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Protein Structure Analysis

by: Nathanael Schowalter

Protein Structure Analysis BINF 731

Marketplace > George Mason University > BioInformatics > BINF 731 > Protein Structure Analysis
Nathanael Schowalter
GPA 3.64

Iosif Vaisman

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Iosif Vaisman
Class Notes
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This 4 page Class Notes was uploaded by Nathanael Schowalter on Monday September 28, 2015. The Class Notes belongs to BINF 731 at George Mason University taught by Iosif Vaisman in Fall. Since its upload, it has received 69 views. For similar materials see /class/215255/binf-731-george-mason-university in BioInformatics at George Mason University.


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Date Created: 09/28/15
BINF 731 Protein Structure Analysis Iosif Vaisman 2007 Structural classes of proteins Tronomyosln all on SCOP Structural Classi cation of Proteins Current release 1 71 27599 PDB Entries October 2006 75930 Domains httpscop mrclmb cam ac ukscop othe structural and evolutionary relationships between all proteins whose structure is known Proteins are classified to re ect both stru ura an evolutionary relatedness Many levels exist in the hierarchy the principal leve s are family superramily and fo d Family Clear Evalutzmtanly relanmtsth Superfamily Probable rorrtrnnrt evalutzmtary nrigirt Fold Major structural similarity Secondary Structure Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classi cation Protein Structure Classi cation SCOP Structural Classi cation ofProteins FSSP Fold classi cation based on StructureStructure alignment ofProteins CATH class architecture topology and homologous superfamily SCOP Structural Classi cation of Proteins Family Clear evalunmtanly relanmtsth proteins clustered together into families are clearly evolutionarily related Generally this means that pairwise residue identities between the proteins are 30 and greater However in some ofcommon descent in the absense ofhigh sequence identity for example many globins form afamily though some members have sequence identities of only 15 es hutwhnse structural ple a 1n the ATPase dnnnatn ufthe heat shnek nnntetn and exam hExakmase togetha39 form a superfam y SCOP Statistics 212 Fnlrls Super Families families A unhanmtstns 179 48D A11 betapmtzms 125 248 452 mnhanndhetanmtetnstah 121 199 542 mnhanndhetanmtetnsmh 234 349 557 Mmddnnnnnnmtstns 38 38 53 Membranz nndeeu wheenntstnsza an 73 snannmtstns an 95 1511 mu sun 1294 2327 Stmcture processing for DaliFSSP i iiEEiE j mam nan msmm ms SCOP Stmctural Classi cation of Proteins Fnld Major Imcmml xmxltmty Proteins are de ned as having aennnnnnn fuld1ftheyhave the the same fuld u en havepenpheral elements f structure and tum reguns snnne eases these d1ffenng n the stxu Cure pmtetns placed together 1n the same may nnt ave aennnnnnn evn1utdnnany ungm the structural nn11antdes d ansejust 39um the physms and ehenntstny of s end nnntetns favunng cenmnpack mg arrangements and ehatn topologies FSSP Database Cunent release September 211115 3724 sequence fannthes nepnesenttng 311524 pnntetn stxuetunes The FSSP database 15 based un exhaustdve allragzmstrall 31 structure ennn e pmtetn Data Bank 121313 The classi catmn and ahnnnnen ts are autnnnatdeany nnatntatned and ennttnunus1y updated ustng e Dah Search engine Dali Domain Dictiona1y http wwa ebl at ukdahdnnnatn Structural dnnnatns are dehneated automatically ustng the entena ufrecunence and ennnnaetness Eaeh dnnnatn 1s assigned a Dumam Class1 cat1un number DCiliminJ w are 1 e fuld space attracturregmn m e globular folding topology n e funetdnna1 fam1ly n 7 sequence fam1ly Hierarchical clustering of folds in DaliFSSP W n M m mm K0 M mm 5 mm mm mm W i Mi llllizrrt39gcm Adapted rm Hatm and Sander i992 Dali Domain Dictionary lmI ltml Fold types 7 1 39 Fold types are de ned as fr jl 710 clusters of structural i J neighbors in fold space with average pairwise Zscores by Dali above 2 Structural neighbours of lumA top left 1mli bottom right has the same topology even though there are shifts in the relative orientation of secondary structure elements Dali Domain Dictionary Sequence families The fourth level ofthe classi cation is a representative subset of the Protein Data Bank acted using a 25 sequence identi threshold Allagainstall structure comparison was carried out within the set ofrepresentatives Homologues are only shown aligned to their representative Dali Domain Dictionary structural domains Fold space attractor regions delineated automatically wquot 11B 1 using the criteria 0 mean er f recurrence and compactness r i l 43 5 3 all 1 Density distribution ofdomains all p in fold space according to Dali Dali Domain Dictionary Functional families The third level ofthe classi cation infers plausible evolutionary relationships from strong structural similarities which are accompanied by functional or sequence identically conserved functional residues E C numbers Swissprot keywords CATH Protein Structure Classification Current release 3 1 0 January 2007 httpwww biochem ucl ac ukbsmcathinew CATH is a novel hierarchical classi cation ofprotein domain structures which clusters proteins at four major levels lass Architecture Topology Homologous superfamily CATH protein saucth classi cation CATH Protein Structure Classi cation class Celevel m to u c D 9 r classrs determined accordingtuthe secunuarystructure i n no th I mnusrtrun andpack mg wrtlnn e structure lt can be u quotM assigned autumatrcally ams uftheknuwn structures and manually u s Threemajur classes A 39 t r mamlyralpha 39 quot mamlyrbeta mnanst Snn wmh Roll A alpharbeta lphzheta annl alnlnalseta i 39 T V A fuurtln class ls alsu ruentr eu wlucn cuntatns nrutern llnvnaaran a unmatns wlncln have luw secunuary structure cuntent lleuctanasa CATH Protein Structure Classi cation CATH Protein Structure Classi cation Arclntecture Arlevel Tupulugy Fuld family Televel nus uescnlses the uyerall slnane ufthe unmatn structure as Struct es are guuped rntu fuld farnrlres at tlus leyel uetermtneu by the unentatruns ufthe secunuary structures uenenurng un bath the uyerall slnane anu cunnectryrty ufthe butler restne cumecnvltybetweenthe secunuary secunuary structures nus ls uune usmgthe structure structures cumpansun alguntlnm SSAF s currently asslgaed manually using asrmnle uescnntrun e arrangement e g barrel Dr Krlzyer s ference ls maue tn the lrterature fur wellrknuwn arclutectures e g the betarpmp ell Br Br alnlna four hellx bundle Sume fuld families are very hlghlypupulated and are currently subdivided using a lngner cutuff un the SSA scure Procedures are being ueyeluneu fur autumatrng tlus step CATH Protein Structure Classi cation CATH Protein Structure Classi cation llumulaguus Superfamlly Helevel nus leyel groups together nrutern unmatns wlucln are thought Sequence farnrlres Selevel 5 335mm Emma mmmf 3 3 3 res wrtlnn eacn Helevel are further clustereu un as homologous Slmllantles are ruentrtaeu rstby sequence sequence denmy Dumm cluster cumpansuns anu subsequmdy by structure cumpansun using S tlnel the smaller murcatrng Structures are clustered rntu the same homologous hlghly similar structures and functruns superfzmllylfthey satrsfy une ufthe fulluwmg cntena Sequence ruentrty gt 3qu nuns uflarger structure e ulvalenttu smaller SAP scure a u and sequence ruentrty gt nuns uflarger structure equryalenttc smaller M SSAF scure gt an u an uflarger structure equryalent tu smaller and numalns which have related functruns


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