Protein Dynamics

Question 1

Protein Dynamics

Answer 1

1. Proteins are not static
2. Continuously undergo conformational changes at varois timescales
3. Dynamic encoded in structure of proteins

Motions:
- local motions: continuous bond formation/breaking in 2 structur
- global motions: large structural change

Question 2

Techniques protein dynamics

Answer 2

1. Forster Resonance Energy transfer
2. Hydrogen Deuterium exchange

Question 3

Forster Resonance Energy Transfer
(FRET)

Answer 3

Objective: Determine protein conformation( oligomeric states), binding interactions, conformational changes

Act as molecular ruler, distance dependence

Principle: when donor and acceptor dye are in proximity. Energy transfer
Emission of donnor zero
Emission of acceptor is dominant

Components
Dyes
At different timepoints: rates opening closing

Question 4

Hydrogen Deuterium exchange

Answer 4

Objectuve: generate map of dynamic regions in target proteins

Principle: amide protons exchange with deuterium when add deuterium water to sanpkem
Only solvent accesible protons are susceptible to exchange
Run over time

Coupled with NMR:
Deuterium not NMR active
See decrease in number of peaks
Can determine rate of unfolding for each aa

Useful for: comparing mutants. Probing folding/unfolding
Protein-ligand interactions