Lecture 6: Protein structure/folding

Question 1

Define supersecondary structure and list some examples:

Answer 1

Elements of a secondary structure are connected by turns or by loops or coils, making up a supersecondary structure
* Helix – turn – helix
* β hairpin
* Greek key
* Strand – helix – strand

Question 2

Example of Helix – turn – helix?

Answer 2

• DNA binding proteins
• Calcium binding proteins

Question 3

Define Beta-hairpin and some examples:

Answer 3

• Common
• Anti-parallel
• Length varies

Examples:
- Bovine pancreatic trypsin inhibitor
- Snake venom toxin

Question 4

What does a Greek key look like?

Answer 4

• 4 antiparallel strands

thinking about a Greek key as one long, bent hairpin with 4 antiparallel strands

Question 5

What is a protein domain or motif?

Answer 5

Super-secondary structure elements combine to form domains, which are independently folded regions that often possess a specific function within the protein.

Small proteins contain usually one domain, larger proteins may have multiple domains

Question 6

What is a protein family, and what are some common examples of such families?

Answer 6

Proteins can be grouped into families based on tertiary structure.
Examples
- alpha domain family: four helix bundle, globin fold
- alpha/beta family: α/β barrel, α/β horseshoe fold
- antiparallel beta family: anti-parallel β barrel

Question 7

What are the key steps involved in the folding of a protein?

Answer 7

Proteins are synthesized as linear polymers that have to
fold into a 3-dimensional functional structure
* Protein are made at the ribosome, and then generally
they fold into their active shape spontaneously
* The only “instructions” needed are embedded in their
amino acid sequence

Question 8

Describe likely folding pathway:

Answer 8

• Formation of short secondary structure segments
• Subdomains form
• Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange, (tertiary structure still partly disordered)
• Final domain structure emerges, small conformational adjustments to give final compact native structure

Question 9

What is the role of the hydrophobic core in protein folding?

Answer 9

The hydrophobic core is likely the most important noncovalent contributor to protein stability in aqueous solution.

Question 10

How is a protein fold stabilised?

Answer 10

• Non-covalent interactions, while individually weak in proteins, collectively make a significant contribution to protein conformational stability
• In some proteins additional covalent bonds (for example, disulfide bonds) may be present that contribute to conformation stability
• The hydrophobic core is likely the most important noncovalent contributor to protein stability in aqueous solution.

Question 11

Tertiary structure is stabilised by short/long range (circle one) interactions which are made up of non-covalent/covalent (circle one) bonds.

Answer 11

The tertiary structure is stabilized by long-range interactions, which are made up of non-covalent bonds.

Question 12

What is a chaperone and what role do they play?

Answer 12

A chaperone is a type of protein that assists other proteins in folding into their proper three-dimensional structures, which is essential for their function. Chaperones are crucial because the folding process can be complex and prone to errors, leading to misfolded proteins that may be non-functional or harmful to the cell.

Question 13

What are the three types of chaperones?

Answer 13

• Chaperone-independent
• Chaperone-dependent e.g. Hsp70
• Chaperonin-dependent e.g. GroEL-GroES

Question 14

What factors can lead to protein unfolding?

Answer 14

Temperature: High temperatures can disrupt the hydrogen bonds and other interactions that stabilize a protein’s structure.

pH Changes: Extreme pH levels can alter the charge of amino acids, disrupting ionic bonds and hydrogen bonding.

Chemical Denaturants: Substances like urea or guanidinium chloride can disrupt the non-covalent interactions within proteins.

Mechanical Stress: Physical forces, such as shear stress, can disrupt the structure of proteins.

Mutations: Changes in the amino acid sequence can destabilize the protein’s structure, leading to unfolding.

Question 15

Give examples of diseases associated with protein unfolding:

Answer 15

Prion Diseases (alpha to beta transformation occurs in abnormal protein)

Alzheimer’s Disease (amyloid)

Type 2 Diabetes (amyloid)

Question 16

Describe Anfinsen’s experiment:

Answer 16

1. Unfolded ribonuclease A in 8M urea and β-mercaptoethanol to break its four disulphide bonds.
2. Dialysis to remove urea and β-mercaptoethanol and air oxidation of sulfhydryl groups.

• Proved that the amino acid sequence of a protein contains all the information required for determining the 3-dimensional structure.