Chapter 6: Structural Proteins

Quick Review-Structure Basics

Phi, Psi, Ramachandran Diagram a-Helix, b-Sheet, b-Turn

Structure-Function of Proteins
Helical Proteins-Keratin, Collagen b-Sheet Proteins- Silk

Tertiary and Quaternary Structure

Higher Order Structures AA Sequence Dictates Function

Phi and Psi Torsion Angles

Rotation or dihedral angles Ca-N phi Ca-C psi When a peptide chain is fully extended the angles are defined as 180 or -180 (these are the same). At 180, one gets a staggered conformation - (trans) e.g., n-butane

Note: alternating C=O pointing in opposite directions.

When viewed down the Ca-N axis, rotation to the right or clock wise increases the angle of rotation.

Must start with the fully extended form which is defined as 180o or -180o

Ramachandran Diagram
If you plot on the Y-axis and on the X-axis, you will plot all possible combinations of , .
You must know the identities of the different regions of the Ramachandran diagram. That is, you must be able to identify them on an exam, since you will be given the figure with no labels. See next slide!

The a-Helix
The most favorable F and Y angles with little steric hindrance. Forms repeated hydrogen-bonds along backbone. n = 3.6 residues per turn p = 5.4 (What is the d for an a-helix?) d=p/n=5.4/3.6=1.5 The C=O of the nth residue points towards the N-H of the (N+4)th residue.

The N

hydrogen-bond is 2.8 and the atoms are 180o in plane. This is almost optimal with favorable Van der Waals interactions within the helix.

b-Sheet Facts
Repeat distance is 7.0 R group on the amino acids alternate up-down-up above and below the plane of the sheet 2 - 15 amino acids residues long 2 - 22 strands per sheet Avg. of 6 strands with a width of 25

parallel less stable than antiparallel

Antiparallel needs a hairpin turn Tandem parallel needs crossover connection which is right handed sense

Non-Repetitive Structures
Turns - coils or loops: 50% of structure of globular proteins are not repeating structures b-bends (b-turns) - type I and type II: hairpin turn between antiparallel sheets

3
3 2 2

Type I 2 = -60o, 2 = -30o 3 = -90o, 3 = 0o Type II 2 = -60o, 2 = 120o

3 = 90o, 3 = 0o

Keratin: A Quasi a-Helical Protein

Nails, hair, horns and feathers a or b-forms Over 30 variants, tissue specific type I and type II acidic negative charge basic positive charge a keratin hair- 20 M diameter macrofibril 2000 parallel to hair microfibril 80 and high sulfur content protein can break -S-S- with mercaptans and reconnect (i.e. can give hair a permanent wave)

a-Keratin proteins are modified a-helix proteins

5.1 vs. 5.4 pitch. Closely associated pairs of helices. Each pair consists of a type I and type II protein Left-handed coiled-coil 310 AA residues 7-residue pseudo repeat. Helical wheel - Look down an a helix and residues stick out from center of helix 3.6 residues/turn 360 = 100 per residue 3.5 residues/turn in a-keratin because of diff pitch

a-b-c-d-e-f-g-a

repeat on side of helix

Dimer protofilament microfibril macrofibril hair

Helical wheel diagram a, d and a, d residues are nonpolar. 3.5 residues/turn 3.6 residues/turn a-helix

Helices align with 18 inclination to each other. Coil around each other.
a-keratin lots of disulfides hard keratin cys content is high soft keratin cys content is low Curly hair has more Cys residues. Perms reform disulfide bonds

Silk Fibroin: b-Pleated Sheet

Spider and insect webs, cocoons, nests, and egg sacks. An almost fully extended b-sheet that cannot stretch and is extremely strong. Fibroin + sericin = web (sericin = amorphous gummy protein)
Adult moths dissolve (hydrolyze) their cocoons by cocoonase, cloth eating moths do the same by digesting sericin. Boiling water also removes sericin and leaves fibroin or silk strand!

Extended parallel b-sheets of (-Gly-Ser-Gly-Ala-Gly-Ala-)N

Ala from one sheet interdigitate with Ala from another sheet
Silks from different species have different interdigitating groups and have differing physical properties.

