvine, Irvine, California, United States of America, 2Max Planck Institute for Molecular Genetics, Berlin, Germany Abstract Much attention has recently been given to the statistical significance of topological features observed in biological networks.Here,weconsiderresidueinteractiongraphs(RIGs)asnetworkrepresentationsofproteinstructureswithresidues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purposeinbiomolecularnetworks.However,suchasinglesummarystatisticofanetworkmaynotbedetailedenoughto capturethecomplextopologicalcharacteristicsofproteinstructuresandtheirnetworkcounterparts.Here,weinvestigatea variety of topological properties of RIGs tofind a wellfitting network nullmodel for them. The RIGs arederived froma structurallydiverseproteindatasetatvariousdistancecut-offsandfordifferentgroupsofinteractingatoms.Wecompare thenetworkstructureofRIGstoseveralrandomgraphmodels.Weshowthat3-dimensionalgeometricrandomgraphs,that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strengthofthefitandvariousproteinstructuralfeatures.Weshowthatthefitdependsonproteinsize,structuralclass,and thermostability,butnotonquaternarystructure.Weapplyourmodeltotheidentificationofsignificantlyover-represented structuralbuildingblocks,i.e.,networkmotifs,inproteinstructurenetworks.Asexpected,choosinggeometricgraphsasa nullmodelresultsinthemostspecificidentificationofmotifs.Ourgeometricrandomgraphmodelmayfacilitatefurther graph-basedstudiesofproteinconformationspaceandhaveimportantimplicationsforproteinstructurecomparisonand prediction.Thechoiceofawell-fittingnullmodeliscrucialforfindingstructuralmotifsthatplayanimportantroleinprotein folding,stabilityandfunction.Toourknowledge,t