Lecture 14 - Protein Structure

Question 1

Bond rotation in primary structure of proteins

Answer 1

• Bonds between N-aC and aC-C can freely rotate
• Partial double bond prevents rotation between the C-N of the amide bond
  (C = carbonyl carbon)

Question 2

a-Helix strutcural characteristics

Answer 2

• Rod-like, tightly coiled
• R groups extend outward
• 3.6 residues per turn
• Stabilized by H-bonds between carbonyl oxygen and amide group 4 residues away
• Usually right-handed
• Prolines rarely found because they introduce destabilizing kink

Question 3

B-Sheet structural characteristics

Answer 3

• Polypeptide chain is extended into zig-zag conformation
• Adjacent R groups protrude in opposite directions
• Stabilized by H bonds
• Chains arranged side-by-side to form a series of pleats
• Adjacent polypeptide chains can run parallel or anti-parallel
• When sheets are layered closely the R groups must be small

Question 4

Tertiary structure is stabilized by

Answer 4

relatively weak interactions which include:

• disulfide bonds
• H-bonds
• salt bridges
• hydrophobic interactions

Question 5

Proteins that facilitate folding:

Answer 5

• Accessory factors - modify specific amino acid side chains to alter the outcome of protein folding
• Chaperones - Do no change the final outcome of the folding process, but prevent protein aggregation prior to completion of folding and prevent formation of non-productive intermediates

Question 6

Accessory factors

Answer 6

modify specific amino acid side chains to alter the outcome of protein folding

- Protein disulfide isomerase (PDI) - catalyzes formation of disulfide bonds
- Peptide polyl cis-trans isomerase - catalyzes the interconversion of the cis and trans isomers of proline peptide bonds

Question 7

Chaperones

Answer 7

Do no change the final outcome of the folding process, but prevent protein aggregation prior to completion of folding and prevent formation of non-productive intermediates

- Originally discovered as heat shock proteins (Hsp)
- HSP70 - bind while still being translated
- Hsp60 (aka Chaperonins)

Question 8

Collagen

Answer 8

• Most abundant protein in mammals
• Rich in glycine (33-35%)
• Collagen helix (polyproline type II helix or a-chain) is left-handed with 3 amino acids per turn
• 3 a-chains are twisted in a right-handed sense to form superhelix with glycines in the shared interior
• Contains hydroxyproline and hydroxylysine (these are Vitamin C dependent)
• Cross-linking of collagen molecules contributes to the strength of the fiber

Question 9

Diseases caused by abnormal collagen synthesis:

Answer 9

• Osteogenesis imperfecta (aka brittle bone disease)
• Ehlers-Danlos syndromes
• Scurvy

Question 10

Osteogenesis imperfecta

Answer 10

• aka brittle bone disease
• characterized by fragile bones susceptible to fracture, thin skin, abnormal teeth and weak tendons
• Most often caused by mutations in the COL1A1 gene encoding collagen I
• The dominance of type I collagen in bone explains why bones are predominately affected

Question 11

Ehlers-Danlos syndromes

Answer 11

• Type IV
  - caused by defects in type III collagen, which is particularly important in skin, arteries, and hollow organs
  - Manifestations may be severe, with arterial rupture, intestinal perforation, rupture of the uterus during pregnancy or labor, and easy bruising of thin, translucent skin
• Type VI
  - caused by a deficiency of lysyl hydroxylase
  - clinical features include marked hyper-extensibility of the skin and joints, poor wound healing, and musculoskeletal deformities

Question 12

Scurvy

Answer 12

• results from dietary deficiency of ascorbic acid
• Ascorbic acid deficiency causes decreased hydroxyproline and hydroxylysine synthesis because prolyl and lysyl hydroxylases require ascorbic acid
• Collagen containing insufficient hydroxyproline and hydroxylysine loses temperature stability and is less stable than normal collagen at body temperature.
• The resulting clinical manifestations are distinctive and understandable: suppression of the orderly growth process of bone in children, poor wound healing, and increased capillary fragility with resultant hemorrhage, particularly in the skin

Question 13

Mass Spectrometry

Answer 13

peptide fragment masses are used to determine the peptide sequence

Question 14

Two-dimensional gel electrophoresis

Answer 14

separates proteins by both charge and size

Question 15

Nuclear Magnetic Resonance (NMR)

Answer 15

can be used to determine structure and monitor dynamics for relatively small proteins (~250 amino acids or less)