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

Amino acid ‘flexibility’

Side chain interactions

-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

Globular proteins are very compact3° structure

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