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The FREAKS Session 3 .1: Repeats Session 3 .2: Biased regions

The FREAKS Session 3 .1: Repeats Session 3 .2: Biased regions. of PROTEIN SEQUENCE. Miguel Andrade Johannes-Gutenberg University of Mainz A ndrade @uni-mainz.de. Definition. 14% proteins contains repeats (Marcotte et al, 1999) 1: Single amino acid repeats.

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The FREAKS Session 3 .1: Repeats Session 3 .2: Biased regions

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  1. The FREAKS Session 3.1: Repeats Session 3.2: Biased regions of PROTEIN SEQUENCE Miguel Andrade Johannes-Gutenberg University of Mainz Andrade@uni-mainz.de

  2. Definition 14% proteins contains repeats(Marcotte et al, 1999) 1: Single amino acid repeats. 2: Longer imperfect tandem repeats. Assemble in structure.

  3. Definition CBRs Perfectrepeat: QQQQQQQQQQQ Imperfect: QQQQPQQQQQQ Aminoacid type: DDDDDEEEDEDEED Compositionallybiasedregions (CBRs) High frequencyofoneortwoaminoacids in a region. Particularcaseoflowcomplexityregion

  4. Function CBRs Conservation => Function Length, amino acid type not necessarily conserved • Frequency: 1 in 3 proteins contains a compositionally biased region (Wootton, 1994), ~11% conserved (Sim and Creamer, 2004)

  5. Function CBRs Conservation => Function Length, amino acid type not necessarily conserved Functions: Passive: linkers Active: binding, mediate protein interaction, structural integrity (Sim and Creamer, 2004)

  6. Structure of CBRs Often variable or flexible: do not easily crystalize

  7. 1CJF: profilin bound to polyP

  8. 2IF8: Inositol Phosphate Multikinase Ipk2

  9. 2IF8: Inositol Phosphate Multikinase Ipk2 RVSETTTSGSL

  10. 2CX5: mitochondrial cytochrome c B subunit N-terminal

  11. 2CX5: mitochondrial cytochrome c B subunit N-terminal FFFFIFVFNF

  12. Types of CBRs More than 6 aa in length, 1.4% of all, 87% of them in Euk (Faux et al 2005)

  13. Types of CBRs Distribution is not random: Eukaryota: Most common: poly-Q, poly-N, poly-A, poly-S, poly-G Prokaryota: Most common: poly-S, poly-G, poly-A, poly-P Relatively rare: poly-Q, poly-N Very rare or absent in both eukaryota and prokaryota: Poly-I, Poly-M, Poly-W, Poly-C, Poly-Y Toxicity of long stretches of hydrophobic residues. (Faux et al 2005)

  14. Filtering out CBRs Normally filtered out as low complexity region: they give spurious BLAST hits QQQQQQQQQQ |||||||||| QQQQQQQQQQ 10/10 id IDENTITIES |||||||||| IDENTITIES 10/10 id

  15. Filtering out CBRs Normally filtered out as low complexity region: they give spurious BLAST hits QQQQQQQQQQ |||||||||| QQQQQQQQQQ Shuffle: 10/10 id IDENTITIES |||||||||| IDENTITIES 10/10 id

  16. Filtering out CBRs Normally filtered out as low complexity region: they give spurious BLAST hits QQQQQQQQQQ |||||||||| QQQQQQQQQQ Shuffle: 10/10 id IDENTITIES | | SIINDIETTE Shuffle: 2/10 id

  17. Filtering out CBRs Option forpre-BLAST treatment SEG algorithm: 1) Identifysequenceregionswithlowinformationcontentover a sequencewindow 2) Mergeneighbouringregions Eliminateshits against common acidic-, basic- or proline-rich regions (Wootton and Federhen, 1993)

  18. Exercise 1. Filtering CBRs for BLAST using SEG • Obtain this protein sequence from NCBI. This is a hypothetical protein from Nematocida sp., a microsporidia (spore-forming fungi) that infects the worm Caenorhabditiselegans. • Can you see funny things in this sequence? • Go to the NCBI's BLAST web page and go to the "protein blast" option • Search for homologs of the protein • Keep the output • Do the same search in another NCBI's BLAST window selecting the filter low complexity regions using SEG option • Compare the outputs: Can you identify different hits? Do matches to the same sequence have relevant differences in the E-value? Comment on the relevance of the differences.

