6BBB0333
L5 – Thermodynamics of Protein Folding
- How do proteins fold?
o Folding pathways and protein mis-folding
- Why do proteins fold and mis-fold?
o The energetics of protein folding
o Why don’t proteins stay unfolded? Why do they adopt a 3D native structure?
- Energetics of unfolded proteins are also very relevant, not just folded protein - must compare
quantitatively: equation below (K =)
- Always focus on folded protein interactions but must consider unfolded protein
- You have to compare them
- Thermodynamics is always about an equilibrium and in order to get an accurate estimate of
where the equilibrium lies and therefore what delta G is, both sides of the equilibrium must
be considered – you MUST look at unfolded state
- While we are usually focussed on H bonds and other enthalpic contributions, we must also
look at entropy (tricky because less visual)
Non-covalent that stabilise the folded protein structure
- Hydrogen bonds
- Electrostatic interactions
- Van der Waals forces
- Hydrophobic effect
Explicitly exclude disulphide bonds from this because only small subset of proteins includes
disulphide bonds
Rest is applicable to any type of protein
, 6BBB0333
Hydrogen Bonds
- Classical H bond between carbonyl group and amide group as you would find in alpha helix
and beta sheet (LHS)
- However H bonds can occur between any positively polarised hydrogen e.g. alcohol group
and negatively polarised heteroatom that can lend its lone pairs to form this obscure bond
- Looking at thermodynamics of formation of this bond from two molecules that are isolated
in the gas phase its about 3kcal per mole = relatively high
- Hydrogen bond’s nature has been disputed:
o We must know their nature to understand how proteins fold and energetics and in
order to model these things on a computer
o Scientists said H bonds are more like charged interactions
o Some think it’s a version of VdW interactions
o Some think more like covalent bond
o NMR was able to answer this:
NMR showed that some hydrogen bonds have covalent character because
otherwise you would not observe scalar couplings
Scalar couplings are communication between different nuclei driven by a
network of covalent bonds in between them
If you observe this between two side of a H bond, means that it must have
some kind of covalent character (electron mediated connection between the
two sides of H bond) – partially covalent
Much weaker than e.g. C-C of C-H bond
There not only is a distance dependency of the energy but also angle-
dependency (strength of hydrogen bond – given same distance – changes
with the angles)
- Hydrogen bonds are relatively strong non-covalent interactions between a hydrogen atom
bonded to an electronegative atom (such as oxygen or nitrogen) and another electronegative
atom. In proteins, hydrogen bonds form between amino acid side chains and the peptide
backbone, helping to maintain the secondary and tertiary structures. For example, in an
alpha-helix, hydrogen bonds between amino acid residues stabilize the helical structure.
L5 – Thermodynamics of Protein Folding
- How do proteins fold?
o Folding pathways and protein mis-folding
- Why do proteins fold and mis-fold?
o The energetics of protein folding
o Why don’t proteins stay unfolded? Why do they adopt a 3D native structure?
- Energetics of unfolded proteins are also very relevant, not just folded protein - must compare
quantitatively: equation below (K =)
- Always focus on folded protein interactions but must consider unfolded protein
- You have to compare them
- Thermodynamics is always about an equilibrium and in order to get an accurate estimate of
where the equilibrium lies and therefore what delta G is, both sides of the equilibrium must
be considered – you MUST look at unfolded state
- While we are usually focussed on H bonds and other enthalpic contributions, we must also
look at entropy (tricky because less visual)
Non-covalent that stabilise the folded protein structure
- Hydrogen bonds
- Electrostatic interactions
- Van der Waals forces
- Hydrophobic effect
Explicitly exclude disulphide bonds from this because only small subset of proteins includes
disulphide bonds
Rest is applicable to any type of protein
, 6BBB0333
Hydrogen Bonds
- Classical H bond between carbonyl group and amide group as you would find in alpha helix
and beta sheet (LHS)
- However H bonds can occur between any positively polarised hydrogen e.g. alcohol group
and negatively polarised heteroatom that can lend its lone pairs to form this obscure bond
- Looking at thermodynamics of formation of this bond from two molecules that are isolated
in the gas phase its about 3kcal per mole = relatively high
- Hydrogen bond’s nature has been disputed:
o We must know their nature to understand how proteins fold and energetics and in
order to model these things on a computer
o Scientists said H bonds are more like charged interactions
o Some think it’s a version of VdW interactions
o Some think more like covalent bond
o NMR was able to answer this:
NMR showed that some hydrogen bonds have covalent character because
otherwise you would not observe scalar couplings
Scalar couplings are communication between different nuclei driven by a
network of covalent bonds in between them
If you observe this between two side of a H bond, means that it must have
some kind of covalent character (electron mediated connection between the
two sides of H bond) – partially covalent
Much weaker than e.g. C-C of C-H bond
There not only is a distance dependency of the energy but also angle-
dependency (strength of hydrogen bond – given same distance – changes
with the angles)
- Hydrogen bonds are relatively strong non-covalent interactions between a hydrogen atom
bonded to an electronegative atom (such as oxygen or nitrogen) and another electronegative
atom. In proteins, hydrogen bonds form between amino acid side chains and the peptide
backbone, helping to maintain the secondary and tertiary structures. For example, in an
alpha-helix, hydrogen bonds between amino acid residues stabilize the helical structure.
