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http://creativecommons.org/licenses/by-sa/2.0/. From Protein Sequence to Protein Properties. Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course: http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/

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  1. http://creativecommons.org/licenses/by-sa/2.0/

  2. From Protein Sequence to Protein Properties Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/

  3. Protein Sequence Database Inferring function from sequence • No Known Homologues in the Database or homologues of unknown function • Oh, $#!¥!!! • Go to the Protein Databank to get structure • & • Live happily ever after Your Sequence

  4. Analyzing the information in the protein sequence • Physical-Chemical Information • Localization of the Protein

  5. Analyzing the physical chemical information in the protein sequence Why are these properties useful? For example, they help identifying your protein in an electrophoresis gel

  6. How to predict protein hidrophobicity

  7. How to predict molecular mass Ala Cys -H2O Molecular Mass: 71.09 71.09+103.15-18

  8. + Protein Charge 0 - 0 16 pH How to predict isoelectric point At each value of pH, calculate the state of hydrogenation of each residue and thus the charge of the whole protein Amino acid pKa is dependent upon environment Buried amino acids do not gain/loose protons as easily as exposed amino acids … Does not work very well Isoelectric point is the pH at which the protein is not charged Ala Cys … ~10 Isoelectric Point: - 9.3 …

  9. Analyzing the information in the protein sequence • Physical-Chemical Information • e.g. http://prowl.rockefeller.edu/prowl-cgi/sequence.exe/.fsa • http://www.expasy.org/tools/ • Localization, modifications & secondary structure Information • E.g. http://seq.cbrc.jp/proteinLocalizationResources/localizationLinks.html • http://www.expasy.org/tools/

  10. Why are localization, secondary structure and modifications important? • Localization tells you where you protein acts • A nuclear protein can not be a membrane receptor • Structure tells you how the protein is assembled • Comparison with other proteins that have similar structure may shed light into the function • Modifications are often important to protein activity • Phosphorylation changes the activity of proteins

  11. Predicting the localization or secondary structure of your protein

  12. How is the localization of a protein predicted? • Search for homology to the relevant TS in your protein • Drawbacks: • Sometimes no signal peptide • Small sequences, divergence, change between organisms • Signal Peptides • Nuclear localization signals at the N-terminal • Mitochondrial TS • Peroxysomal TS • …

  13. 17 aa residues How are transmembrane regions predicted? • Transmembrane segments are 17 residues long Hydrophobic Hydrophobic Two Transmembrane helices

  14. How is membrane orientation predicted? Signal Peptide NH Outside HN- Cytosol NH 15 aa 15 aa +++ --- 17 aa

  15. Predicting transmembrane helices

  16. Protein Modification: Phosphorylation • Phosphorylation is a highly effective means of regulating the activity of target proteins. • ~ 30% eukaryotic proteins are phosphorylated. • Protein kinases: The enzymes that catalyze phosphorylation reactions. one of the largest protein families • ~ 100 in yeast • ~ 500 in human beings • Kinases: specificity • Ser/Thr kinases: acceptor is -OH of Ser or Thr • Tyr kinases: acceptor is -OH of Tyr • Tyr kinases are unique to multicellular organisms, important in growth regulation. Tyr kinase mutations often occur in cancer cells

  17. Protein Modification: Methylation Important for example in modifying histones and silencing genes

  18. Protein Modification: Acetylation Important for example in modifying histones and preventing methylation that leads to the silencing of genes

  19. Protein Modification: Ubiquitination Important in marking proteins for destruction

  20. Protein Modification: Hydroxilation Important for example in regulating the elasticity of your skin and the activity of Adiponectin (reduces insulin tolerance)

  21. Protein Modification: Glycosylation • Adding sugars is a highly effective means of regulating the activity of proteins and of targeting them to specific compartments. • Important in cell wall biosynthesis • Important for anchoring to membranes • Important for folding • http://en.wikipedia.org/wiki/Glycosylation

  22. Predicting post translational modifications to your protein

  23. How are post translational modifications to a protein predicted? • Signal sequences or content • Search for homology to pattern peptides

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