Module 1-Structural Organization of Membrane Proteins (Lectures 1-3)

Functions of membrane proteins

Receptors, transporters, enzymes

Peripheral protein

pH change of adding chelator which removes stabilizing Ca releases a membrane protein it is considered

Integral protein

if detergent is needed to remove a membrane protein: monotopic, bitopic, polytopic

Amphitropic proteins

Associate reversibly with the membrane

Soluble proteins

are folded in such a way to have hydrophilic amino acids in the exterior and hydrophobic amino acids in the interior

How do membrane proteins manage their H-bond groups?

C=O and N-H groups of the peptide bonds and the side chains of several amino acids can act as hydrogen bond donors or acceptors, need to minimize unpaired H bonding

What are the types of structural possibilities for membrane proteins

A helix that crosses the whole membrane, closed b-barrel with the connecting loops outside the membrane

The alpha helix

C=O of each amino acid H-bonds with NH of the amino acid 4 residues down from it, rise of 1.5 A

Why can solutes not be transported through an a helix?

it is not hollow and there is no hold in the middle, tightly packed atoms in centre in van der waals distance from each other

In a single spanning helix what AA are favoured in this interfacial region?

Aromatics like Trp and Tyr

What is the structure of the single spanning helix?

The section of helix traversing the membrane is made up of hydrophobic amino acids; Weakly hydrophilic residues tolerated in small numbers (Thr, Ser)

what is concentrated at the solution/membrane interface in Multi-spanning Trans-membrane proteins?

Aromatic residues (esp. Tyr and Trp)

Why can hydrophilic side chain be in TMD?

by having them face the interior of the bundle and interact with hydrophilic groups from the other strands

The TMD of the glucose transporter has a

channel lined with polar residues

Annular lipids

Form a bilayer shell(annulus) around the protein

What interaction do lipid annuli?

head groups interact with POLAR aa at the inner and outer membrane, tails interact with non polar residues

What is the result of proteins with wide hydrophobic bands on membrane?

Will repack lipids so that hydrophobic side chains are covered by lipid tails

What is the result of proteins with narrow hydrophobic bands on membrane?

encourage lipids to take on less extended conformations

Single TM proteins, however, will tilt to accommodate

he preferred default membrane thickness

Monotopic membrane proteins

have small hydrophobic domains that interact with only one leaflet of the membrane

What irregularities do membrane helices in multi spanning proteins have?

over-wound regions, under-wound regions, kink, local unfolding

Ramachandran plots

allows us to visualize dihedral angles φ (phi) and ψ (psi) associated with each residue completely described secondary structure

the 3 10 helix

case of over-winding, side chains line up with each other, sensitive to voltage in channel which allows for it to open and close

pi helices

case of under-winding, pi helix in the middle of an alpha helix causes a pi bulge

What is the result of a pi bulge

the extra residue in the pi helix bulges out with its C=O not having a corresponding NH to H-bond with, introduces kink into the helix

What is the result of a proline in the middle of the helix?

there is a kink as of the N of proline residues in a peptide bond does not contain a H to allow for H bonding

The two sets of ridges in an a-helices make what angles to the helix?

25 degrees and 45 degrees

4-4 packing

The two helices are oriented with their long axes crossing at an angle of 50°(25°+25°)

3-4 packing

The two helices cross at an angle of 20°(45°-25°). 20 is more common in membrane proteins as it is closer to parallel

knobs into holes packing

side chains in one helix (knobs) pack into the spaces between the side chains (the holes) in the other

What is the purpose of a GXXXG motifs?

this will bring two glycine residues to the same face of the helix, the lack of a side chain will leave a groove for another helix

B-strands

no H bonds in a given b-strand, h bonding occurs between adjacent strands of a sheet

B-barrels

extended anti-parallel β-sheets that wrap around so that the last strand hydrogen bonds with the first

In beta strands how would you describe the residues on the exterior?

generally aromatic (Tyr, Phe, Trp; together ~40 %) or small, branched hydrophobic(Val/Leu/Ile)

amino acid sequences of amphipathic beta strands alternate in

polarity, alternate between hydrophobic and hydrophilic residues

Structure of barrels with 8-10 strands

have a solid core filled with hydrophilic residues, no channel

Structure of intermediate side b-barrels (16-18)

strands have aqueous pores, generally with inserted loops

Structure of large barrels (22-26)

generally have a plug domain (orange) that inserts into and closes (most) of the channel

Charged residues (Lys, Arg, Glu, Asp) are found

almost exclusively in the aqueous phases

Positive-inside rule

Lys, His, Arg occur more commonly on the cytoplasmic face

Trp and Tyr residues often found at the

interface between the lipid and water for both types of proteins

amphipathic helices

helices that are hydrophobic on the side buried in the membrane, and hydrophilic on the side facing the cytosol

lipid-anchored proteins

Proteins can be anchored to the membrane via long chain fatty acids, isoprenoids, sterols, or glycosylated derivatives of phosphatidylinositol

Pseudosymmetry

occurs when a single protein (monomer) consist of two structurally identical folds with different sequences

Quasi-symmetry

could have multiple copies of the same protein with each subunit adopting a different conformation