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Lecture about kinasesFormation of project groups

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Protein kinases

Before we describe how protein kinases work, first an interlude dealing with the representation of protein structure

Proteins are made of a chain (or chains) of covalently bound amino acids

Proteins are made of a chain (or chains) of covalently bound amino acids

5

N

H

H

CH

O

H NH CH

O

CH3 CHH3C CH3

N

O

CH

OO

CHCH3CH

2

CH3Ala Val Pro Ile

AVPI

NHN

H

H

CH

O

H NH CH

O

N CH

O

CH

OO

Ala Val Pro Ile

AVPI

NH

The -N-C-C-N-C-C- acts as the main chain or « backbone »

the atom groups that define the type of amino acid form the « side chains »

Backbone representation

The string of amino acids folds either in the form of a helix, a b-strand or as a non-structured loop (not shown)

An example of a short polypeptide comprising a-helices, b-sheets and loops

loop

a-helix

b-sheet

The amino acid sequence of a protein kinase

>P06213| 1023-1298 (=275 amino acids)...ITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSF…

The folded string of the amino acids that constitute a protein kinase can be represented in different ways

Show all atoms of the amino acid

in a stick representation

Show all atoms of the amino acid

in a sphere representation

Show the surface of the protein

Show only the back-bone of the amino acid

in a ribbon representation

Phosphorylation and dephosphorylation : protein kinases and protein phosphatases

Protein kinases

What do they do?What do they look like?How do they do it?

This is what they do

Understanding enzymes as nano-machines;

ATP is nicely buried inside the protein kinase whereas the substrate (only a short peptide shown in blue) is fixed onto the surface of the protein

The tyrosine residue, shown in green, is perfectly positioned to receive the g-phosphate

ATP

tyrosine containing substrate

This is what they look like

Understanding enzymes as nano-machines;

Protein kinases have two lobes, the upper one is the N-terminal lobe, the bottom one the C-terminal lobe.

the catalytic cleft sits at the interface between the two; the catalytic residue (not shown) as well as ATP reside in the cleft (ready for action)

N-terminal lobe

C-terminal lobe

catalytic cleftATP

This is what they look like

Understanding enzymes as nano-machines;

A ribbon representation illustrating the position of highly conserved amino acids

As their level of conservation indicates, these amino acids are vital for the functioning of the protein kinase

They control the position of ATP (lys, asp, glu), substrate (blue ribbon) and the transfer of electrons (asp*) leading to hydrolysis of ATP

*

And this is how they do it (understanding enzymes as nano-machines)

serine/threonine versus tyrosine protein kinases

Certain protein kinases are multidomain enzymes

Kinases exist in an incompetent state and require activation before they can phosphorylate substrate

Different modes of activation of protein kinases