Protein-Ligand Interactions

Question 1

What is affinity and what is specificity?

Answer 1

A = STRENGTH of molecular interaction (greater decrease in free energy upon binding –> greater affinity).

S = MOLECULAR COMPLEMENTARITY between S and S binding site.
relative strength between one protein and alternative ligands.

Question 2

What are the dominant forces in;

• protein;nucleic acids
• protein;ligands
• protein folding.

Answer 2

• electrostatic
• none
• hydrophobic.

Question 3

What is the assumption when carrying out a binding assay?

Answer 3

That labelling radioactively doesn’t affect binding.

Question 4

What is the link between Kd and biological activity?

Answer 4

Proteins switch from empty to fully blind when [ligand] is close to Kd

Kd mainly lower than physiological [ligand] by factor of 10-100

(ATP = 1 MM and Kd = 10 um)

Question 5

What mutations can affect Kd?

Answer 5

Increase affinity for ligand but no appreciable increase in binding so mutation disappears.

Kd increases - ligand fails to bind and loss of function.

Question 6

Why can some RNAs form enzymes?

Answer 6

SS nuclei a cuss are fairly flexible

Cellular RNA forms secondary and tertiary structures (depend on primary)

Question 7

What activeatable functional groups are found in RNA and protein enzymes?

Answer 7

Proteins have 20 AAs - more diverse than nucleic acids

RNA has 2’OH of ribose frequently featuring in RNA catalysis.

Question 8

How do proximity and orientation differ?

Answer 8

Proximity describes reaction in which no improbable collision is required as reactants already in contact.

Orientation - reactants optimally aligned for reaction.