Globular Proteins

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Globular Proteins
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Figure 8-35 X-Ray diffraction photograph of a
single crystal of sperm whale myoglobin.
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Figure 8-39a Representations of the X-ray
structure of sperm whale myoglobin. (a) The
protein and its bound heme are drawn in stick
form.
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Figure 8-39b Representations of the X-ray
structure of sperm whale myoglobin. (b) A diagram
in which the protein is represented by its
computer-generated Ca backbone.
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Figure 8-39c Representations of the X-ray
structure of sperm whale myoglobin. (c) A
computer-generated cartoon drawing in an
orientation similar to that of Part b.
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Figure 8-43a The H helix of sperm whale
myoglobin. (a) A helical wheel representation in
which the side chain positions about the a helix
are projected down the helix axis onto a plane.
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Mb
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Cut-away view
surface
Stryer Fig. 3.45 Mb yellow hydrophobic,
bluecharged, whiteothers
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Stryer Fig. 3.46 Porin
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Porin
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Structural features of most globular proteins
1. Very compact e.g. Mb has room for only4
water molecules in its interior.
2. Most polar/charged R groups are on the
surface and are hydrated.
3. Nearly all the hydrophobic R groups are on
the interior.
4. Pro occurs at bends/loops/random structures
and in sheets
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Figure 9-1
Chapter 9!!!
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Figure 9-2 Reductive denaturation and oxidative
renaturation of RNase A.
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Figure 9-3 Plausible mechanism for the thiol- or
enzyme-catalyzed disulfide interchange reaction
in a protein.
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Figure 9-14b Reactions catalyzed by protein
disulfide isomerase (PDI). (b) The oxidized
PDI-dependent synthesis of disulfide bonds in
proteins.
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Figure 9-4 Primary structure of porcine
proinsulin.
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H-bond Fun Fact

• 1984 survey of protein crystal data shows that
  almost all groups capable of forming H-bonds do
  so. (main chain amides, polar side chains)

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Many conformational states
Fewer conformational states
A single conformational state
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High energy
Many conformational states
Fewer conformational states
A single conformational state
Low energy
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Figure 9-11c Folding funnels. (c) Classic
folding landscape.
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Figure 9-11d Folding funnels. (d) Rugged energy
surface.
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Ideal
Real ?
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Figure 9-12 Polypeptide backbone and disulfide
bonds of native BPTI.
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Figure 9-13 Renaturation of BPTI.
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Figure 9-26 Secondary structure prediction.
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Figure 9-28 Conformational fluctuations in
myoglobin.
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Figure 9-30a The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(a) The Ca backbone and the heme group.
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Figure 9-30b The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(b) An a helix.
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Figure 9-32a Amyloid fibrils. (a) An electron
micrograph of amyloid fibrils of the protein PrP
27-30.
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Figure 9-32bc Amyloid fibrils. (b) and (c) Model
and isolated b sheet.
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Figure 9-34a Evidence that the scrapie agent is a
protein.(a) Scrapie agent is inactivated by
treatment with diethylpyrocarbonate, which reacts
with His side chains.
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Figure 9-34b Evidence that the scrapie agent is a
protein.(b) Scrapie agent is unaffected by
treatment with hydroxylamine, which reacts with
cystosine residues.
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Figure 9-34c Evidence that the scrapie agent is a
protein.(c) Hydroxylamine rescues
diethylpyrocarbonate-inactivated scrapie reagent.
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Figure 9-35a Prion protein conformations. (a) The
NMR structure of human prion protein (PrPC).
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Figure 9-35b Prion protein conformations. (b) A
plausible model for the structure of PrPSc.
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Figure 9-36 Molecular formula for
iron-protoporphyrin IX (heme).
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Figure 9-37 Primary structures of some
representative c-type cytochromes.
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Figure 9-38 Three-dimensional structures of the
c-type cytochromes whose primary structures are
displayed in Fig. 9-37.
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