Protein Conformation

Question 1

What forces are involved in protein folding and interactions?

Answer 1

1. Covalent
2. Hydrogen bonding
3. Entropic (hydrophobic)
4. Electrostatic

Question 2

2 Types of Covalent Interactions:

Answer 2

1. Backbone Bonds: Peptide bonds are planar and due to the partial double bond character they cannot rotate freely but instead can be in either:
   Lower energy trans conformation OR
   Higher energy cis conformation
2. Side Chain Bonds: Side chain bonds can rotate, but there will be low energy conformers and the energy of the different states is dictated by the interactions with the backbone atoms and with other side chains.

Question 3

Ramachandran plot

Answer 3

Shows the conformational space owned by different combinations of Phi and Psi rotations.
Alpha helices show with a negative Phi and a negative Psi.
Beta strands show with a negative Phi and a positive Psi.

Question 4

Beta sheets are composed of?

Answer 4

Beta strands, in either a parallel or antiparallel fashion. Hydrogen bonds hold the strands in place.

Question 5

Hydrogen Bonding, in relation to protein conformation:

Answer 5

Hydrogen bonds are weak bonds, meaning that they can make and break at body temperature.

Hydrogen bonds are an essential component of protein structure.
In both beta sheets and alpha helices the hydrogen bond forms between the carbonyl oxygen and the amino group.

The typical length of a hydrogen bond in water is 1.97 Angstroms.

Question 6

Entropic (Hydrophobic) Bonding, in relation to protein conformation:

Answer 6

Hydrophobic interactions can also be described as entropic as hydrophobic groups exposed to water lead to a decrease in entropy.
Therefore burying hydrophobic residues away from water leads to an increase in entropy.
Almost all proteins have hydrophobic cores, stabilising their folded state.

Question 7

Electrostatic Interactions, in relation to protein conformation:

Answer 7

Electrostatics deals with the interaction between charges (or partial charges). A number of amino acids are fully charged but most (if not all) exhibit partial charge due to the polarity of the individual amino acids.
Electrostatic effect is complicated in biological macromolecules.

Question 8

Protein Folding and Protein Assembly: 2 alternative processes

Answer 8

1. Simultaneous folding of two random coil peptides to give folded dimer (Folding AND Assembling).
2. Binding of pre-folded monomers (Folding THEN Assembling).

Both processes lead to the same result, but start differently.

Question 9

Possible methods to examine protein folding pathways:

Answer 9

NMR, Fourier-transform infrared spectroscopy (FTIR), Fluorescence.

Question 10

Examples of stabilisation of protein structure:

Answer 10

GCN4 protein is a homo-dimer held together by a parallel alpha helical coiled coil using a leucine zipper to hold the helices together.

Histones: H3 and H4 not stably folded by themselves, fold together to form a more stable heterodimer. Becomes even more stable as an octamer (H3H4H2AH2B). This octamer becomes even more stable with the addition of DNA.