Protein Dynamics 1

Question 1

What are chemical shifts defined by in IDPs?

Answer 1

Their sequence.

Question 2

What program is used to predict the chemical shifts of IDPs?

Answer 2

CamCoil

Question 3

What does CamCoil do?

Answer 3

Defines how much the actual IDP has deviated from the ultimate random coil - identifies amounts of secondary structure in proteins.

Question 4

What is Gab2 involved in?

Answer 4

Cellular signalling.

Question 5

Why are IDPs important in cellular signalling?

Answer 5

Can form lots of protein-protein interactions.

Question 6

Describe the structure of Gab2/

Answer 6

Very large - small helical domain (120aa) and rest of protein is disordered.

Question 7

Give examples of proteins Gab2 mediates interactions between.

Answer 7

Tyrosine kinase, GCPRs, cytokine receptor, multi chain immune recognition and integrins.

Question 8

Upon stimulation what can Gab2 interaction with?

Answer 8

Grb2

Question 9

What does Gab2 do after interacting with Grb2?

Answer 9

Recruits SH2 domain containing molecules (e.g. tyrosine phosphatase/PI3K) to activate signalling pathways.

Question 10

What domains does Grb2 contain?

Answer 10

Two SH3 domains (proline rich) and one SH2 domain (tyrosine phosphorylated sequences).

Question 11

What happens upon binding of Gab2 to Grb2 via its SH3 domain?

Answer 11

Gab2 folds.

Question 12

What does Gab2 fold into?

Answer 12

Poly-proline helix once bound.

Question 13

What method was used to characterise the disorderd Gab2 protein?

Answer 13

NMR.

Question 14

What was discovered about Gab2 structure when studied by NMR?

Answer 14

There is residual secondary structure of beta sheets and poly proline helix.

Question 15

What did this residual secondary structure tell you about Gab2?

Answer 15

Showed that the bound state conformation was semi-present in the disordered state - prone to adopt this conformation.

Question 16

What protein is associated with Parkinson’s?

Answer 16

Alpha-synuclein

Question 17

What happens to alpha synuclein to cause Parkinson’s?

Answer 17

Amyloid.

Question 18

What are the amyloids formed in?

Answer 18

Lewy bodies - inclusion bodies.

Question 19

What do these amyloids do?

Answer 19

Kill neurones in the brain.

Question 20

What is the difference between membrane bound and solution form?

Answer 20

Membrane bound - active form, thought to be helical.

Solution - disordered - not naturally found like this.

Question 21

What is the suggested function of alpha synuclein?

Answer 21

Involved in neurotransmitted release in synaptic cleft.

Question 22

Are some membranes more likely trigger aggregation of alpha synuclein?

Answer 22

Yes.

Question 23

What kind of helix is in alpha synuclein?

Answer 23

Amphipathic.

Question 24

What can be used to monitor transition from disordered protein to membrane bound protein?

Answer 24

Circular Dichroism.

Question 25

Is a portion of the protein still disordered in membrane bound form?

Answer 25

Yes.

Question 26

What is the disordered part of the protein?

Answer 26

Protein-protein interactions - SNARE formation cannot occur if protein is truncated.

Question 27

What is used to probe transient interactions?

Answer 27

Paramagnetic relaxation enhancement in solid state NMR.