FOM 1.3.1 Flashcards
What is an apo-protein?
protein not bound to anything
What is a ligand?
Anything that binds a protein.
What is a holo-protein?
A complex of all components (proteins, subunits, and all ligands) needed for function
Give examples of some of the things that proteins bind.
small sugars, nucleotides, RNA, water, organic molecules, O2, large carbs, metal ions, proteins, lipids, CO2, protons, DNA, drugs, photons, NO
What constitutes a protein binding site?
A well-defined region of the protein that contacts a ligand. These contacts are made by specific AA side chains or backbone.
Give an example of a protein binding site interaction with a ligand.
An aromatic tryptophan ring stacking against the hexose ring of the sugar ligand.
How does ATP show chemical complementarity?
ATP has numerous domains that interact with binding sites including: Hydrophobic regions, positive charges, accepting and donating H bonds.
What happens when an ATP tries to bind in an inverted manner?
Chemical repulsion and steric clashes. ATP won’t bind
How can mutations alter binding? (2)
It can affect how tightly the ligand is bound (affinitiy) It can affect which ligand is bound most tightly (specificity, similar to selectivity)
What has occurred in patients who present with Vitamin D resistant rickets?
A mutation has occurred in the receptor that alters binding stability b/t receptor and ligand.
In the example with Vitamin D resistant rickets, how were doctors able to increase vitamin D uptake by cell lines? What’s the limitation or obstacle with this route?
The doctors were able to alter the vitamin D to better fit w/ the cells mutant receptor. The obstacle is that patients may have different mutations.
Can ligands affect the protein structure?
Yes and they most likely will.
How do ligands affect the equilibrium of proteins b/t their folded and unfolded form?
Shift equilibrium in favor of the folded forms.
What type of roles can metal ions play in proteins? Would we use drugs to mimic these effects?
“structural” roles Yes, drugs that mimic these effects are used in unfolding dz’s (e.g. CFTR)
Can different ligands affect the way a protein will fold? If so, how much of a folding difference could be achieved?
Yes 1000-fold difference
P + L PL , give the dissociation and association reaction contants, k
Ka = [PL]/[P][L], units M-1 Kd = [P][L]/[PL], units M
In the dissociation reaction, when [P]free = [PL], what is Kd equal to?
[L]
Where can Kd be found on a sigmoidal curve?
At the 50/50 point, the point where half of the protein is bound.
When looking at differentiation curves, what is important to note about the axises? How could it affect the curve?
Standard unit distribution = hyperbolic shape Logarithmic distribution= sigmoidal curve
What is the slope around the half-way point of an uninfluenced sigmoidal curve?
1
When looking at a single ligand-protein binding sigmoidal dissociation curve, what do shifts to the left (smaller []) and right indicate?
Left: Tighter affinity Right: Weaker affinity
When analyzing the capability of a drug to bind a protein, what type of concentration is desirable?
A drug that can achieve a concentration higher than its midpoint inside a cell is desirable.
What is the midpoint of a drug concentration in vivo called?
EC50 instead of Keq
What type relationship exists when the binding of the first has no effect on the binding of the subsequent?
Independent
