Protein analysis and proteomics Friday, 27 January 2006 Introduction to Bioinformatics
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Transcript of Protein analysis and proteomics Friday, 27 January 2006 Introduction to Bioinformatics
Protein analysis and proteomics
Friday, 27 January 2006
Introduction to Bioinformatics
protein
[1] Protein families
[4] Protein function
[2] Physical properties
[3] Protein localization
Fig. 8.1Page 224
Perspective 1: Protein families
(domains and motifs)
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Definitions
Signature: • a protein category such as a domain or motif
Domain: • 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 domain
Motif (or fingerprint):• a short, conserved region of a protein• typically 10 to 20 contiguous amino acid residues
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15 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 226 Table 8-3
Page 227Source: Integr8 program at www.ebi.ac.uk/proteome/
Definition of a domain
According 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 226
According 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 domains
Fig. 8.2Page 228
Extending along the length of a protein
Occupying a subset of a protein sequence
Occurring one or more times
Example of a protein with domains: Methyl CpG binding protein 2 (MeCP2)
MBD
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TRD
The 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 228
Result of an MeCP2 blastp search:A methyl-binding domain shared by several proteins
Are proteins that share only a domain homologous?
Fig. 8.3Page 228
ProDom entry for HIV-1 pol shows many related proteins
Fig. 8.7Page 231
Proteins can have both domains and patterns (motifs)
Domain(aspartylprotease)
Domain(reversetranscriptase)
Pattern(severalresidues)
Pattern(severalresidues)
Fig. 8.7Page 231
Fig. 8.8Page 232
Definition of a motif
A 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.
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Perspective 2: Physical properties of proteins
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Fig. 8.9Page 234
Posttranslational modifications:
Fig. 8.11Page 235
Fig. 8.11Page 235
Fig. 8.12Page 236
Fig. 8.13Page 238
Fig. 8.13Page 238
Fig. 8.13Page 238
Syntaxin, SNAP-25 and VAMP are three proteins that interact via coiled-coil domains
Introduction to Perspectives 3 and 4: Gene Ontology (GO) Consortium
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The Gene Ontology Consortium
An 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 compartment
You 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.
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GO terms are assigned to Entrez Gene entries
Fig. 8.14Page 241
Fig. 8.14Page 241
Fig. 8.14Page 241
Fig. 8.14Page 241
The Gene Ontology Consortium: Evidence Codes
IC 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 statement
Table 8-7Page 240
Perspective 3: Protein localization
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protein
Protein localization
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Protein localization
Proteins 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.
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Fig. 8.15Page 242
PSORT: searches for sorting signals that are characteristic of proteins localized to particular cellular compartments
Fig. 8.16Page 244
Fig. 8.16Page 244
Localization of 2,900 yeast proteins
Michael 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.
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Perspective 4: Protein function
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Protein function
Function refers to the role of a protein in the cell.We can consider protein function from a varietyof perspectives.
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1. Biochemical function(molecular function)
RBP binds retinol,could be a carrier
Fig. 8.17Page 245
2. Functional assignmentbased on homology
RBPcould bea carrier
too
Othercarrier proteins
Fig. 8.17Page 245
3. Functionbased on structure
RBP forms a calyx
Fig. 8.17Page 245
4. Function based onligand binding specificity
RBP binds vitamin A
Fig. 8.17Page 245
5. Function based oncellular process
DNA RNA
RBP is abundant,soluble, secreted
Fig. 8.17Page 245
6. Function basedon biological process
Analyze a gene knockout phenotype;RBP is essential for vision
Fig. 8.17Page 245
7. Function based on “proteomics”or high throughput “functional genomics”
High throughput analyses show...
RBP levels elevated in renal failureRBP levels decreased in liver disease
Fig. 8.17Page 245
Functional assignment of enzymes:the EC (Enzyme Commission) system
Oxidoreductases 1,003Transferases 1,076Hydrolases 1,125Lyases 356Isomerases 156Ligases 126
Table 8-8Page 246Updated 9/04, 9/05
Functional assignment of proteins:Clusters of Orthologous Groups (COGs)
Information storage and processing
Cellular processes
Metabolism
Poorly characterized
Table 8-9Page 247See Chapter 14 for COGs at NCBI