Intro to Protein Dynamics Flashcards
Why do we know protein structures are accurate models?
- different technaiques produce the same structure
- crystals under different conditions make same structure
- proteins from the same family have same structure
- protein crystals can bind ligands and many are enzymatically active
Where do proteins usually exist in the 3D energy landscape?
At the bottom of the well
Why is the bottom of the energy well in the 3D energy landscape bumpy?
Because proteins are constantly moving
What dictates the rate of interconnection between different protein conforms?
The ΔG between the comforms
What alters the energy landscape?
A change in the system e.g temperature or pH
How long does it take for a protein to move from one stable state to another?
Microseconds
How does O2 get to the heme centre in myoglobin?
Through ‘breathing’, extended fluctuations which provide multiple transient channels
Where does the evidence for myoglobin breathing come from?
- H/D exchange on the backbone N-H
- Measure the change in mass by mass spec
What does H/D exchange show about myoglobin?
- Surface residues exchange immediately
- many deeper buried residues also exchange, though this is much slower
Does protein ‘breathing’ occur in crystals?
Yes
How can crystal structures provide information on protein dynamics?
- some structures have regions of electron density that are weak
- these regions are not uniquely defined in space
- disorder at each residue can be calculated, more disorder=more dynamic
What is a B factor/B value?
A temperature factor which measures disorder at each residue in a protein
At what temperature does protein ‘breathing’ cease to occur?
220k (-53°C)
How can you test if protein breathing is necessary for function?
- Take protein down to 220k
- Add inhibitor and see if it is bound
- e.g. RNAse A