Gly
Ala Gly Ala

Silk fibers are strong when extended but cannot be stretched because of the fully extended sheet form of fibroin, however, they are pliable because of the hydrophobic contacts between b -strands

Collagen A Triple Helical Cable

Bones, Teeth, Cartilage, Tendon, Ligament, Blood Vessels, Skin Matrix: Strong, Flexible, Stretchy I II III [a1(I)]2a2(I) [a1(II)]3 [a1(III)]3 skin, bone tendon, cornea vessels cartilage vessels, fetal skin

Type I 285 kDa

14 wide

3000 long 30 distinct peptide types 16 variants

1/3 gly; 15-30% 4-hydroxyproline (Hyp); some 3-hydroxyproline (3-Hyp), and some 5-hydroxylysine (Hyl)

Gly-X-Y X often Pro Y often Hyp Small percentage of Hyl at X and Y

Human Pro Alpha 1 (I) Collagen GPP-GPA-GFA-GPP-GAD-GQP-GAK-GEP

Left-Handed 3.0 residues/turn pitch 9.4 extended conformation the prolines avoid each other. 3 left handed helices combine in a triple right handed coil.

Rope twist or metal cable longitudinal force (pulling) is supported by lateral compression opposite twisted strands prevents twists from pulling out.

Vitamin C is Required for Hydroxyproline

Without prolyl hydroxylase, collagen denatures at 24C instead of 39 to form gelatin. Hydroxyproline gives collagen stability and strength by H-bonding. Scurvy-skin lesions, broken blood vessels, wounds dont heal, teeth fall out, cannot stand.

Crosslinking requires lysine oxidase N C - CH2 - CH2 - NH2 pea b-Aminopropionitrile, from sweet

Inhibits lysine oxidase i.e. no crosslinking several diseases: Lathyrism (abnormalities in bones, joints, etc.) Osteogenesis imperfecta, brittle bone, A single amino acid change could be lethal Ehlers-Danlos syndromes, hyperextensible joints and skin, Indian rubberman

Osteoarthritis - cartilage.

Tertiary Protein Structure

Describes folding of secondary structural elements Determined via X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy 3D structures of many proteins are available at http://www.rcsb.org/pdb

X-ray Crystallography
X-rays are bounced off of the protein and deflected by electrons in the various atoms/bonds. The diffraction pattern of the Xrays is measured and an electron density map is created (blue in the figure to the left). Amino acids structures are fit into the electron density.

NMR Spectroscopy
Paramagnetic nuclei have interactions with external magnetic field. Nuclei can absorb energy at particular frequencies (resonance frequencies). Resonance frequencies are sensitive to chemical environment and nearby nuclei. Constraints for distances between nuclei = structure information.

Family of Structures

Motifs and Domains

a-helix
from whale hemoglobin has non-polar residues (yellow) and polar residues (purple) on opposite sides of the helix.

b-sheet
with protein binding domain on the side with non-polar residues (orange) leaving the polar ones (purple) facing solvent water

Sidechain Locations in Proteins

Non-polar sidechains (Val, Leu, Ile, Met, and Phe) occur mostly in the interior of a protein keeping them out of the water (hydro-phobic effect) Charged polar residues (Arg, His, Lys, Asp, and Glu) are normally located on the surface of the protein in contact with water. Uncharged polar residues (Ser, Thr, Asn, Gln, and Tyr) are usually on the protein surface but also occur in the interior of the protein.

Selected Protein Structures

Cytochrome b562 Immunoglobulin Fab Lactate dehydrogenase

Beta-Barrel Proteins
Retinol binding protein Triose phosphate isomerase

Peptide amidase F

All b -Sheet (looks like b-clam)

Jack Bean Concanavalin A

Orange spheres are metal ions

bab

Supersecondary Structural Motifs

b-hairpin

aa

Most common Common

Nucleotide binding Rossman Fold babab

b-barrels

Zinc finger - DNA binds to a-helix

Protein Domains
Many single polypeptide proteins fold into multiple structural domains, each with their own function glyceraldehyde-3-phosphate (GAP) dehydrogenase The blue domain binds NAD+

The orange domain binds GAP

A glycolysis pathway enzyme

Structure is Conserved more than Sequence

C-type cytochromes

Quaternary Protein Structure

4o structure is the relative placement of different polypeptide segments Hemoglobin is shown to the left (a1-yellow, a2-green, b1-cyan, b2-blue), heme groups are in red - bind O2

Protein Folding
We will not cover this section. However, be aware that proteins can be unfolded/denatured. Denatured proteins can be refolded, sometimes requiring helper proteins, and this refolding takes place via preferred pathways. Common thought is that secondary structures form first, eventually collapsing due to the formation of hydrophobic cores