Protein Dynamics Flashcards
What types of proteins dynamics are there?
Atomic vibrations
Collective movement of domains
Triggered conformational changes of whole subunits
Transient unfolding
How fast do individual atoms vibrate?
10^15 to 10^11 per second
What distance do atoms vibrate?
0.01 to 1A
How fast do domains move?
10^12 to 10^3 per second
How far do domains move?
0.01 to 5A
How far do subunit conformational changes move?
0.5 to 10A
How fast do subunits move?
10^-3 to 10^9 per second
Why are dynamics important?
Catalysis
Ligand binding
Formation of complexes
Active site availability
What effect do dynamics have on a reaction progression energy plot?
Not smooth as rapid interconversions
What effect does temperature have on an energy diagram?
More energy so smoother
How can dynamics be measured?
Empirical measurements of ligand release
Quenching of aromatic amino acids
HX NMR
What small molecules can be used for quenching?
I-, O2, acrylamide
Why is quenching not a good measurement?
Some non-specific binding
What molecules are used for HX NMR?
D20 exhanges with amides
Why is deuterium used for HX?
Different spin for NMR
different mass for MS
What is rate of HX determind by?
Ki exchange,
Ko opening
Kc closing
Which residues exchange first?
Exposed, un-bonded ones
How is rate of HX dependant on pH?
10x increase for each pH unit above pH3
Why is 2D NMR used for large proteins?
To separate overlapping peaks of similar environments
What are the types of 2D NMR?
COSY
NOESY
TOCSY
HSQC
What spectrum does HSQC produce?
15N-1H spectrum of all amino acids except Proline
What spectrum does COSY produce?
Protons coupled by 3 or fewer bonds
What spectrum does NOESY produce?
Protons within 5A space
What spectrum does TOCSY produce?
protons coupled by bonds and all protons in a spin system
