Protein Folding I Flashcards
Name the 4 non-covalent interactions that are involved in protein folding stability.
- short range repulsion
- hydrogen bonds
- Van der Walls interactions
- electrostatic forces
What are the 4 determinants of protein folding?
> secondary structure allows for very efficient packing
folding is hierarchical
somehow context dependent
hydrophobic effect
What is the molten globule state?
An intermediate conformational state between the native and the fully unfolded states of a globular protein.
***Thus, in short, the molten globule is a compact globule with a “molten” side-chain structure that is primarily stabilized by nonspecific hydrophobic interactions.
How do you calculate frequency and propensities for amino acids forming secondary structures?
frequency = amino acid in alpha-helix / all amino acids
propensity = frequency / all amino acids
True or False:
The molten globule state is in-between the native and fully unfolded state of a globular protein.
True
True or False:
Protein folding is not a cooperative process that obeys the thermodynamics’ laws and prefers a lower energy state.
False – protein folding IS a cooperative process that obeys the thermodynamics’ laws and prefers a lower energy state. Thus, the folding funnel is a good example to look at to understand this.
How many conformations does lymphotactin exist in?
Two
1) chemokine structure
2) glycosaminoglycan-binding structure
What does the term “metamorphic protein” mean?
That the same primary structured protein can exist in multiple conformations and depending on the conformation will have different functions within the organism.
** An example is lymphotactin (slide 16 protein folding I lecture)
What are the 4 characteristics that describe a protein in the molten globule state?
1) the presence of a native-like content of secondary structure.
2) The absence of a specific tertiary structure produced by the tight packing of amino acid side chains.
3) Compactness in the overall shape of the protein molecule, with a radius 10% to 30% larger than that of the native state.
4) The presence of a loosely packed hydrophobic core that increases the hydrophobic surface area accessible to solvent. (thus, water can still get in)
True or False:
A protein in the molten globule state has a specific tertiary structure produced by the tight packing of amino acid side chains?
False – a protein in the molten globule state has an absence of a specific tertiary structure produced by the tight packing of amino acid side chains. (This is one of the characteristics of a protein in the molten globule state)
How much bigger is the protein’s radius when it’s in the molten globule state than the radius of that protein in it’s native state?
10%-30%
(this is a characteristic of a protein in its molten globule state – compactness in the overall shape of the protein molecule, with a radius 10%-30% larger than that of the native state)
True or False:
A protein in the molten globule state must have a presence of a loosely packed hydrophobic core that increases the hydrophobic surface area accessible to solvent.
True – this is a characteristic of a protein in its molten globule state.
(the presence of a loosely packed hydrophobic core that increase the hydrophobic surface area accessible to solvent)
True or False:
The presence of a native-like content of a secondary structure for that specific protein must be present for that protein to be in it’s molten globule state?
True – (the presence of a native-like content of a secondary structure)
This is a characteristic of a protein in its molten globule state.
What are the two main types of bonding that govern protein folding stability?
1) Non-covalent interactions
>Short range repulsion
>Electrostatic forces
>Van der Walls interactions
>Hydrogen bonds
2) Hydrophobic interactions
