Protein modifications Flashcards
Name 3 methods by which protein structure may be determined
- X-ray crystallography
- Nuclear magnetic resonance (NMR)
- cryo-electron microscopy (crys-EM)
Describe the process by which X-ray crystallography is carried out
- Protein is purified
- Crystallisation
- Freezing of crystal
- Data collection
- Measure diffraction
- Visualise electron density
- Build structure
How does NMR reveal protein structure?
- Certain nuclei (H1, C13, N11, N15) are intrinsically magnetic, spinning causes magnetic moment when a magnetic field is applied
- Nuclear Overhauser Effect (NOE) shows information on protons in close proximity
What is cryo-EM most useful for?
Looking at large structures (e.g a virus) however low resolution
What is the function of post-translational protein modification?
Add extra layer of functionality/regulation
Describe the process of proteolytic processing
- Proproteins (zymogens) translated in an inactive form to ensure that enzymes do not get degraded
- ‘pro’ sequence cleaved off by enteropeptidase
- Some proteins translated with ‘pre’ signal sequence which targets them to correct cellular compartments
How does phosphorylation occur?
- Covalent addition of phosphate group to serine, threonine and sometimes (rarely) tyrosine
- Added by kinases and removed by phosphatases
What is phosphorylation important for?
Intracellular signalling
Where does acetylation occur and what are its functions in each case?
N-terminal - synthesis, stability & locomotion of proteins
Amino group of lysine - reversible modification important in the regulation of proteins (e.g histones)
What is glycolysation?
- The covalent addition of a carbohydrate moiety which is either N-linked (amino group of asparagine residues) or O-linked (hydroxyl group of serine/theonine)
- Mostly occurs through secretory pathway, produces cell membrane proteins
What is acylation and what are its two types?
- Covalent addition of a fatty acid group
- Increases hydrophobicity, plays a role in membrane targetting and protein-protein interactions
- Most commonly: meristoylation and palmitoylation
What is meristoylation?
- Addition of meristoyl group to amino-group of an N-terminal glycine with an amide bond
What is palmitoylation?
Addition of palmitic acid to cysteine/serine/threonine via a thioester/ester bond
What is prenylation?
- Covalent addition of prenyl group to C-terminal cysteine residue
- Increases hydrophobicity and play a role in membrane targetting and protein-protein interactions
What is methylation?
- Covalent addition of methyl group to amino group of lysine and arganine residues, not reversible
- When present on histones can act epigenetically to repress/activate gene expression
When are co-factors used for proteins?
- Required for enzymes to regulate activity
- Can be metal ions or small molecules
What occurs in the oxidation of a protein?
- Covalent disulphide bond between 2 cysteine residues
- Either co/post-translational
- Reversible
How do proteins interact with eachother? Provide an example
- Commonly mediated by tetratricorepeat domains folds
e. g Ribonuclease complexes with an inhibitor with femtomolar affinity
What are the 4 common motifs/folds in protein-nucleic acid interactions?
- zinc finger
- leucine zipper
- helix-turn-helix
What are the properties of the Zn finger?
Zn ion coordinated by 2histidine and 2cysteine which binds to the major groove in DNA, with the + charge neutralising it. Can recognise 3 bases
What is the helix-turn-helix?
2* helix joined by a short strand important for gene regulation. Alpha-helix is inserted into the major groove of DNA
How does the leucine zipper function?
- Interacts with the major groove of DNA via basic residues of the N-terminus in order to neutralise the negative charge
- Leucine every 7-8 residues creates zipper (2 chains whcih dimerise to form an amphipathic helix)
- Hydrophobic side chains interact with eachother and polar chains interact with eachother
Why do protein complexes with nucleic acids need to be very specific?
In order to ensure fidelity
