Protein interactions

Question 1

What can proteins interact with?

Answer 1

Small ligands - metabolites, metal ion, neurotransmitter, antigenic peptide.
Proteins - hormone, receptor, cell surface.
DNA and RNA.
Lipids.
Sugars and carbohydrates.

Question 2

How do proteins interact with proteins, DNA or lipids?

Answer 2

Mainly non-covalent interactions - ionic, hydrogen/electrostatic, hydrophobic, van der Waals.
Two proteins are rarely joined by covalent disulfide bonds.

Question 3

What affects the strength of interaction?

Answer 3

The more non-covalent interactions, the stronger the interaction.

Question 4

What is Calmodulin?

Answer 4

A small ligand that protein interacts with.
It is found in all eukaryotic cells.
It is activated by Calcium binding to a variety of targets, which changes its shape and allows it to interact with other things like membrane transport proteins and enzymes.

Question 5

What are multimeric proteins?

Answer 5

Proteins made from more than 1 of the same subunit.
The subunits are very similar and interact together to form the complex.

Question 6

What are filaments?

Answer 6

Structural filaments interact together to form the structure of the cell.
Actin filaments in the nucleus are made from small subunits that join together to form rigid structures.

Question 7

What are protein complexes?

Answer 7

Made from different proteins to form a specific function.

Question 8

Why do proteins associate with DNA?

Answer 8

DNA must be packaged in a way that can be accessed so it can be translated.
It is packaged around histone proteins in order to pack into the nucleosome into the nucleus.

Question 9

What are DNA sequence non-specific proteins?

Answer 9

Histones, Helicases, Polymerases, Transcription factors.
Any DNA sequence can interact with the protein.

Question 10

What are DNA sequence specific proteins?

Answer 10

Restriction enzymes, Transcription enzymes.
These proteins only bind when the specific sequence is present.

Question 11

How do proteins interact with lipids?

Answer 11

Receptor proteins interact with lipids through hydrophobic interactions.

Question 12

What proteins are anchored in cell membranes?

Answer 12

For example GDP, is involved in covalent modification with lipids and targets proteins to cell membranes.

Question 13

How do proteins interact with sugars?

Answer 13

Glycoproteins are proteins modified with sugars to help the interaction of external sugars with proteins in the membrane.

Question 14

What factors affect the likelihood and strength of binding?

Answer 14

Availability - concentration, and co-localisation.
Matching non-covalent interactions.
Competition from alternative partners.

Question 15

What are domains?

Answer 15

Proteins interact with other molecules through specialised domains.
Domains are fragments of proteins folded in a particular way that forms a unit for a particular interaction.

Question 16

How can pH regulate protein interactions?

Answer 16

If pH is altered so that there is less ionisation - then the charge between different amino acids will be less and therefore the ionic interaction is weaker.

Question 17

What are post-translational modifications of proteins?

Answer 17

Changes to proteins after they have been synthesised:
Phosphorylation, methylation, ubiquitylation, acetylation, SUMOylation, hydroxylation.
This gives variety to the function of proteins, as there is a limited number that are made.

Question 18

What is phosphorylation?

Answer 18

Adding phosphate to a positive amino acid will add a negative charge so there is no attraction between a negative amino acid and the interaction is lost.

Question 19

What are modification-specific protein domains?

Answer 19

BRCT recognises phosphorylated proteins.
UBA recognises ubiquitylated proteins - has pigment attached.
Bromodomain recognises acetylated proteins.

Question 20

How do ligands modify protein interactions?

Answer 20

For example calmodulin, when Ca2+ binds it changes the shape and so affects which proteins calmodulin interacts with.

Question 21

How is protein regulation complicated?

Answer 21

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 22

How can protein interactions be measured?

Answer 22

Look at the % of protein bound to the ligand. Use Kd.

Question 23

What is Kd?

Answer 23

Dissociation constant - this indicates affinity.
It is the concentration of ligand required to achieve half saturation of protein population.
The smaller the dissociation the stronger the affinity.