Protein Interactions

Question 1

What can proteins form interactions with?

Answer 1

• small ligands
• DNA and RNA
• proteins
• membranes=lipids
• sugars/carbohydrates

Question 2

What are protein interactions that occur which are sequence specific?

Answer 2

• restriction enzymes

- transcription factors

Question 3

What are protein interactions which are not sequence specific?

Answer 3

• histone
• helicase
• polymerase

Question 4

How do proteins interact with other proteins or DNA or lipids?

Answer 4

• usually using non-covalent interactions such as ionic, Hydrogen, van der waals bonding/forces
• sometimes two proteins can be joined by disulphide bonds

Question 5

What affects the likelihood and strength of binding of protein interactions?

Answer 5

• availability (conc) and co-localisation
• matching non-covalent interactions
• competition from other partners

Question 6

What affects the lifetime of the complex and therefore its affect?

Answer 6

• extent of contributing stabilising interactions

- regulators= PH, modification, other ligands

Question 7

What are some examples of post-translational modification of proteins?

Answer 7

• phosphorylation
• methylation
• ubiquitylation
• acetylation
• SUMOylation
• hydroxylation

Question 8

How does calmodulin work?

Answer 8

-once it binds to calcium it changes structure in a way that enables it to bind to other partners

Question 9

What factors make protein interactions more complicated to understand?

Answer 9

• one protein can have many interaction domains
• one protein can interact at the same time with many substrates and ligands
• all of the interactions influence each other and form a complex matrix

Question 10

What can we measure ligand-protein interaction?

Answer 10

• proteins and ligands have reversible affinity for each other
• they are in equilibrium because always part of them interacts and part does not
• the equilibrium is dynamic and regulated by surroundings, other interactors and modification

Question 11

What is Protein interaction affinity indicated by?

Answer 11

Kd (disassociation constant)

Question 12

What is the Kd?

Answer 12

the concentration of substrate/ligand required to achieve half (50%) saturation of protein population

Question 13

What does a low value of Kd mean?

Answer 13

that the interaction is strong

Question 14

What are protein-protein complexes?

Answer 14

Proteins interacting with other proteins forming multimers/multimeric proteins.
There proteins have a quaternary structure

Question 15

What are protein-lipid associations?

Answer 15

Proteins associate themselves with phospholipids in the membrane producing integral/peripheral transmembrane proteins.

Question 16

What are protein sugar interactions?

Answer 16

Some membrane proteins may get modified to form glycoproteins.

Question 17

What does more non-covalent interactions between a protein and its ligand mean?

Answer 17

There is a stronger interaction between them

Question 18

What interaction stabilies 2’ structure of proteins?

Answer 18

Hydrogen bonds either intra in alpha helicies or inter in beta sheets

Question 19

What interaction stabilise 3’ structure of proteins?

Answer 19

Ionic bonds between 2 ionisable R groups of amino acids.

Question 20

What are protein domains?

Answer 20

Specific fragments /domains that have evolved to interact with specific proteins.

They have specialised and specfic domains

One protein may have multiple different domains each with a different job.

Question 21

What are some properties of protein interactions?

Answer 21

Highly Regulated
Highly fluid
Both associate and dissociate with its substrates.

Question 22

What is the saturation point of a protein?

Answer 22

The point where the addition of a ligand will not affect the percentage bound to a protein.

Question 23

How do you measure protein affinity?

Answer 23

Have an amount of protein
React with varying substrate concentrations
Measure the proportion of ligand bound to the protein
Draw a graph.