Protein Structure 1

Question 1

Key concepts in protein structure

Answer 1

• Primary structure – the actual amino acyl sequence.
• Secondary structure – the natural in vivo folding of the primary structure as it falls off of the ribosome (+/- chaperone proteins/inside GroEL/GroES complex) -(stops them sticking to other hydrophobic proteins, being kept safe) based on the sequence to form 3D structures.
• Tertiary structure – amino acid side-chain interactions to give polypeptide domains in complete folded shape.
• Quaternary structure – multiple polypeptide domains interacting to form a complete protein and/or the binding of biochemical cofactors (FMN, FAD, PQQ, heme B, retinaldehyde etc) and/or metals to the tertiary structure

all proteins have a quaternary structure even if its the same as the tertiary structure

Question 2

Secondary structures

Answer 2

• Formed by hydrogen-bonding from amino –H and carboxyl =O in protein backbone.
• Broadly divided into:
• Helices there are also tertiary structure helices!]
• Sheets (composed of beta-strands – don’t mix up “strand” and “sheet”: a very, very common error is to conflate the beta strand (secondary structure) and the beta pleated sheet (tertiary structure)).
  alpha helix equivalent is beta strands
  turns are neight helix or beta pleated sheets

Question 3

Secondary structure helices (right-handed)

pitch=how many amino acyl residues per turn of the helix

WHY malgl aac?

Answer 3

*The alpha helix (α-helix) – 3.6 amino acyl residues per turn; 2.3 Å helix radius.
-Perutz (1951) Nature 167: 1053-1054.
- Most common helix in proteins.
- Usually about 10 aa residues, but can be 4-40+.
- Usually contains Methionine, Alanine, Leucine, Glutamate, and Lysine amino acids (alpha helix form because of side chains) but Proline and Glycine disrupt a helix (they cant hydrogen bond with anything could split helix and make turns).
-very stable and selected for

• The 3(10) helix (rare) – 3.0 amino acyl residues per turn; 1.9 Å helix radius
  -Bragg et al. (1950) Proc. Roy. Soc. A 203: 321-357.
• Very strained structure.
• Found in e.g. myoglobin and hemoglobin.
• Small radius but long
• Usually very short - <4 aa residues.
• The pi helix (π-helix) – 4.4 amino acyl residues per turn; 4.4 Å helix radius. always found in an alpha helix never by itself.
  -Low and Baybutt (1952) J. Am. Chem. Soc. 74: 5806-5807.
• Widest
• Energetically unfavourable – selected against unless functionally critical, so found near active-sites. Tends to break and degrade so organisms have to remake it.
• Usually seen as a bulge on a long alpha helix.
• Usually short – 7-10 aa residues, usually.

Question 4

(learn!) Give some examples of
*Alpha helicies
3(10)
Pi helix

Answer 4

*Alpha helicies (many!)
Isocitrate dehydrogenase (NAD+) (EC 1.1.1.41, Icd) from Acidithiobacillus thiooxidans

3(10) helix (circled)
Myoglobin (Mb) from Physeter microcephalus L.

Pi helix (circled)
Bacterioferritin (Bfr) (EC 1.1.1.41) from Blastochloris viridis
always found within an alpha helix wider part is the pi
Bacteriorhodopsin

Question 5

Beta-pleated sheet (β-sheet)
what do the aas have in common (side chain)

Answer 5

*They are Beta-strands connected by hydrogen bonds. shown as arrows
* Can be parallel or antiparallel and complex structures can form.
* Each strand is usually 3-10 aa in length.
* Usually contains Tryptophan, Tyrosine, Phenylalanine, Isoleucine, Valine and Threonine amino acids.
* Examples of different variations on this theme are on coming slides.

Question 6

Greek key motif (β-sheet)
A motif is a short conserved sequence pattern associated with distinct functions of a protein or DNA.
Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.

Answer 6

Greek key motif (β-sheets)
Greek key motif (circled)
Anthrax-toxin lethal endopeptidase (EC 3.4.24.83, Lef) from Bacillus anthracis.

• Four antiparallel strands and linking-loops.
• Richardson (1977) Nature 268: 495-500.

Question 7

Beta meander (β-sheets)

Answer 7

Beta meander (β-sheets)
Beta meander (circled)
Immunoglobin G-binding protein [aka Protein A]
(Spa) from Staphylococcus aureus
subsp. aureus
* 2+ anti-parallel strands linked by hairpin loops.
* Richardson (1977) Nature 268: 495-500.
* Can form tertiary domain structures e.g. beta barrel,
beta propeller.
*quite hydrophobic

Question 8

Beta helix (β-sheets)
Beta helix (right-handed)

Answer 8

Beta helix (β-sheets)
Beta helix (right-handed)
Thermal hysteresis protein
YL-1 [aka antifreeze protein YL-1]from Tenebrio molitor L.

• Parallel strands in tandem repeat structure – has 2-3 faces
• Kisker et al. (1996) EMBO J. 15: 2323-2330.

Beta helix (right-handed)
Ice-binding protein (IBP) from Flavobacterium frigoris

Beta helix (left-handed)
Antifreeze protein isoform 501 from Choristoneura fumiferana Clemens.

They all stop ice crystals forming so stop damage to cells in that way. they still freeze but without crystals
the faces are very hydrophobic.
More faces means it can bind to more ie crystals

Question 9

What are psychrotolerant and psychrophilic organisms?

Answer 9

psychrotolerant can live in the cold and psychrophilic requires the cold.