2o structure

1
2o structure

• Most all structural elements described by ? and ?
• Glycine exception
• AAs may occur more often in certain 2o structures
  than others
• Strong correlation
• Only Gly, Pro

2
3o and 4o structure

• 3o structure
• Overall 3-D arrangement
• 4o structure
• Arrangement of separate chains/subunits
• 2 classes of proteins
• Fibrous proteins
• Globular proteins

3
Fibrous proteins

• Structural roles
• Repeating 2o structure (sequence?)
• Insoluble in H2O
• ? conc of H-phobic on interior and surface
• Buried by packing chains together
• a-keratin, silk fibroin, and collagen

4
Collagen

• Major constituent of connective tissues (bone,
  tendon, ligaments, skin)
• Left-handed helix with 3 AA/turn (very tight vs.
  a)
• 3 chain helices twist (right)? collagen triple
  helix ? tropocollagen

5
Collagen

• Gly (35), Ala (11) and Pro or HyPro (21)
• Every 3rd residue is a Gly (GlyX-Pro-GlyX-HyPro-
  Gly X-HyPro)
• Genetic defects when G?A
• Chains linked by H-bonds
• Backbone NH of Gly and backbone CO of X in
  another chain
• HyPro? also involved in intrachain H-bonds
• Vitamin C dependent synthesis
• Prolyl hydrolase (Fe2 metalloprotein)

6
Collagen

• Triple helix aligns and crosslinks? collagen
  fibrils
• Crosslinked via covalent bonds between Lys, HyLys
  and His
• Too many crosslinks?
• flexibility?

7
Silk Fibroin

• Webs of insects and spiders
• Antiparallel b-sheets
• Rich in Ala and Gly
• Close packing of b-sheets
• H-bonding between all backbone N-H and CO
• ? extended, but flexible

8
Globular proteins

• Variety of structures/functions
• Enzymes, transport proteins, motor, regulatory,
  immunoglobulin
• Folding is compact
• H philic? outside
• H phobic ? inside

Human serum albumin
Alcohol dehydrogenase
N-acetylglucosamine acyltransferase
9
Myoglobin

• Stores/diffuses O2 in contracting muscle
• 153 AA
• 1 Heme group (Fe protoporphyrin)
• 8 a helices and b turns
• Hydrophobic vs hydrophilic?
• Fe is not water accessible

10
3o structure determination

• X-ray diffraction (crystallography)
• Crystalize protein
• X-ray beam diffracts based on electron density of
  atoms
• Computer analysis (construct e- density map)
• Build structural model
• Problems??

11
3o structure determination

• NMR
• 30 kDa or less in MW
• In solution
• Monitor atoms with a nuclear spin (1H, 13C,
  15N..)
• Spin generates a dipole
• Apply a magnetic field to align
• Radiation pulse to flip nuclei
• 1H NMR ? complex
• 2-D NMR
• Monitor atom coupling through space (NOESY) and
  covalent bonds (TOCSY)

12
3o structure determination

• 2-D NMR

13
3-D structure

• Classify according to substructure
• How 2o elements come together
• Motifs/supersecondary structures
• Stable, common arrangements of 2o elements
• b-a-b loop
• a-a corner
• b-barrels
• Greek key
• Jellyroll
• b-meander
• a-a unit