secondary structure elements helices strands/sheets/barrels turns the type of 2° structure is...
TRANSCRIPT
Secondary structure elements
• helices
• strands/sheets/barrels
• turns
• The type of 2° structure is determined by the amino acid sequence– Chemical & physical characteristics– How? Area of research
-turn
• Proteins up to 1/3 turns and loops
• Common linker for -sheets and -helices
• 180o turn involving 4 residues– H-bond between
C=O and N-H
• Which AA?
-turn
• Proline – Imino N cis
conformation (6%)
• Glycine– Very flexible
• Often found on the exterior of the folded protein: solvent exposed
3° and 4° structure
• 3° structure
– Overall 3-D arrangement– Interaction of 2° structural elements
• 4° structure
– Arrangement of separate chains/subunits– Non-covalently linked
• Possible exception: disulfide bonds
• 2 classes of proteins– Fibrous proteins (extended)– Globular proteins (~spherical)
Fibrous proteins
• Structural roles• Typically single type of 2° structure
– Long strands of helices (eg. -keratin/collagen)– Big sheets of structure (eg. silk)
• Insoluble in H2O conc of H-phobic on interior and surface– Buried by packing chains together
• Strong and flexible– (eg. hair, silk, cartilage)
Collagen
• Major constituent of connective tissues (bone, tendon, ligaments, skin…)
• Helical 2° structure distinct from helix– 3 AA/turn (tighter– Left-handed (opposite
twist)• collagen “triple helix”
tropocollagen– Helix: 2° structure– Triple helix: 4° structure
Collagen
• Gly (35%), Ala (11%) and Pro (or HyPro) (21%)• Every 3rd residue is a Gly (Gly–X-Y-Gly–X-Y)
– Genetic defects when G is changed (“mutated”)• eg. osteogenesis imperfecta
• Chains linked by H-bonds – Backbone NH of Gly and backbone C=O of X in another
chain
• Chains also linked by uncommon covalent bonds– Side chain linkage
Collagen• Triple helix aligns and
crosslinks collagen fibrils– Crosslinked via
covalent bonds between Lys, HyLys and His
• Too many crosslinks?– ↓ flexibility– aging
NH2
CH
C
H2C
OH
O
H2C
H2C C
HN
NH2
CH
C
H2C
OH
O
H2C
HCH2C
OH
Lys HyLys
Silk Fibroin
• Webs of insects and spiders
• Antiparallel -sheets– Rich in Ala and Gly– Close packing of -sheets– H-bonding between all
backbone N-H and C=O
• Extended but flexible
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
How is the 3D structure determined?
• X-ray crystallography– Form ‘crystals’ of the protein
• Regularly repeating lattice• X-ray beam is diffracted by the lattice• Just like a microscope
– Much shorter wavelength (higher energy) light– Computer acts as a ‘lens’
• Size of protein is theoretically unlimited
How is the 3D structure determined?
• X-ray crystallography– Get a ‘snapshot’ of the protein in a solid-ish
phase– Need highly ordered crystals– Proteins come in close contact: may influence
the structure
How is the 3D structure determined?
• NMR– Nuclear spins of 1H, 13C, 15N, etc.
• Detect via energetic response to a magnetic field• Response depends on chemical environment
– Distance between all pairs of atoms within the molecule– Software (with plenty of help from the user) determines
structures that satisfy these distances
How is the 3D structure determined?
• NMR– Only fairly small (<25kDa) proteins– Need highly concentrated sample
• Lots of protein• Very soluble
• NMR and crystallography are complementary techniques