Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Slide 47Slide 48Slide 49Protein analysis and proteomicsFriday, 27 January 2006Introduction to BioinformaticsDA [email protected][1] Protein families[4] Protein function[2] Physical properties[3] Protein localizationFig. 8.1Page 224Perspective 1: Protein families(domains and motifs)Page 225DefinitionsSignature: •a protein category such as a domain or motifDomain: •a region of a protein that can adopt a 3D structure•a characteristic fold or functional region•a family (superfamily) is a group of proteins that share a domain•examples: zinc finger domain immunoglobulin domainMotif (or fingerprint):•a short, conserved region of a protein•typically 10 to 20 contiguous amino acid residuesPage 22515 most common domains (human)Zn finger, C2H2 type 1093 proteinsImmunoglobulin 1032EGF-like 471Zn-finger, RING 458Homeobox 417Pleckstrin-like 405RNA-binding region RNP-1400SH3 394Calcium-binding EF-hand 392Fibronectin, type III 300PDZ/DHR/GLGF 280Small GTP-binding protein 261BTB/POZ 236bHLH 226Cadherin 226Table 8-3Page 227Source: Integr8 program at www.ebi.ac.uk/proteome/Definition of a domainAccording to InterPro at EBI (http://www.ebi.ac.uk/interpro/):A domain is an independent structural unit, found aloneor in conjunction with other domains or repeats.Domains are evolutionarily related. Tables 8-1,8-2Page 226According to SMART (http://smart.embl-heidelberg.de):A domain is a conserved structural entity with distinctivesecondary structure content and a hydrophobic core.Homologous domains with common functions usuallyshow sequence similarities.Varieties of protein domainsFig. 8.2Page 228Extending along the length of a proteinOccupying a subset of a protein sequenceOccurring one or more timesExample of a protein with domains: Methyl CpG binding protein 2 (MeCP2)MBDPage 227TRDThe protein includes a methylated DNA binding domain(MBD) and a transcriptional repression domain (TRD).MeCP2 is a transcriptional repressor.Mutations in the gene encoding MeCP2 cause RettSyndrome, a neurological disorder affecting girls primarily.Fig. 8.3Page 228Result of an MeCP2 blastp search:A methyl-binding domain shared by several proteinsAre proteins that share only a domain homologous?Fig. 8.3Page 228ProDom entry for HIV-1 pol shows many related proteinsFig. 8.7Page 231Proteins can have both domains and patterns (motifs)Domain(aspartylprotease)Domain(reversetranscriptase)Pattern(severalresidues)Pattern(severalresidues)Fig. 8.7Page 231Fig. 8.8Page 232Definition of a motifA motif (or fingerprint) is a short, conserved region of a protein. Its size is often 10 to 20 amino acids.Simple motifs include transmembrane domains andphosphorylation sites. These do not imply homologywhen found in a group of proteins.PROSITE (www.expasy.org/prosite) is a dictionary of motifs (there are currently >1300 entries)(9/05). In PROSITE,a pattern is a qualitative motif description (a proteineither matches a pattern, or not). In contrast, a profileis a quantitative motif description. We will encounterprofiles in Pfam, ProDom, SMART, and other databases.Page 231-233Perspective 2: Physical properties of proteinsPage 233Fig. 8.9Page 234Posttranslational modifications:Fig. 8.11Page 235Fig. 8.11Page 235Fig. 8.12Page 236Fig. 8.13Page 238Fig. 8.13Page 238Fig. 8.13Page 238Syntaxin, SNAP-25 and VAMP are three proteins that interact via coiled-coil domainsIntroduction to Perspectives 3 and 4: Gene Ontology (GO) ConsortiumPage 237The Gene Ontology ConsortiumAn ontology is a description of concepts. The GOConsortium compiles a dynamic, controlled vocabularyof terms related to gene products. There are three organizing principles: Molecular functionBiological processCellular compartmentYou can visit GO at http://www.geneontology.org.There is no centralized GO database. Instead, curatorsof organism-specific databases assign GO termsto gene products for each organism.Page 237GO terms are assigned to Entrez Gene entriesFig. 8.14Page 241Fig. 8.14Page 241Fig. 8.14Page 241Fig. 8.14Page 241The Gene Ontology Consortium: Evidence CodesIC Inferred by curatorIDA Inferred from direct assayIEA Inferred from electronic annotationIEP Inferred from expression patternIGI Inferred from genetic interactionIMP Inferred from mutant phenotypeIPI Inferred from physical interactionISS Inferred from sequence or structural similarityNAS Non-traceable author statementND No biological dataTAS Traceable author statementTable 8-7Page 240Perspective 3: Protein localizationPage 242proteinProtein localizationPage 242Protein localizationProteins may be localized to intracellular compartments,cytosol, the plasma membrane, or they may be secreted. Many proteins shuttle between multiple compartments. A variety of algorithms predict localization, but thisis essentially a cell biological question. Page 242Fig. 8.15Page 242PSORT: searches for sorting signals that are characteristic of proteins localized to particular cellular compartmentsFig. 8.16Page 244Fig. 8.16Page 244Localization of 2,900 yeast proteinsMichael Snyder and colleagues incorporated epitopetags into thousands of S. cerevisiae cDNAs,and systematically localized proteins (Kumar et al., 2002).See http://ygac.med.yale.edu for a database including2,900 fluorescence micrographs.Page 243Perspective 4: Protein functionPage 243Protein functionFunction refers to the role of a protein in the cell.We can consider protein function from a varietyof perspectives. Page 2431. Biochemical function(molecular function)RBP binds retinol,could be a carrierFig. 8.17Page 2452. Functional assignmentbased on homologyRBPcould bea carriertooOthercarrier proteinsFig. 8.17Page 2453. Functionbased on structureRBP forms a calyxFig. 8.17Page 2454. Function based onligand binding specificityRBP binds vitamin AFig. 8.17Page 2455. Function based oncellular processDNA RNARBP is abundant,soluble, secretedFig. 8.17Page 2456. Function basedon biological processAnalyze a gene knockout phenotype;RBP is essential for visionFig. 8.17Page 2457. Function based on “proteomics”or high throughput “functional genomics”High throughput analyses show...RBP levels elevated in renal