Fibrous Proteins
Examples
1. a-keratins
Hair, nails, horns, skin
2. Silk Fibroin
3. Collagen
4. Elastin
Saw Varsity’s a-keratins off
Amino Acid Composition of Fibrous Proteins
Gly
Ala
Ser
Glu + Gln
Cys
Pro
Arg
Leu
Thr
Asp + Asn
Val
Tyr
Ile
Phe
His
Met
Trp
a-Keratin Fibroin
(Wool)
(Silk)
8.1
44.6
5.0
29.4
10.2
12.2
12.1
1.0
11.2
0
7.5
0.3
7.2
0.5
6.9
0.5
6.5
0.9
6.0
1.3
5.1
2.2
4.2
5.2
2.8
0.7
2.5
0.5
0.7
0.2
0.5
0
1.2
0.2
Collagen Elastin
(Tendon) (Aorta)
32.7
32.3
12.0
23.0
3.4
1.3
7.7
2.1
0
tr.
22.1
10.7
5.0
0.6
2.1
5.1
1.6
1.6
4.5
0.9
1.8
12.1
0.4
1.7
0.9
1.9
1.2
3.2
0.3
tr.
0.7
tr.
0
tr.
a-Keratin
Keratin: an Intermediate Filament Protein
What’s in Hair
and Wool?
H
H N
Collagen
N H
C (CH2) 3 C=C (CH2) 2 C
CHO
O= C
C= O
Covalent Crosslink
Intramolecular Crosslinks
Left hand
a-helix
b a’
a
Gly-X-Y
X=Pro
Y=HO-Pro
Intermolecular Crosslinks
Quarter Stagger
ELASTIN
Property of Resilience
4-way Stretch
Aorta
Lung
Ligamentum Nuchae
H H O
N C C
N
H C (CH2)2
O= C
Elastin network
(CH2)3
N
(CH2)4
N C C
H H O
N H
(CH2)2 C H
C= O
Desmosine
Overall Shape (applies mainly to globular proteins)
Structural Motifs
Alpha helix
Beta barrel
Beta structure
Beta-alpha-beta
Globular Protein Molecules
3-Dominant Structural Features
a Helix
Beta Sheet
Packs
Framework
Turns or loops
Connects
Typical Protein
Rules Governing Protein Folding
Can we predict how a protein will fold on the
basis of amino acid sequence data alone?
1. Globular Proteins have a defined outside and inside
Hydrophobic buried inside
Hydrophilic outside
Folding and Biological Activity
Enzyme Active Site
Z
X
Y
Random Coil
Denatured
Z
X Y
Folded
Biologically Active
TURNS (on Surfaces)
Reverse direction abruptly
Beta Bends or Turns (4 residues to execute sharp turn)
H-bonding between carbonyl residue1 and
amide N on residue 3.
Glycine not in loop (Type I turn)
Glycine in loop
(Type II turn)
Gamma (very tight turn)
Proline in loop, bonding between 1 and 2
Tight Turn
N
O= C
C= O
N
Reverse Turn in Polypeptides
Glycine
H-bond
between
1 and 4
Twice more common than type 2
Chou-Fasman Rule for Predicting Secondary
Structure
Propensity
Amino Acid
Pa
Helix
Pb
Pt
Beta Sheet Beta Turn
Ala
Cys
Leu
Met
Lys
1.29
1.11
1.30
1.47
1.23
0.90
0.74
1.02
0.97
0.77
0.78
0.80
0.59
0.39
0.96
Val
Ile
Thr
0.91
0.97
0.82
1.49
1.45
1.21
0.47
0.51
1.03
Gly
Ser
Asp
Pro
0.56
0.82
1.04
0.52
0.92
0.95
0.72
0.64
1.64
1.33
1.41
1.91
Protein Folding Mystery
To fold a protein is negative entropy with
respect to the protein. You go from a disordered
to an ordered state.
Folding is away from a natural tendency
to exist in a random state?
Where is the energy driving protein folding?
ANSWER IN TEXTBOOK
Folded
Unfolded
N
N
C
ORGANIZED WATER
DSTotal = DSsys - DSsurround
C
QUATERNARY STRUCTURE
SUBUNIT STRUCTURE
Multisubunit
Proteins
HOMODIMER
HETERODIMER
WEAK FORCES IN PROTEIN
Hydrogen Bond: A hydrogen bond is a linear dipole that result when hydrogen atom
bond covalently to either N or O is attracted by an electron pair from a neighboring N or
O. The attracting force is basically electrostatic.
Disulfide Bond: A strong covalent bond formed by two –SH groups of cysteines. This
bond can only be broken to component -SH groups by reducing agents.
Electrostatic Bond: This bond is based force of attraction between oppositely charged
ions. Each charged ion has an electric field that can be penetrated by a field of opposite
polarity or repelled by like polarity.
Hydrophobic Bond: This bond’s strength is attributed to water avoidance.
Consequently, hydrophobic bonds are move evident in a protein’s interior.
Hydropathic Index
hydrophobic
hydrophilic
+
_
Determining Hydropathic Index
Sum 1-9 (window)
Sum 2-10
Sum 3-11
Sum 4-12
Sum 5-13
Sum 6-14
(-)
(+)