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Structure and Function
of Proteins
Ora Schueler-Furman
2009-2010
1
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3
PROTEINS
From the Greek word
proteio
“Proteios”
- first rank, most important
Play central roles in all biological processes
4
Introduction into
Protein Structure
• The chemical nature of polypeptides
• Forces that determine protein structure
5
The 4 Hierarchical Levels of
Protein Structure
6
Primary Structure: Sequence
7
Formation of a Peptide Bond
H
+H N
3
Ca
O
C
O-
R
cpk colors
O - oxygen
H - hydrogen
N - nitrogen
C - carbon
8
Dihedral Angles F and 
define Backbone Geometry

w
F
The peptide bond w is planar and polar
9
Basic Facts
Polypeptide chain:
But also >20000 aa:
50-10’000 aa
34’350 aa (Titin)
Average MW of aa :
110 daltons
Average MW of a protein of length n aa:
n X110
Distance (Cai – Cai+1) <=3.63Ǻ
aa – amino acid
10
Basic Terms
Main chain, backbone, side chain, residue
bb
sc
Peptide:
a small # of connected aa
Polypeptide: a longer chain of aa
Protein:
polypeptide chain with defined
aa sequence & conformation
11
The Protein Alphabet: 20 letters
A
C
D
E
F
G
H
I
K
L
Ala
Cys
Asp
Glu
Phe
Gly
His
Ile
Lys
Leu
Alanine
Cysteine
Aspartate
Glutamate
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
M
N
P
Q
R
S
T
V
W
Y
Met
Asn
Pro
Gln
Arg
Ser
Thr
Val
Trp
Tyr
Methionine
Aspargine
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophane
Tyrosine
amino acids vary in:
volume, shape, chemical nature
(charge, hydrogen bonding capability, etc.)
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Special Amino Acids
CO
N
C
H
H
H
• The simplest aa
• No sc
• Very flexible bb
CO
N
C
H2C
CH2
H
• Cyclic aa
• sc Connects bb N
• Very constrained bb
CH2
13
Aliphatic Amino Acids
• sc contains only carbon and hydrogen atoms
• hate water
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Amino Acids with Hydroxyl Group
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Negatively Charged Amino Acids
different size → different tendency for 2. structure
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Amide Amino Acids
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Positively Charged Amino Acids
• pKa 11.1
• pKa 12
• large sc
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Aromatic Amino Acids
• pKa 7
• benzene
ring
• sc contains aromatic ring
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Amino Acids with Sulfur
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Cystine
Oxidation of Sulfur
atoms creates
covalent disulfide
bond (S-S bond)
between two
cysteines
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S-S Bonds Stabilize the Protein
A chain s
s
GIVEQCCASVCSLYQLENENYCN
s
s
B chain
s
s
F V N Q H L C G S H L V E A L Y L V C G E R G F..
N
C
A chain
Insulin
B chain
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Post-Translational
Modifications
• Processing (proinsulin/insulin)
– control of protein activity
• Glycosylation
– protein trafficking
• Phosphorylation (Tyr, Ser,
Thr)
– regulation of signaling
• Methylation, Acetylation
– histone tagging
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Metal Binding Proteins
• aa: HCDE
• Fe, Zn, Mg, Ca
• Fe
– blood: red hemoglobin
– electro-transfer: cytochrome c
• Zn
– in DNA-binding “Zn-finger” proteins
– Alcohol dehydrogenase: oxidation of
alcohol
24
Forces that
Determine Protein
Structure
25
Non-Covalent Forces Add up
Each bond is
weak
Large number
of bonds
From: the Molecular Biology of the Cell, 4th ed.
26
E(r) = K/rp
p=1: Coulomb interaction
between two charges
E(r) – energy of
attraction
Attractions between molecules
p=1
p=6
r – distance between molecules
p>1: delocalized charges – weaker interactions
p=6: interaction between neutral molecules
Short-range interactions: p>=3
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1. Van der Waals Interactions
(Lennard Jones Potential)
Attractive:
weak, due to transient
dipoles
rij
Repulsive:
Atoms do not penetrate
each others →
spheres (VdW-radii)
1Ǻ = 0.1nm
0.5-1kcal/mol
From: the Molecular Biology of the Cell, 4th ed.
28
2. Hydrogen Bonds
d
H
N
O
C


Donor
Acceptor
Hydrogen “shared”
between two
electronegative atoms
Important for 2nd struct.
Interaction with water
1-3kcal/mol
From: the Molecular Biology of the Cell, 4th ed.
29
3. Electrostatic Forces
(Salt Bridges)
Coulomb’s law:
E = kqAqB/Dr
qA, qB : point charges
r: distance
k=332 (for units of kcal/mol)
D: dielectric constant
(water:80; protein: ~4)
Solvent screening: D’ = DrAB
qA
qB
r
3Ǻ: ~1.4
kcal/mol
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4. Aromatic Rings: p-p and
Cation-p Interactions
Aromatic ring: cloud of p
electrons: negative charge
From: wikipedia.
Can interact with
• positive charge of Lys,
Arg, His
• edge of other aromatic
ring
31
5. Water
• polar
• cohesive
•competes with interactions in the
protein (Hb, SB)
• high D – reduces electrostatic
forces
• hydrophobic effect
• explicit modeling difficult
From: the Molecular Biology of the Cell, 4th ed.
32
Accessible Surface Area
Van der Waals surface
• Roll ball (radius = 1.4Ǻ; H2O) over molecule
• polar vs apolar: well solvated protein – polar
atoms at surface, apolar atoms in the core
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Non-Covalent Forces: Summary
• VdW: Many small contributions sum up to
significant energy
• Salt bridges and hydrogen bonds: polar
interactions are reduced by competing water
at the surface
• Surface of protein: hydrophobic atoms
should be all buried
34