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Jan 13, 2016
http://creativecommons.org/licenses/by-sa/2.0/
From Protein Sequence to Protein Properties
Prof:Rui [email protected]
973702406Dept Ciencies Mediques Basiques,
1st Floor, Room 1.08Website of the
Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/
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
Analyzing the information in the protein sequence
• Physical-Chemical Information
• Localization of the Protein
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
How to predict protein hidrophobicity
How to predict molecular mass
Ala
Molecular Mass: 71.09
Cys
71.09+103.15-18
-H2O
How to predict isoelectric point
Ala
Isoelectric Point:
Cys …
- 9.3 … pH
Pro
tein
Cha
rge
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
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/
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
Predicting the localization or secondary structure of your protein
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
How are transmembrane regions predicted?
• Transmembrane segments are 17 residues long
17 aa residues
Hydrophobic Hydrophobic
Two Transmembrane helices
How is membrane orientation predicted?
HN-
Outside
Cytosol
NH
NH
Signal Peptide
17 aa
15 aa 15 aa
+++ ---
Predicting transmembrane helices
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
Protein Modification: Methylation
Important for example in modifying histones and silencing genes
Protein Modification: Acetylation
Important for example in modifying histones and preventing methylation that leads to the silencing of genes
Protein Modification: Ubiquitination
Important in marking proteins for destruction
Protein Modification: Hydroxilation
Important for example in regulating the elasticity of your skin and the activity of Adiponectin (reduces insulin tolerance)
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
Predicting post translational modifications to your protein
How are post translational modifications to a protein predicted?
• Signal sequences or content
• Search for homology to pattern peptides