BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah

Protein Structure

Protein Structures

A study in the structure-function of proteins.

Amino acid sequence dictates function.

Structures are not “static” but breath and vibrate

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

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.}

Fibrous (structural) proteins 



 keratin proteins are helical

  but spacing differs from an  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

Left­handed coil   coiled­coil

310 AA residues 7­residue 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

Helical wheel diagram

a and d residues are nonpolar.

a ­ d are non­polar 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

Protein helices are stretchy and can elongate

When keratin is stretched it can form a more sheet like structure.

keratin of feathers and nails are extended and have a

more rigid and stiff consistency

epidermolysis bullosa simplex and epidermolytic

Silk Fibroin a



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.

Extended parallel  sheets of (­Gly­Ser­Gly­Ala­Gly­Ala­)_N 

Ala from one sheet interdigitates with Ala from another sheet

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

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

4­Hydroxyprolyl   3­Hydroxyproylyl

(4­Hyp) (3­Hyp)

Gly­X­Y   X often Pro    Y often Hyp  like a poly Gly or poly Pro helix

Left­handed 3.0 residues/turn pitch 9.4 extended 

conformation the prolines avoid each other.

Rope twist or metal cable 

longitudinal force (pulling) is  supported by lateral 

Collagen helices are  organized into fibrils.

689 A hole repeat

100 ­ 2000 A diameter 

different types make different 

Collagen is 0.4  12% 

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.