Lecture 19 - Proteins III

What did Anfinsen's experiment with denaturing and renaturing ribonuclease teach us?

If you denature a protein everything needed to reestablish correct protein structure is found in the sequence of the primary structure. The function of the protein is also reestablished by the amino sequence.

what is a protein domain?

It is not yet a tertiary protein but is higher in organization than a motif. It is typically between 40-400 amino acids.

What happens to the C terminus of P-53 as it comes into close proximity with its binding partner proteins?

Its C terminus changes conformation. These changes in conformation allow it to bind with different binding partner proteins.

What is a super secondary structure?

This describes how two or more secondary structures of the same protein interact. Folds or motifs which are particularly stable such as a helix turn helix.

This image describes the formation of an amyloid nucleus. Describe this image.

1. Natively folded proteins begin to form secondary structures - - including beta sheets. 2. In the molten globule state, the beta sheets from one protein interact with another protein in the molten globule state. This interaction will prevent it from folding into its correct tertiary structure. 3. This happens multiple times, leading to an aggregate of mis-folded proteins. This is an amyloid nucleus.

Describe the secondary structures involved in the tertiary structure of myoglobin.

8 segments of alpha-helices are connected by beta-turns.

What is protein renaturation?

A denatured protein refolding and returning to its proper tertiary structure.

What is a molten globule state?

A molten globule state is the result of hydrophobic collapse. Basically hydrophobic and hydrophilic interactions push hydrophobic residues to the center of a protein and hydrophilic residues toward the exterior. This state is found early in the process of protein folding - - often before secondary structure has been defined.

What is another name for a super secondary structure?

A motif or a fold.

What is a prion?

A prion is an "infectious protein." This sounds totally crazy, but a prion is a protein that can actually induce other proteins to un-fold (losing their correct folding) and re-fold in an incorrect conformation. These proteins, once re-folded are resistant to proteases and aggregate in cells. Denaturing a prion protein requires boiling it (no joke) in nitric acid.

Are the alpha helices of myoglobin right handed or left handed?

All of the alpha helices in myoglobin are right handed.

Describe the distribution of amino acids in a hydrophilic porin transmembrane protein?

All of the hydrophobic amino acids point away from the "donut hole" making the channel hydrophilic. Environment always influences conformation.

What causes Alzheimer's Disease? What are important factors in the disease?

Alzheimer's Disease is caused by the formation of amyloid plaques in the brain. These plaques are mis-folded versions of brain proteins. Proteins with large traces of Phenylalanine tend to be involved in these amyloids and may promote aggregation.

What is hydrophobic collapse?

An event that scientists believe occurs early in the folding process of globular proteins. Hydrophobic residues orient toward the center of a protein (hydrophobic interactions) while hydrophilic residues orient near the outside of the protein. The result of hydrophobic collapse is defined as a molten globule state.

What is an intrinsically unstructured protein (IUP)?

An intrinsically unstructured protein is a protein that has more than one possible conformation. These proteins do not have a defined structure until they interact with something. In other words, these are proteins who do not assume their final structure until they encounter other molecules.

What is cumulative selection?

As a protein folds, correctly folded portions remain the same, while incorrectly folded portions are re-folded. In other words, at each step parts of the protein fold correctly and parts do not. Those parts that fold correctly are retained and those that fold incorrectly are unfolded so that they can re-fold.

What types of secondary structures are most likely to be involved in the formation of an amyloid structure?

Beta sheets.

What is Creutzfeldt-Jacobs's Disease?

Creutzfeldt-Jacobs's Disease is a prion disease. It results in aggregates of mis-folded proteins.

True or false: compared to an un-folded protein, a folded protein is entropically favored.

False. Folded proteins are more ordered. This makes the folding process entropically unfavorable. The folding process, it should be noted, takes advantage of entropy. Hydophilic and hydrophobic interactions, for example, are entropically favored (to prevent increased structure in the water lattice).

True or false: protein folding is a trial-and-error process.

False. If proteins assembled randomly, it could take millions or even billions of years for one protein to find the correct orientation.

How can you denature a protein?

Heat Organic solvents (Alcohol) Detergents Extreme acidic or basic pH Urea

What is Levinthal's paradox?

Levinthal calculated that, if a protein of 100 residues were to use a trial-and-error folding process AND if each of the residues could take three different conformations, it would require 1.6*10^27 years for that protein to arrive at the correct structure. The paradox part of this is that most proteins fold within milliseconds. The point of the paradox is that protein folding is NOT random.

What is a metamorphic protein?

Metamorphic proteins are proteins that can exist in multiple forms. These forms are energetically similar (stable.) Additionally, these different metamorphic conformations exist in equilibrium.

How many polypeptides is myoglobin made up of?

Myoglobin is made up of one polypeptide.

In what way is protein denaturing a cooperative process?

Once a protein starts unfolding, the remainder of the protein begins unfolding very quickly. In other words, once a protein begins denaturing, the process moves rapidly.

What is the significance of a high PONDR score?

The PONDR scale shows the length of a protein by residue and rates the order of the structure. A high PONDR score corresponds to protein regions that are intrinsically un-structured. Basically, a high PONDR score means that a segment is NOT structured. A low score indicates a structured area.

Describe the distribution of amino acids in myoglobin referring to their hydrophobicity and hydrophilicity.

The core of myoglobin is hydrophobic and the exterior is hydrophilic. There are only two hydrophobic side chains on the outside.

What are amyloidoses?

These are diseases that are caused by the formation of protein aggregates called amyloid fibrils or plaques. Common examples include: Alzheimer's, ALS (Lou Gehrigs), and Parkinson's Disease. Prion diseases are another example of amyloid plaque disease.

True or false: the presence of certain amino acid residues can make secondary structure formation more likely.

True. For example, a high concentration of glutamate residues is often associated with an alpha helix. Similarly, cysteine is a common residue in proteins that contain beta sheets.

What is protein denaturing? How does it do this?

unfolding of the protein or making it lose its tertiary structure. It does it by disrupting hydrophobic interactions, hydrogen bonds, and disulfide bonds etc.