Languages of cell communication 2 Flashcards
Localisation within the cell
Protein localisation can affect their activities
Post-translational modifications
- what are they?
- different forms?
= reversible covalent modifications
> addition of small chemical groups - phosphorylation ,acetylation etc > addition of large molecules - sugars, lipids etc > cleavage of proteins > isomerisation
Post-translational modifications
- huge variety
Increases no. of potential molecular states
- > provides versatility
- different proteins can be encoded by 1 gene
expands diversity + dynamic behaviour of proteins encoded by genome
Post-translational modification
- consequences
Conformational changes
Altered protein-protein interactions
- promote or prevent protein binding
Subcellular localisation
Proteolytic stability
Conformational changes
In polypeptide backbone
OR
in intramolecular arrangement of different folded domains of protein
Altered protein-protein interactions
create or destroy a binding site
- due to effects on charge, H-bonding + shape on binding surface
can have secondary effects
- e.g. changes in subcellular localisation or further PTMs
Subcellular localisation
PTM alters dynamics of shuttling of proteins between different sub-cellular compartments (aka Protein Trafficking)
Subcellular localisation
- example
Lipid modification directs many proteins to stably interact w/ cellular membranes
Proteolytic stability
Alters expression of level of a protein
Phosphorylation (often coupled to ubiquitination) can target a protein for proteolytic degradation
Other modifications can stabilise a protein
Common PTMs
Addition of simple functional groups
- Phosphorylation
- Methylation
- Acetylation
Addition of large molecules
- glycosylation
- ubiquitination
Proteolysis + isomerisation
Phosphorylation
- as a regulatory mechanism
Specific +
Tightly regulated +
Flexible control
… of protein function
Provides points of kinetic control
Phosphorylation
- general protein names
Writer enzyme
= protein kinases adding P
Eraser enzyme
= protein phosphatases removing P
Kinases
- most common
Ser/Thr + Tyr protein kinases
Phosphate group
- charge
- effects
-vely charged
Attracted to +vely charged groups nearby +can disrupt hydrophobic interactions
OR repel -vely charged groups
Phosphorylation
- secondary structures
Local disruption (steric or electrostatic effects)
= P group disrupts a H bond between an alpha helix + a beta-pleated sheet
-> helix unfolds
Local ordering (forming new structures)
= P group H-bonds w/ 2 +vely charged residues
-> allows previously unstructured region to fold into alpha helix
Phosphorylation
- tertiary + quaternary structures
Long range disruption:
= P group prevents binding of a protein + partner molecule OR another domain of same protein
Long range ordering:
= P group can promote new long-range intramolecular + intermolecular interactions
(creates a docking site)
What makes intracellular signals precise + specific?
- Specificity of interaction between signalling molecules
- High threshold
- for signal activation maintained by constitutively active eraser enzymes - Back up mechanisms
- 2 parallel pathways to activate a single downstream target protein - Signal integration
SRC family kinase
- inactive shape
SH2 binds to phosphate group on C-terminal of tyrosine
Linker domain tightly bound between SH2 + SH3
SRC family kinase
- phosphatase acts…
P removal
-> loosens structure
- > activating ligand can bind to SH3 domain
- > conformation change
- > Tyrosine loop phosphorylated = activated
- > moves out of kinase active site
= Active kinase
What determines kinase substrate specificity?
- i.e. mechanisms that control which Ser, Thr or Try residues get phosphorylated
Active site
- complementary
Docking sites
- elsewhere in kinase domain
Modular binding domains
- appended to the kinase domain to recruit target substrates
Scaffolds/adaptors
- different proteins stabilise complex between kinase + substrate
Phosphorylation coupled w/ ubiquitination
- process
Phosphate attracts ubiquitin
- > recognition signal for proteasome
- > binds + degrades into peptides
Phosphorylation coupled w/ ubiquitination
- important e.g.
Cell cycle
- transitions between phases regulated by Cyclin-CDKs
When Cyclin-CDK is required
- > CK inhibitor phosphorylated
- > Cyclin-CDK activated
Changes in localisation influence..?
Probability of interaction between molecules
Co-localisation of reacting components…?
Drives reactions much more efficiently
2 most common cellular translocations involved in signalling
Movement of proteins to + from nucleus
Movement of proteins to + from cell membranes
Movement of proteins to + from nucleus
Access to nucleus essential for activity of proteins that act on chromatin
- e.g. chromatin modifiers + TFs
Movement of proteins to + from cell membranes
Many signalling proteins + their substrates from only on membranes
Confining molecules to the membrane
-> increases the local concentrations
