Proteins and carbohydrates 3 Flashcards
What is ΔG* and what can it also be considered a measure of?
The unfolding activation energy of the protein. It can be considered as a measure of the kinetic stability of a protein.
How can the mechanical properties of a protein be investigated?
By pulling the protein using single molecule force spectroscopy until unfolding and examining the force to extension relationship of the protein.
How can a protein domain be identified?
Different types of protein domain have different values of force required to unfold so measuring this variable using single molecule force spectroscopy can be used to identify protein domains by referring to a database.
How can the bonds between proteins be investigated?
By pulling the proteins using single molecule force spectroscopy until bond rupture (unbinding) and examining the force to extension relationship of the proteins.
Describe and explain the mechanical strength of α-helices.
α-helices are mechanically weak as the hydrogen bonds connecting the secondary structure together are in series so they break independent of each other.
Describe and explain the mechanical strength of β-sheets.
β-sheets are mechanically strong when the external force is applied from opposite ends of the protein as the hydrogen bonds connecting the secondary structure together are in parallel so they reinforce each other in resisting pulling forces.
If the forces are pulling from opposite sides of the β-sheet, then it is mechanically weak as the bonds break in a zipper arrangement.
What is the advantage of using optical tweezers over AFM?
They are more sensitive to low forces.
Describe the feature unique to the free energy landscape of weak and soft proteins and its significance.
Weak and soft proteins have a large distance between the folded and unfolded states (i.e. a more broad transition state peak) so a lot of extension is required to unfold weak and soft proteins.
Describe the feature unique to the free energy landscape of strong and brittle proteins and its significance.
Strong and brittle proteins have a shorter distance between the folded and unfolded states, so require less extension but more force to unfold.
What factors determine the mechanical stability of a protein?
Intramolecular interactions, the direction of the applied force, and for β-sheets: the length of the β-sheet. The longer the β-sheets, the greater the number of inter-strand hydrogen bonds that share the mechanical load, and the more mechanically stable the protein is.
What is the persistence length of a protein?
A measure of the stiffness of the protein backbone chain. The distance that the chain does not change direction.
What is the persistence length of all unfolded proteins?
0.4nm (very similar to contour length of each amino acid)
What is the contour length of a protein?
The length of the amino acid chain/protein backbone (distance not displacement).
What is the lifetime of a protein?
The time until a bond in a protein breaks.
What can the force of unfolding be considered as a measure of?
The force of unfolding is a measure of the mechanical stability of a protein.
