The Wonderful World of Proteins

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The Wonderful World of Proteins

• Elements of protein structure.
• Forces that assemble proteins.
• Protein secondary structures
• Intro to hemoglobin
• Importance of cooperativity

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Primary Sequence Structure
-Leu - Arg - Asp - Asp - Ser - Leu - Ala - Asp -
Glu - Leu - Tyr - Phe - Glu -
Proteins can self-assemble! All the information
needed to make a working 3-D machine is encoded
in the amino acid sequence!
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What holds proteins together?
All the atoms of the polypeptide chain interact
with each other to guide the folding of the
protein into its native state.
Some interactions that are important in
stabilizing proteins include

• The hydrophobic effect

• Hydrogen bonds

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The hydrophobic effect
Water and oil They dont like each other.
When you drop oil into water, it tends to glob up
into little droplets. Proteins act the same way.
All the greasy hydrophobic residues tend to up
in the middle of the protein making a
hydrophobic core. The polar and charged
residues tend to line the outside of the protein
as they are happy interacting with water.
Polar and charged residues on the
outside. Greasy residues on the inside.
A protein cross-section.
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Hydrogen bonds
Hydrogen bonds occur when a proton (hydrogen) is
shared between a donor group and the unpaired
electrons of an acceptor oxygen. Proteins fold
such that all hydrogen bonding groups participate
in a hydrogen bond.
Donors N-H O-H
AcceptorO
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The Protein Folds Itself.
These forces work in combination to direct the
assembly of the polypeptide into a complicated
functional structure.
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Secondary Structure in Polypeptides
Polypeptides are often found in periodic
structures where each amino acid adopts the same
backbone conformation. These periodic structures
are known as secondary structure. The criterion
for a secondary structure 1. Must satisfy
hydrogen bonding of the backbone amide and
carbonyl. 2. Must form a compact structure
without internal cavities.
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The Alpha Helix
By model building, Linus Pauling guessed that the
alpha helix, a right-handed helix with 3.6
residues per turn, would be the most stable
secondary structure.
The hydrogen bonding of the backbone is
completely satisfied with intramolecular bonds.
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The Alpha Helix
It forms a compact structure with no internal
cavities.The side-chains of each residue stick
out like little decorations.
Example of a mostly alpha-helical protein
Myoglobin.
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Helices without Hydrogen Bonds
Homopolymers of the freaky residues proline and
glycine can form left-handed helices with 3
residues per turn that do not use hydrogen bonds.
These conformations are important in structural
proteins like collagen.
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Beta Structures
Pauling and Corey continued thinking about
periodic structures that could satisfy the
hydrogen bonding potential of the peptide
backbone. They proposed that two extended peptide
chains could bond together through alternating
hydrogen bonds.
Alpha, Beta, I got ALL the letters up here,
baby!
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Beta sheets are pleated.
And the ruffles add flavor!

• Facts about B-sheets
• Each strand is usually 6-12 residues long.
• Unlike the local interactions in helices, beta
  sheets are composed of long-range interactions
  adjacent strands can come from completely
  different sections of a polypeptide chain or even
  different polypeptides.
• The side chains of adjacent residues in the
  polypeptide sequence extend on opposite faces of
  the sheet more on this in a bit.

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Steric vs H-bonding
The local interactions in the peptide backbone
are a bit strained in the ideal conformation
shown here. As a result, beta sheets tend to be
distorted into a right-handed twist
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Hemoglobin, my best friend.Something that red
has got to have a heart.

• Oxygen Delivery System.
• Structural Basis of Protein Function.
• Paradigm for Allosteric Regulation.
• Structural Basis of Disease.

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Oxygen and How You Get It.
Oxygen diffusion limits the size of an organism
or tissue thickness to 1mm. Larger organisms
require specialized oxygen delivery systems -
like blood. What do you need in an oxygen
delivery system? Must accept oxygen from lungs
(pO2 100 torr, 1mm Hg) Then give oxygen away
in capillaries (pO2 30 torr) Oxygen must then
be donated to respiring tissues like muscle (pO2
lt20 torr).
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What could we use to carry oxygen? How about
Iron! It binds to oxygen! But its largely
insoluble and quite toxic. Solution put it in a
heme. Heme porphyrin - made of four pyrrole
rings. Four nitrogen coordination to metal
center. Problem Oxidation of Fe (II) to Fe
(III) and formation of free radicals nasty.
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When two hemes get together, they auto-oxidize
through an intermediate where an oxygen bridges
between two Fe centers. Oxidation forms Fe(III)
heme irreversibly no more reversible oxygen
binding.
Solution James Collman and his picket-fence
Fe(II) porphyrins. Bulky groups keep hemes from
sharing an oxygen. Reversible O2 binding!
N
N
N
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Natures Solution Globins

• Myoglobin
• First protein structure determined.
• Alpha helical polypeptide.
• Associates with heme through coordination with a
  histidine side chain.

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Details of Mb-O2 binding site.
Distal Histidine hydrogen bonds to bound oxygen.
Proximal Histidine coordinated to heme iron.
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Myoglobin - O2 binding is described by a simple
equilibrium.
Dissociation constant, K
Fractional saturation of Mb
1.0
0.5
pO2
p50
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Fraction O2 binding
O2 Free
O2 Bound
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P50 O2 binding affinity
P50 6 mmHg
P50 24 mmHg
P50 105 mmHg
PaO2 (mmHg)
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Myoglobin gives O2 to respiring tissue.
50 transfer of O2 between 30 mmHg and 2 mmHg
PaO2 in Air
PaO2 in Tissue
PaO2 in Respiring Tissue
PaO2 (mmHg)
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If Hemoglobin were a single globin.
Needs to transfer O2 from Air to tissues.
Must have a P50 high enough to bind O2 in Lungs,
but low enough to release O2 in tissues. A single
globin with a P50 of 26 mmHg would have an O2
transfer efficiency of 25
PaO2 (mmHg)
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It would be better if Hb could change its
affinity for O2.
The O2 transfer would be more efficient if Hbs
affinity for O2 was high when PaO2 was high
then Hb affinity became much weaker when PaO2
was lower.
PaO2 (mmHg)
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Hbs affinity for O2 does change!
Affinity is high when PaO2 is high Affinity
low when PaO2 is low. (Curve is a bit exaggerated)
PaO2 (mmHg)
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Structural Basis for Cooperativity
Hemoglobin is a heterotetramer of myoglobin like
monomers. Two alpha subunits and two beta.
X 4
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Cooperative binding of O2
As O2 binds to each globin subunit, the O2
affinity of the other globins increases.
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Structural Basis for Cooperativity
The structures of deoxy- and oxy-Hb are
different! The a/b dimers rotate as rigid
bodies.
C
F/G
Deoxy form has low O2 affinity
Oxy form has high O2 affinity
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Deoxy
Breath Out
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Oxy
Breath In