1. http://creativecommons.org/licens es/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. Inferring function from sequence Your Sequence Protein Sequence Database No Known Homologues in the Database or homologues of unknown function Oh, $#!¥!!! Go to the Protein Databank to get structure & Live happily ever after

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

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

6. How to predict protein hidrophobicity

7. How to predict molecular mass Ala Molecular Mass: 71.09 Cys 71.09+103.15-18 -H 2 O

8. How to predict isoelectric point Ala Isoelectric Point: Cys… -9.3… pH Protein Charge 0 0 16 - + ~10 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 At each value of pH, calculate the state of hydrogenation of each residue and thus the charge of the whole protein

9. Analyzing the information in the protein sequence Physical-Chemical Information e.g. http://prowl.rockefeller.edu/prowl- cgi/sequence.exe/.fsahttp://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/loc alizationLinks.html http://seq.cbrc.jp/proteinLocalizationResources/loc alizationLinks.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? Signal Peptides Nuclear localization signals at the N- terminal Mitochondrial TS Peroxysomal TS … Search for homology to the relevant TS in your protein Drawbacks: Sometimes no signal peptide Small sequences, divergence, change between organisms

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

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