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From Protein Sequence to Protein Properties

Prof:Rui Alvesralves@cmb.udl.es

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