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Biomedical genomics lecture

Bimoedical Genomics 1
Lecture on protein structure investigations with online tools

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Biomedical genomics lecture

  1. 1. Biomedical Genomics 1 - Investigating protein structure using online tools Dr L. Therese Bergendahl Research Fellow Joseph Marsh Lab MRC Human Genetics Unit Medical Research Council Human Genetics Unit MRC Institute of Genetics and Molecular Medicine www.igmm.ac.uk
  2. 2. Me Computational Photochemist
  3. 3. GENOTYPE PHENOTYPE Post transcriptional Post translational DNA RNA Protein Individual Population SEQUENCING Epigenetics
  4. 4. Protein Structure – Ultrafast recap A Linear sequence of amino acids forms a stable 3D structure fold All α - helices All β - strands Combination of the two, either alternating (α/β) or mixed (α+β) Membrane proteins Disordered Proteins Classified by SCOP or CATH Classic examples are the globin fold, immunoglobulin fold, SH2 domain and TIM barrel
  5. 5. Laurents et al., Protein Sci, 1994 3 % RMS difference (Cα) is 1.6 Å Sequence similarity is: Ovomucoid (green) and the C-terminal of the L7/L12 ribosomal protein (red)
  6. 6. Protein Structure Domains are analogous to folds, from the point of view of the full protein – essentially the units of folds that can function independently Proteins interact! With ligands crucial for function As members of transient protein signaling networks As subunits in stable protein complexes
  7. 7. Protein Structure Disordered Proteins are also important, and are overrepresented in signalling networks Lack any recognisable 3D structure either entirely or in parts of the structure. Data. What is it good for? Sequence Folds/ Motifs/ Domains Interaction with other proteins or macromolecules Stability Function Phenotype
  8. 8. Pick a Protein…
  9. 9. My protein: inositol-1,4,5-triphosphate receptor 1 (IP3R1) IGMM crew used exome sequencing and found a set of interesting de-novo mutations in the ITPR1 gene in individuals with Gillespie Syndrome Iris hypoplasia and cerebral volume loss common phenotypes in GS patients
  10. 10. 1, Uniprot My protein: IP3R1
  11. 11. http://www.rcsb.org/
  12. 12. http://www.rcsb.org/
  13. 13. http://genome3d.eu
  14. 14. Domains Homologues and other annotations
  15. 15. http://d2p2.pro
  16. 16. www.predictprotein.org If you don’t want to sign up, use the open version, here: https://ppopen.informatik.tu-muenchen.de
  17. 17. This can take a frustratingly long time for a large protein..
  18. 18. No joke.. Its STILL going…
  19. 19. http://string-db.org
  20. 20. http://genetics.bwh.harvard.edu/pph2/
  21. 21. 206

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