Protein Structure. Lecture 2/26/2003. Protein Structures. A study in the structure-function of proteins. Amino acid sequence dictates function. Structures are not “static” but breath and vibrate Protein dynamics (movement) can be linked to function. Globular proteins = enzymes and catalysts
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A study in the structure-function of proteins.
Amino acid sequence dictates function.
Structures are not “static” but breath and vibrate
Protein dynamics (movement) can be linked to function
Fibrous proteins = structural or connective role.
Structure - function relationships
Some residues and chains are just disordered “Floppy” flexible which maybe required for function
but spacing differs from an a helix
a 5.1 Å vs. 5.4 Å pitch.
This change in pitch forms closely associated pairs of helices. Each pair consists of a type I and type II protein
Left-handed coil coiled-coil
310 AA residues 7-residue pseudo repeat.
Helical wheel - Look down an helix and residues stick out from center of helix 3.6 residues/turn 360 = 100 per residue
a - b - c - d - e - f - g a repeat on side of helix
a and d residues are nonpolar.
Protofilaments antiparallel strands
3.5 residues hydrophobic repeat
The hydrophobic strip aligns between two helices with 18 inclination from one to another.
They fit well together
Dimer protofilament microfibril macrofibril hair
keratin rich in cys and forms disulfides
hard keratin cys content is high
soft keratin cys content is cyst low
Perms reduce R-S---S-R bonds to 2R-SH
Curly hair has more Cys residues.
When keratin is stretched it can form a more sheet like structure.
b-keratin of feathers and nails are extended and have a more rigid and stiff consistency
epidermolysis bullosa simplex and epidermolytic hyperkeratosis are keratin related diseases involved in the loss of mechanical integrity of the shin.
From spider and insect webs, cocoons, nests and egg sacks.
An almost fully extended sheet that cannot stretch and is strong.
This is why spiderman can support his weight on the web material!!
Fibroin and sericin = web
sericin is an amorphous gummy protein
Adult moths dissolve (hydrolyze) their cocoons by cocoonase, this digests sericin, clothmoths do the same.
Boiling water also removes sericin and leaves fibroin or silk.
Ala from one sheet interdigitates with Ala from another sheet
Silks from different species have different interdigitating groups and have differing physical properties.
Silk fibers are strong when extended but cannot be stretched because of the fully extended sheet form of fibroin
Bones, teeth, cartilage, tendon, ligament, blood vessels and skin matrix
Strong, flexible, stretchy
I [1 (I)]2 2I skin, bone tendon, cornea vessels
II 1 (II)3 cartilage
III [1 (III)]3 vessels, fetal skin
Type I 285 kDA 14A wide
3000 A long 30 distinct peptide types 16 variants
like a poly Gly or poly Pro helix
Left-handed 3.0 residues/turn pitch 9.4 extended conformation the prolines avoid each other.
3 left handed helices combine in a triple rt handed coil.
Rope twist or metal cable longitudinal force (pulling) is supported by lateral compression opposite twisted strands prevents twists from pulling out.
689 A hole repeat
100 - 2000 A diameter different types make different arrays dark us light areas on fibril
Hydrophobic repulsion drives fibril formation possible Van der Waals attraction due to packing.
Collagen is 0.4 12% carbohydrate (linked sugars)
Hydroxyproline gives collagen stability and strength by H-bonding.
Without prolyl hydroxylase collagen denatures at 24C instead of 39 to form gelatin.
Scurvy-skin lesions, broken blood vessels, wounds don’t heal, teeth fall out, one cannot stand.