today lecture about kinases formation of project groups discussion about project content
TRANSCRIPT
Today
Lecture about kinasesFormation of project groups
Discussion about project content
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
O
O
CHCH3CH
2
CH3Ala Val Pro Ile
AVPI
NHN
H
H
CH
O
H NH CH
O
N CH
O
CH
O
O
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