  19. A particular analysis… AIR9 (1708 aa) Ser rich + basic conserved region LRR A9 repeats Δ1 Δ3 Δ2 Δ15 Δ9 Δ10 Δ6 Δ11 • Buschmann, et al (2006). • Current Biology. Buschmann, et al (2007). Plant Signaling & Behavior Δ12 Δ14 Δ16 Microtubule localization of Δx-GFP

  20. …triggers a tool

  21. http://sourceforge.net/projects/biasviz/ Huska, et al. (2007). Bioinformatics A particular analysis… …triggers BiasViz

  22. A particular analysis… …triggers BiasViz http://sourceforge.net/projects/biasviz/ Huska, et al. (2007). Bioinformatics

  23. ADAM15

  24. Binds SH3 of endophilin and SH3 PX1 PMID:10531379 Binds SH3 of endophilinI and SH3 PX1 PMID:10531379 Binds SH3 of Fish PMID:12615925 Binds SH3 of Grb2 PMID:11127814 Binds SH3 of Fish PMID:12615925 Binds SH3 of Fish PMID:12615925 Binds SH3 of ArgBP1/ABI2 PMID:12463424

  25. 0.4 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.2 0.2 0.2 0.2 0.1 0.1 0.1 0.1 0.0 0.0 0.0 0.0 a b ADAM19 ADAM11 ADAM20 ADAM9 c

  26. Exercise 2. Viewing CBRs in an alignment with BiasViz2 • Go to the BiasViz2 web page • Launch BiasViz2 • Load this alignment on the step 1 section • Hit the "Go to graphical view" button • Try to find combinations of parameters that reveal CBRs • Try hydrophobic residues and window size 10. If I tell you this is a transmembrane protein, what is this result telling you? • Can you see other biased regions?

  27. Martin Schaefer Function of polyQ polyQ in Huntingtin Human Dog Mouse Opossum Chicken Frog Zebrafish Trout Fugu Stickleback Lancelet Capitella Limpet Nematostella Trichoplax Cionaintestinalis Cionasavignyi D. melanogaster D. mojavensis D. sechellia D. erecta D. yakuba D. grimshawi D. pseudoobscura D. persimilis D. ananassae D. willistoni D. virilis Schaefer et al (2012) NucleicAcids Res.

  28. human 1 5 10 50 100 500 1000 partners polyQ TFs long non polyQ

  29. human yeast 1 5 10 50 100 500 1000 1 5 10 50 100 500 1000 partners polyQ TFs long non polyQ polyQ TFs long non polyQ 1 5 10 50 100 500 1000 1 2 5 10 20 50 100 200 500 partners polyQ >14 polyQ 4-14 no polyQ polyQ >14 polyQ 4-14 no polyQ

  30. polyQprotein unbound N-terminal coiled coil polyQ disordered polyP C-terminal

  31. polyQprotein bound protein X polyQprotein unbound N-terminal coiled coil polyQ coiled coil polyQ polyP disordered polyP C-terminal

  32. ATXN1Q82NT is toxic ATXN1Q82NT aggregates Spyros Petrakis Petrakis et al (2012) PLoS Genetics

  33. interactors that change ATXN1Q82NT toxicity

  34. Normal polyQ protein CC polyQ disordered CC partner

  35. Normal polyQ protein CC polyQ disordered CC partner

  36. Normal polyQ protein CC polyQ disordered CC partner polyQ alpha-helix non-CC partner

  37. Normal polyQ protein Toxic polyQ protein CC polyQ disordered CC partner polyQ alpha-helix non-CC partner

  38. Normal polyQ protein Toxic polyQ protein CC polyQ disordered CC partner polyQ alpha-helix non-CC partner

  39. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix non-CC partner

  40. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ beta-aggregates non-CC partner

  41. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ beta-aggregates non-CC partner

  42. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ increased beta-aggregates non-CC partner

  43. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ increased beta-aggregates non-CC partner

  44. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ increased beta-aggregates non-CC partner

  45. Normal polyQ protein Toxic polyQ protein CC polyQ polyQ beta-aggregates disordered CC partner polyQ alpha-helix polyQ increased beta-aggregates non-CC partner

  46. BiasViz2

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