Lecture 3: Membrane Proteins

Question 1

Learning Objectives

Answer 1

• Understand the properties of membrane proteins
• Appreciate the diversity of ways in which these proteins interact with the membrane
• Understand the molecular basis of interaction with the membrane
• Appreciate broad classes of membrane proteins

Question 2

Describe the structure of integral membrane proteins.

Answer 2

Integral proteins need hydrophobic and hydrophilic parts to be soluble inside the bilayer and outside.

Question 3

What ratio of lipids to proteins is there in the membrane?

Answer 3

50:1, Lipids:Proteins

Question 4

What percentage of the mass of the membrane is from the proteins?

Answer 4

Normally 50%, but it can range from 25% to 75% depending on the membrane.

Question 5

Compare the structural features of membrane proteins and lipids.

Answer 5

Both are amphipathic and asymmetrical. However, the asymmetry of proteins is absolute and cannot change (essential for function, e.g. G proteins), whereas the asymmetry of membrane lipids can change to relay external signals into the cell.

Question 6

What are the two broad classes of membrane proteins?

Answer 6

Integral (has transmembrane domains) and Peripheral (post-translational modification to protein gives it a lipid anchor or non-covalently bonded to an integral protein. Much more loosely bound to membrane than integral proteins). Peripheral proteins can also be bound via an oligosaccharide linker to Phosphatidylinositide (PI) in the non-cytosolic leaflet.

Question 7

What is a monotropic protein?

Answer 7

A protein which only inserts into one of the monolayers of a membrane lipid bilayer.

Question 8

Define transmembrane domain.

Answer 8

A hydrophobic region of a molecule which cross the membrane from one side to the other. These are usually a-helices or beta-strands.
This does NOT include lipid modifications to proteins (peripheral) or monotropic proteins (does not cross the membrane).

Question 9

Give an example of an a-helical membrane protein.

Answer 9

Aqp0, which is an aquaporin (water channel) in humans

Question 10

Give an example of a beta-barrel membrane protein.

Answer 10

OmpF, which is found in outer membrane of bacterial cells

Question 11

Why is it so important that there are many hydrogen bonds between the turns of an a-helix in a membrane? Give a short description of the hydrogen bonding in a-helices.

Answer 11

There are hydrogen bonds between the C=O group of residue n and NH group of residue n+4, which is in the next turn of the helix. All of the hydrogen bond donors and acceptors are used. This stabilises the a-helix and means that there is no need for hydrogen bonds to be formed with the aqueous environment, so the a-helix can exist in the lipid membrane.

Question 12

Discuss the width and length of a-helices in the cell membrane.

Answer 12

Normally a-helices are between 20 and 30 amino acid residues long. The variation is due to the fact that the a-helix can be slanted or bent. The a-helix is a comparatively wide transmembrane domain. The non-helix part of the protein can adopt many different conformations and affects the solubility of the protein.

Question 13

Which amino acids are likely/unlikely to be present in the lipid membrane? Give specific examples.

Answer 13

Amino acids with hydrophobic side chains are likely to be found in the lipid membrane. This includes Phe, Met, Ile, Leu, Val, Cys, Trp, Ala.

Amino acids with hydrophilic side chains are unlikely to be found in the lipids membrane as this would be highly energetically unfavourable. This includes His, Gln, Glu, Asn, Asp, Lys and Arg.

Question 14

How can the structure of an a-helix be predicted from the amino acid sequence?

Answer 14

If the sequence is heavily hydrophobic (contains amino acids with hydrophobic side chains) and is 20 to 30 aa residues, TMHMM prediction is possible.

Question 15

How many a-helices does Bovine rhodopsin have?

Answer 15

7. Bovine rhodopsin is found in the retina of the eye, meaning that vision is possible in darker conditions.

Question 16

Describe the structure and location of beta barrel proteins.

Answer 16

Beta barrels are formed from curved beta-strand regions.
These form rigid structures which act as pores (porins) and are found exclusively in the bacterial, chloroplast and mitochondrial outer membrane. Beta barrels are less common than a-helices.

The arrangement of amino acid residues in beta barrels is very different to the arrangement in a-helices and cannot be identified or predicted easily.

Hydrophobic residues point towards the lipid environment (outside of pore, touching membrane), whereas hydrophilic residues point towards the hydrophilic core (centre of pore, aqueous environment).

Question 17

Comment on the variety in the structure and function of outer membrane proteins.

Answer 17

Outer membrane proteins (OMPs) have a rigid structure with not much variety in the structure. However, there is a huge variety of functions.

Question 18

Describe how G-protein coupled receptors work.

Answer 18

The receptor is an integral membrane protein and its correct orientation in the membrane is essential for its function. The signalling molecule, e.g. adrenaline, binds to the extracellular side of the receptor, stimulating a conformational change. This conformational change causes the three intracellular domains bound to the receptor protein (alpha, beta and gamma) to exchange GDP for GTP. This exchanges causes the alpha-GTP complex to break off from the protein receptor (dissociate) and diffuse along the inner side of the membrane to adenyate cyclase, where the ATP converted to cyclic AMP, starting a signalling cascade inside the cell when cAMP activates cAMP-dependent protein kinase.

Question 19

How easy is it to study membrane proteins? Explain.

Answer 19

It is very difficult to study membrane proteins, because functional and structural analysis requires a soluble protein and the lipid environment of the membrane is essential for the structure and function of membrane proteins. If a membrane protein is removed from the lipid bilayer it falls apart. Detergents, such as sodium dodecyl sulphate (SDS) and lauryl sulphate, can be used to disrupt interactions between the membrane and membrane protein. The detergents molecules, have a hydrophilic head and hydrophobic tail like phospholipids will form micelles around the exposed membrane protein, preventing it from falling apart.