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4. Protein Structure
Dr. Dale Hancock
[email protected]
How does a protein hold its 3D
shape?
• Proteins are only biologically active when
they have the right shape or 3D
conformation.
• It is no use having the correct amino acid
sequence if the shape is wrong!
Forces that maintain 3-D
protein conformation
•
•
•
•
•
Hydrogen bonding
Electrostatic or ionic interactions
Van der Waal’s interactions
Hydrophobic interactions
Disulphide bridges
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Weak Forces that maintain
3-D protein conformation
• Hydrogen bonding
– (12 -30 kJ/mol)
• Electrostatic or ionic interactions
– (20 kJ/mol)
• Van der Waal’s interactions
– (0.4 - 4 kJ/mol)
• Hydrophobic interactions
– (<40 kJ/mol)
Covalent Bond Energies
What are the bond energies of covalent bonds?
Energy kJ/mol
Bond
H-H
436
C-H
414
C-C
343
C-O
351
Hydrogen Bonding
• This results from the small dipole (uneven
electron distribution) that exists in certain
side chains and in the peptide bond itself.
• (12 -30 kJ/mol)
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Hydrogen Bonding:
the peptide bond
• The amide N of the peptide bond is an H
bond donor while the carbonyl O (from
another peptide bond) can act as an
acceptor.
• This interaction is largely sequence
independent.
Hydrogen Bonding
δ-ve
O
H3N+
CH
O
δ+ve
C
CH3
N
CH
C
H
CH
CH3
O-
CH3
Hydrogen Bonding
O
-O
C
O
CH
N
R
H
C
O
HN
CH
CH
NH
R
R
C
N
R δ-ve
H
CH
C
N
O
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Hydrogen Bonding: side chains
• The polar non-ionic side chains can also
participate in H bonding. Side chains with
–OH (Ser, Thr, Tyr), -SH (Cys) and amide
N-H (Asn, Gln) all act as H bond donors.
Side chains with –C=O (Asn, Gln) and
-OH can also act as acceptors.
• Side chain interactions are sequence
dependent.
H Bonding
Tyrosine
O
HN
CH
C
CH2
δ-ve
O
H
δ+ve
H Bonding
Cysteine
Tyrosine
O
HN
CH
C
O
HN
CH
C
CH2
CH2
SH
O
δ-ve
H
δ+ve
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H Bonding
Tyrosine
Cysteine
O
Glutamine
O
HN
CH
O
C
HN
CH
C
CH2
HN
CH2
CH
SH
CH2
C
δ-ve
O
δ+ve NH2
δ-ve
O
C
CH2
H
δ+ve
H Bonding
Tyrosine
Cysteine
O
Glutamine
O
HN
CH
O
C
HN
CH
C
CH2
HN
CH2
CH
SH
CH2
C
δ-ve
O
δ+ve NH2
δ-ve
O
C
CH2
H
δ+ve
Donors
H Bonding
Tyrosine
Cysteine
O
Glutamine
O
HN
CH
O
C
HN
CH
C
CH2
CH2
Acceptor
SH
HN
CH
CH2
C
O
δ+ve NH2
δ-ve
C
CH2
δ-ve
O
Acceptor
H
Acceptor
δ+ve
Donors
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Electrostatic interactions
(20 kJ/mol)
O
HN
• Side chains with
a positive charge
(His, Arg or Lys)
can interact with
those side chains
with a negative
charge (Asp or
Glu) if they are
close enough.
CH
C
CH2
CH2
CH2
NH
+NH2
C
NH2
OO
C
CH2
C
CH
NH
O
Electrostatic interactions
• Side chains with like charges will repel each
other.
HN
O
O
CH
H2C
C
-O
C
C
CH
HN
O
CH2
O
CH2
C
O-
Electrostatic interactions
• The strength of the interaction is also
dependent on the local environment. The
presence of high concentrations of salts
(high ionic strength), particularly on the
protein surface tend to weaken or dampen
down the strength of this force.
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Hydrophobic interactions
(<40 kJ/mol)
• Non-polar side chains will tend to cluster
together rather than mix with polar
solvents.
• This is an entropic effect: polar solvent
molecules (usually water) have more
options when the non-polar groups are
clustered than when they are scattered
throughout the polar solvent.
