Protein analysis and proteomics Friday, 27 January 2006 Introduction to Bioinformatics DA McClellan david_mcclellan@byu.edu
[1] Protein families [2] Physical properties protein [3] Protein localization [4] Protein function Fig. 8.1 Page 224
Perspective 1: Protein families (domains and motifs) Page 225
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 Page 225
15 most common domains (human) Zn finger, C2H2 type 1093 proteins Immunoglobulin 1032 EGF-like 471 Zn-finger, RING 458 Homeobox 417 Pleckstrin-like 405 RNA-binding region RNP-1 400 SH3 394 Calcium-binding EF-hand 392 Fibronectin, type III 300 PDZ/DHR/GLGF 280 Small GTP-binding protein 261 BTB/POZ 236 bHLH 226 Cadherin 226 Table 8-3 Page 227 Source: 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 alone or in conjunction with other domains or repeats. Domains are evolutionarily related. According to SMART (http://smart.embl-heidelberg.de): A domain is a conserved structural entity with distinctive secondary structure content and a hydrophobic core. Homologous domains with common functions usually show sequence similarities. Tables 8-1,8-2 Page 226
Varieties of protein domains Extending along the length of a protein Occupying a subset of a protein sequence Occurring one or more times Fig. 8.2 Page 228
Example of a protein with domains: Methyl CpG binding protein 2 (MeCP2) MBD 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 Rett Syndrome, a neurological disorder affecting girls primarily. Page 227
Result of an MeCP2 blastp search: A methyl-binding domain shared by several proteins Fig. 8.3 Page 228
Are proteins that share only a domain homologous? Fig. 8.3 Page 228
ProDom entry for HIV-1 pol shows many related proteins Fig. 8.7 Page 231
Proteins can have both domains and patterns (motifs) Pattern (several residues) Pattern (several residues) Domain (aspartyl protease) Domain (reverse transcriptase) Fig. 8.7 Page 231
Fig. 8.8 Page 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 and phosphorylation sites. These do not imply homology when 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 protein either matches a pattern, or not). In contrast, a profile is a quantitative motif description. We will encounter profiles in Pfam, ProDom, SMART, and other databases. Page 231-233
Perspective 2: Physical properties of proteins Page 233
Posttranslational modifications: Fig. 8.9 Page 234
Fig. 8.11 Page 235
Fig. 8.11 Page 235
Fig. 8.12 Page 236
Fig. 8.13 Page 238
Fig. 8.13 Page 238
Fig. 8.13 Page 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 Page 237
The Gene Ontology Consortium An ontology is a description of concepts. The GO Consortium compiles a dynamic, controlled vocabulary of terms related to gene products. There are three organizing principles: Molecular function Biological process Cellular compartment You can visit GO at http://www.geneontology.org. There is no centralized GO database. Instead, curators of organism-specific databases assign GO terms to gene products for each organism. Page 237
GO terms are assigned to Entrez Gene entries Fig. 8.14 Page 241
Fig. 8.14 Page 241
Fig. 8.14 Page 241
Fig. 8.14 Page 241
The Gene Ontology Consortium: Evidence Codes IC Inferred by curator IDA Inferred from direct assay IEA Inferred from electronic annotation IEP Inferred from expression pattern IGI Inferred from genetic interaction IMP Inferred from mutant phenotype IPI Inferred from physical interaction ISS Inferred from sequence or structural similarity NAS Non-traceable author statement ND No biological data TAS Traceable author statement Table 8-7 Page 240
Perspective 3: Protein localization Page 242
Protein localization protein Page 242
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 this is essentially a cell biological question. Page 242
PSORT: searches for sorting signals that are characteristic of proteins localized to particular cellular compartments Fig. 8.15 Page 242
Fig. 8.16 Page 244
Fig. 8.16 Page 244
Localization of 2,900 yeast proteins Michael Snyder and colleagues incorporated epitope tags into thousands of S. cerevisiae cDNAs, and systematically localized proteins (Kumar et al., 2002). See http://ygac.med.yale.edu for a database including 2,900 fluorescence micrographs. Page 243
Perspective 4: Protein function Page 243
Protein function Function refers to the role of a protein in the cell. We can consider protein function from a variety of perspectives. Page 243
1. Biochemical function (molecular function) RBP binds retinol, could be a carrier Fig. 8.17 Page 245
2. Functional assignment based on homology RBP could be a carrier too Other carrier proteins Fig. 8.17 Page 245
3. Function based on structure RBP forms a calyx Fig. 8.17 Page 245
4. Function based on ligand binding specificity RBP binds vitamin A Fig. 8.17 Page 245
5. Function based on cellular process DNA RNA RBP is abundant, soluble, secreted Fig. 8.17 Page 245
6. Function based on biological process Analyze a gene knockout phenotype; RBP is essential for vision Fig. 8.17 Page 245
7. Function based on “proteomics” or high throughput “functional genomics” High throughput analyses show... RBP levels elevated in renal failure RBP levels decreased in liver disease Fig. 8.17 Page 245
Functional assignment of enzymes: the EC (Enzyme Commission) system Oxidoreductases 1,003 Transferases 1,076 Hydrolases 1,125 Lyases 356 Isomerases 156 Ligases 126 Table 8-8 Page 246 Updated 9/04, 9/05
Functional assignment of proteins: Clusters of Orthologous Groups (COGs) Information storage and processing Cellular processes Metabolism Poorly characterized Table 8-9 Page 247 See Chapter 14 for COGs at NCBI
