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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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protein structure

Protein Structure

Lecture 2/26/2003

protein structures

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

slide3

Globular proteins = enzymes and catalysts

Fibrous proteins = structural or connective role.

Structure - function relationships

Some residues and chains are just disordered “Floppy” flexible which maybe required for function

slide4

Fibrous (structural) proteins

Keratin

  • Nails, hair, horns and feathers
  •  or  forms
  • 30 variants, tissue specific
  • type I and type II
  • acidic negative charge basic positive charge
  •  keratin -
  • hair- 20 M diameter
  • macrofibril 2000 Å parallel to hair
  • microfibril 80 Å and high sulfur cement protein.
slide6

 keratin proteins are helical

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

3.6

a - b - c - d - e - f - g a repeat on side of helix



slide8

Helical wheel diagram

a and d residues are nonpolar.

Protofilaments antiparallel strands

slide9

a - d are non-polar and face the same side of helix.

3.6 residues/turn

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.

slide10

Protein helices are stretchy and can elongate

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.

silk fibroin a b pleated sheet
Silk Fibroin a b pleated sheet

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.

slide12

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

Ala from one sheet interdigitates with Ala from another sheet

Silks from different species have different interdigitating groups and have differing physical properties.

slide13

Silk fibers are strong when extended but cannot be stretched because of the fully extended sheet form of fibroin

collagen triple helical cable
Collagen - Triple helical cable

Bones, teeth, cartilage, tendon, ligament, blood vessels and skin matrix

Strong, flexible, stretchy

Several types

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

slide15

1/3 Gly 15-30% -4-Hydroxyproline (Hyp) some 5-Hydroxylysyl (Hyl)

4-Hydroxyprolyl 3-Hydroxyproylyl

(4-Hyp) (3-Hyp)

C

C

N

CH

N

CH

1

2

1

2

H

3

CH2

H3C

5

5

3

C

H3C

4

OH

4

C

C

OH

H

H

H

slide16

Gly-X-Y X often Pro Y often Hyp

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.

slide18

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

slide19

Collagen helices are organized into fibrils.

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)

slide20

Vitamin C is required for hydroxyproline formation

Hydroxyproline gives collagen stability and strength by H-bonding.

Without prolyl hydroxylase collagen denatures at 24C instead of 39 to form gelatin.

Scurvy-skin lesions, broken blood vessels, wounds don’t heal, teeth fall out, one cannot stand.

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