Protein Function Repeat (Whoops)

Question 1

Ligand

Answer 1

A molecule that binds reversibly to a protein

(can be any kind of molecule, including a protein)

Question 2

Where do ligands bind?

Answer 2

To a protein’s BINDING SITE

Question 3

Binding Site

Answer 3

The location on a protein molecule that interacts with the ligand

(the crevice or pocket where a ligand binds)

Question 4

A protein’s 3D structure is designed to…

Answer 4

Interact with specific molecules (ligands)

Question 5

Ligand binding process for:

Monomeric protein + ligand

Answer 5

1) L bind to the binding site on P

2) Forms the PL complex

3) Formation of the PL complex usually triggers a conformational change in the P (NOT ALWAYS)

Question 6

Ligand binding process for:

Dimeric protein + ligand

Answer 6

1) L1 binds to binding site #1 on one of the P subunits

2) Triggers a conformational change in the L bound subunit

3) Conformational change in the one subunit is communicated to the other subunit via the inter-subunit interface

4) Conformational change occurs in the second subunit

5) This change alters the binding affinity for the second ligand (cooperativity)

Question 7

Inter-Subunit Interface

Answer 7

A network of interactions between subunits of a given protein

Question 8

Why are inter-subunit interfaces important?

Answer 8

They allow for conformational changes in one subunit to be communicated to the other subunit/s == allows for cooperativity

(it causes other subunit/s to change shape upon binding to one subunit, impacting the binding of ligand/s to other subunit/s

Question 9

Cooperativity

Answer 9

When the binding of one ligand affects the binding of other ligands to other subunits on the same protein

(**binding of one ligand changes the affinity for other ligands)

Question 10

(+) vs. (-) Cooperativity

Answer 10

(+) = Binding of one ligand to a subunit INCREASES the binding affinity for another ligand (usually on another subunit)

(-) = Binding of one ligand to a subunit DECREASES the binding affinity for another ligand (usually on another subunit)

Question 11

What is the equilibrium expression for non-cooperative protein-ligand interactions?

Answer 11

Free protein + Free ligand <===> Protein-Ligand Complex

(reversible rxn)

Question 12

Rate Constant vs. Equilibrium Constant

Answer 12

Rate Constant = (little k) A proportionality factor in the rate law of a rxn that relates the rate of a rxn to the concentration of the REACTANTS (has to do with rxn order)

Equilibrium Constant = (BIG K) The ratio of the product concentration to reactant concentration at a state of chemical equilibrium
== HOW FAR (to the left or right) will a rxn go before it levels off at equilibrium?

Question 13

Equation for the equilibrium constant in terms of rate constants

Answer 13

Question 14

Dissociation Constant

Answer 14

The equilibrium constant for the dissociation of the protein-ligand complex (the release of a ligand from the PL complex)

(Ratio of the product of free reactant concs. to the conc. of protein-ligand complex)

Question 15

Association vs Dissociation Constants

Answer 15

Question 16

Why do we NOT use the association constant to describe binding affinity?

Answer 16

Because K_a is NOT in easily interpretable units whereas K_d is in units of [L] Molar (more easily understood)

Question 17

What is the dissociation constant equal to in terms of rate constants?

Answer 17

(Rate constant of dissociation) / (Rate constant of association)

Question 18

What is the fractional binding equation?

(non-cooperative)

Answer 18

Frac. of total protein that is bound to ligand = [L] / [L] + K_d

Question 19

When [L] = K_d, this means….

Answer 19

[L] = K_d means that HALF of the total protein is bound to ligand!

Question 20

What is the definition of K_d in terms of fractional binding curves?

Answer 20

K_d = The concentration of free ligand at which HALF of the available ligand binding sites are occupied! (half-saturation point)

Question 21

What do we use as a measure of affinity?

WHY?

Answer 21

K_d!