Lecture 5 - Protein Folding Part I

Question 1

What is the most important amino acid sequence in the myoglobin structure?

Answer 1

Appears to be histidine. There is the proximal histidine, which binds the Fe group, and the distal histidine, which binds the oxygen.

Question 2

What is the biggest purpose for a protein to fold, and what is the largest contributor to the folding of a protein?

Answer 2

Proteins need to fold to reach maximum possible stability, and the biggest contributor of folding is the hydrophobicity of the “inner” side of the protein, which retreats away from the polar water into itself so only the exterior hydrophilic amino acids are on the outside.
- In addition to the side chain hydrophobicity, the main chains also have an effect, as an unpaired N or C group will prefer a polar solution and be hydrophilic. So in order for a hydrophobic side chain to be properly buried, the main chain needs to be “connected” to other main chains to become nonpolar.

Question 3

When is the “exception” that allows proteins to have hydrophobic exteriors and hydrophobic interiors?

Answer 3

When the protein operates in a non-polar solution or environment, and some do, this makes perfect sense.

An example includes Porins, which are the main component of membrane channels, which need water-filled centers

Question 4

What are motifs?

Answer 4

Also known as supersecondary structures, this is the classification of multiple secondary structures that don’t quite qualify as tertiary. The most common example is the helix-turn-helix subunit that separates two alpha helices by a “twist”. This type of unit is found in proteins that bind DNA. This type of shape has been compared to “pearls on a string” and these gaps in the structures are referred to as Domains.

Question 5

What are the advantages of the peptide bond between the N and C terminus?

Answer 5

The amide bond is highly resistant to hydrolysis, and cancels out the charges of both, allowing the link to be nonpolar.

Question 6

What are the main segments that secondary structures are comprised of?

Answer 6

• Alpha helices, Beta sheets, loops and turns
• Alpha helices are linked by hydrogen bonds between an amine and a Carbonyl group (in the side chains?) every 4 links.
• Beta Sheets - Hydrogen bonds connect beta sheets at their strands in one of three forms, parallel, antiparallel, or mixed.

Question 7

Besides hydrophobic interactions, what are 4 other noncovalent factors that govern protein folding stability?

Answer 7

• Short range repulsion
• Van der Waals interactions
• Hydrogen bonds
• Electrostatic forces (i.e. ion pairs and salt bridges)

Question 8

Very Briefly describe Short-Range Propulsion

Answer 8

At too far of a distance, atoms don’t interact at all, but they have a finite “optimum distance” where they attract. If they get too close, they start to repel each other. Protein folding works to avoid that.

Question 9

What are the 3 types of potential hydrogen bond donors? Which one’s seen the least.

Answer 9

O-H, N-H, and F-H, the latter of which is rare.

Question 10

Briefly describe what is meant by ion pairs and salt bridges

Answer 10

Ion pairs are simple enough, the link/bond created with a negatively charged Carboxyl and a positively charged amine in the side chains of amino acids that cause “bridged connections” help link bonds together. Salt bridges are similar but since they’re salts, they don’t actually “link”. I think.

Question 11

What is the basic difference between alpha helices and beta sheets?

Answer 11

Alpha helices tend to be more bendy and flexible, whereas beta sheets are usually more rigid and unmoving. However, beta sheets can have Beta Loops or Beta Turns outside of their main sheets that are a bit disorganized and are a bit looser. These are usually found on the Exterior of the protein.

Question 12

Describe the characteristics of disulfide bonds in a protein structure.

Answer 12

Disulfide bonds can be interchain, which link an alpha structure with a beta structure
or Intrachain, where two cysteines in the (only alpha?) chain separated by 4 other amino acids between them can link together.

Extracellular proteins tend to have frequent disulfide bonds, while intracellular proteins usually lack any disulfide bonds.

Question 13

What is Beta-Mercaptoethanol used for

Answer 13

Cleaves the disulfide bonds in a secondary structure. Which is often useful for protein denaturation.

Question 14

List the steps the average protein takes to fold into it’s most stable form and approximate times.

Answer 14

1. Formation of the secondary structure from the primary
2. Formation of “domains” through cooperative aggregation
3. Formation of assembled domains (known as a molten globule)
4. Conformation is adjusted
5. Structure settles and becomes more rigid.

(Steps 1-4 occur in msecs. Step 5 occurs after about 1 second)

Question 15

Give an example of a repeating motif

Answer 15

Calmodulin - a calcium sensor containing 4 similar domains of alpha helices - with turns in between each to separate them. Each domain is able to bind to one calcium ion.

Question 16

Describe what is noteworthy about lymphotactin

Answer 16

An amino acid sequence (and there’s more like this) that have different conformations that give it completely different functions. As a combination of alpha-sheets/beta-sheets, it becomes the Chemokine structure. When conformed into purely folded beta sheets, it becomes Glycosaminoglycan binding structure.

Question 17

What is a molten globule?

Answer 17

When a protein is being folded into it’s globular form, it briefly hits an intermediate state where it becomes a molten globule.

• Within the molten globule, the native structure of the secondary structure is conserved, and the amino side chains are tightly packed without forming a tertiary structure.
• However, the protein is about 30% larger than the native state, and is stabilized by nonspecific hydrophobic interactions inside the globule.