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Flashcards in Proteins and molecular recognition Deck (29):

What are the interactions involved in intermolecular interactions?

- Ionic interactions

- Hydrogen bonding

- Van der Waals interactions

- Hydrophobic interactions


What are the vital features of intermolecular interactions?

1. Affinity: They need to be sufficiently strong to carry out function.

2. Specificity: Ligands should only bind to complementary receptors.

3. Control: Ligands should only bind when there is a functional requirement. There is tight control over this process.


What are the characteristics of permanent intermolecular interactions?

They use mostly hydrophobic interactions.


What are the characteristics of transient intermolecular interactions?

Combination of hydrophobic and charged interactions.


What are the advantages/disadvantages of hydrophobic interactions?

- Advantage: They produce high affinity interactions.

- Disadvantage: They are not very specific as there are a large number of hydrophobic amino acids.


What are the advantages/disadvantages of charged interactions?

- Advantage: High specificity created with specific combination of charges.

- Disadvantage: Weaker than hydrophobic interactions.


What is the relationship between [L], KD and the fractin bound?

- When [L] < KD, fraction bound < 50%.

- When [L] = KD, fraction bound =50%.

- When [L] > KD, fraction bound > 50%.


What are the relative ranges of KD for different cellular interactions?

- Intracellular interactions: µM - nM

- Antibody interactions: µM - nM

- Drug (e.g. inhibitor): nM - pM


What are the methods used to quantify interaction affinities?

1. Isothermal titration calorimetry: Heat change in ligand binding can be used to quantify KD.

2. Surface plasmon resonance: Change in refractory index of a surface as ligands bind to their protein.


What is the structure of the EGF receptor?

- It has 4 extracellular domains.

- It has a transmembrane and jusxtamembrane domain.

- It has an intracellular tyrosine kinase domain.

- It has a regulatory region.


What happens when EGF binds to the EGF receptor?

1. EGF ligand binds to domain 3 of the EGF.

2. This induce conformational change whereby domain 1 is also bound to domain 3.

3. Domain 2, a dimerisation domain, is unmasked by this process.

4. Dimerisation of 2 activated EGF receptors induces autophoshorylation of the intracellular protein kinase domains.

5. This triggers the EGF pathway.


What are the processes that occur in the EGF pathway?

1. Grb 2 is recruited and binds to the phospho-tyr residue on the PTK domains via SH2 domains.

2. SOS recruited to grb 2 via SH3 domains. This activates SOS.

3. SOS catalyses exchange of GDP for GTP on membrane-bound G-protein RAS.

4. RAS activates RAF, which is a membrane-bound kinase.

5. RAF activates MEK by phosphorylation.

6. MEK activates MAPK by phosphorylation.

7. MAPK activates c-Fos and c-Jun by phosphorylation that subsequently promote transcription of a number of growth-related genes including Myc.


What is the structure of SH2?

- Contains 100 amino acids.

- Consists of antiparallel β-sheets surrounded by α-helices.

- Has conserved Arg/Lys residues involved in interaction with phospho-Tyr residue.

- Has variable residues that contribute to specificity.

- Has 2 pockets, one for phospho-Tyr and one for specificity.



What is the structure of SH3 domains?

- Contains 50-75 amino acids.

- Consists of 5 anti-parallel β-sheets.

- Specificity determined by differential charges and variable regions.


What type of interactions occur between Grb 2 and SOS?

Strong, hydrophobic.


What happens when Ras binds to Raf?

1. Raf contains 2 domains, a catalytic and an inhibitory.

2. The inhibitory domain usually blocks the catalytic domain.

3. When Ras binds to Raf, conformational change occurs whereby the inhibitory domain unblocks the catalytic domain.

4. Raf is activated and can phosphorylate downstream signalling particles.


What are the types of interactions between DNA and DNA-binding domains?

- Non-specific ionic interactions between the domains and the phosphate backbone.

- Specific hydrogen bond interactions between the domains and the bases.


How do antibodies interact with their effector cells?

Through binding between their constant regions (Fc) and receptors on effector cell surface (FcRs). These protect the antibodies from degradation.



What are the different interactions between different antibodies and FcRs?

- IgG → FcγR

- IgA → FcαR

- IgA/IgM → Fcα/μR

- IgE → FcεR


What is the same given to the site on an antigen onto which an antibody binds?



What are the problems with using murine antibodies in therapeutics?

1. Murine antibodies seen as foreign and gives rise to immune response.

2. Murine Fc regions do not interact well with FcRs. This results in poor interactions.

3. Murine Fc regions do not interact well with FcRns. Results in short half-life.


What is a chimaeric antibody?

Human constant regions with murine variable regions.


What is a humanised antibody?

Human antibodies with murine CDRs.


How are human antibodies produced from transgenic mice?

Human Ig genes are introduced into mice with their Ig genes knocked out.


Whar are the different types of human antibody?

1. Whole antibody

2. FAb = VH + VL + CH + CL

3. Fv: VH + VL

4. scFv = VH + VL + linker


What is the mechanism of pertuzumab (Omnitarg action? 

Omnitarg binds to the EGFR dimerisation domain and inhibits dimerisation.


What is the mechanism of trastuzumab (herceptin) action?

Herceptin binds to ErbB2 (which is over-expressed in 25-30% cancers) and is thought to induce receptor internalisation.


What is the mechanism of tarceva action?

Tarceva is an EGFR PRK inhibitor. It binds to ATP binding site in EGFR and prevents kinase action.


What is the general mechanism behind kinase control?

Kinases have activation loops that block the active site. Phosphorylation causes unblocking which then activates kinase.