Non-polar solutes organise the
water into a cage surrounding them
Hydrophobic interactions
• In order to minimize the loss of entropy the
non-polar groups cluster together and bury
themselves in the core of a water soluble
protein.
• It is this interaction which drives
soluble proteins to fold.
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Van der Waal’s interactions
(0.4 - 4 kJ/mol)
• occurs when a charged or polar group
comes in close proximity with a non polar
group. The charged group will induce a
small dipole on the non-polar group.
• A transient dipole can be induced just from
fluctuations in the electron distribution in
neighbouring atoms.
Van der Waal’s interactions
• While these interactions are quite weak
singly, they make a major contribution in a
macromolecule like a protein where many
of these interactions occur.
Disulfide bonds
• In a reducing
environment such as
the cytosol of the
cell, cysteine
residues would exist
in a reduced form
i.e. as –SH.
O
HN
CH
C
CH2
SH
SH
CH2
C
CH
NH
O
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Disulfide bonds
• In a reducing
environment such as
the cytosol of the
cell, cysteine
residues would exist
in a reduced form
i.e. as –SH.
O
HN
CH
C
CH2
SH
SH
CH2
C
CH
NH
O
Disulfide bonds
• In an oxidising
environment such as
the cell surface or
exported proteins,
cysteine residues
would exist as
disulfide bonds
O
HN
CH
C
CH2
S
S
CH2
C
CH
NH
O
Disulfide bonds
• In an oxidising
environment such as
the cell surface or
exported proteins,
cysteine residues
would exist as
disulfide bonds
O
HN
CH
C
CH2
S
S
CH2
C
CH
NH
O
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What 3D structures can
proteins assume?
What 3D structures can
proteins assume?
psi
phi
O
+H3N
CH
O
O
H
N
C
CH
R1
H
N
C
CH
R2
C
O-
R3
What 3D structures can
proteins assume?
α carbon
α carbon
O
+H3N
CH
R1
C
α carbon
O
H
N
CH
C
O
H
N
R2
Peptide bond,
restricted rotation
CH
C
O-
R3
Free rotation
A tripeptide at pH 7.
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What 3D structures can
proteins assume?
α carbon
α carbon
O
+H3N
CH
C
O
H
N
R1
CH
C
O
These atoms
are all in one
plane
C
O-
α carbon
H
N
R2
Peptide bond,
restricted rotation
CH
R3
Free rotation
A tripeptide at pH 7.
The angles phi
and psi are
shown here
Figure 6.2
The amide or peptide bond planes are
joined by the tetrahedral bonds of the
-carbon. The rotation parameters are
and . The conformation shown
corresponds to = 180°and = 180°.
Note that positive values of and correspond to clockwise rotation as
viewed from C . Starting from 0°, a
rotation of 180°in the clockwise
direction (+180°) is equivalent to a
rotation of 180°in the counterclockwise
direction (-180°). (Illustration: Irving Geis.
Rights owned by Howard Hughes Medical
Institute. Not to be reproduced without
permission.)
Hierarchy of Protein Folding
• Primary
Amino acid sequence
• Secondary
Local structures
Alpha helix & Beta sheet
• Tertiary
Overall 3D arrangement of a polypeptide
chain
• Quaternary
Organisation of subunits
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Alpha Helix
Side chain
Backbone
Ribbon format
Properties of alpha helices
• All alpha helices found in naturally
occurring proteins are right handed due to
L-amino acids.
• Rigid structure with a single polypeptide
chain
• Side chains all face outwards
• All peptide C=O H-bond to an amide N
Beta Sheets
parallel
Anti parallel
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The Beta-Pleated Sheet
Composed of beta strands
• Also first postulated by Pauling and Corey,
1951
• Strands may be parallel or antiparallel
• Backbone almost fully extended
• Side chains orientate above and below the
plane of the sheet.
Figure 6.10 A “pleated sheet” of paper with an antiparallel β-sheet drawn on it. (Irving
Geis)
Figure 6.11 The arrangement
of hydrogen bonds in (a)
parallel and (b) antiparallel βpleated sheets.
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Tertiary Structure
Tertiary Structure
• The backbone links between elements of
secondary structure are usually short and
direct
• Proteins fold to make the most stable
structures (make H bonds and minimize
solvent contact)
Quaternary Structure
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