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Sections in Voet to Study or Read

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Title: Sections in Voet to Study or Read


1
Sections in Voet to Study or Read Study Read
Ch 8 pp. 219-233 Collagen pp. 233-240 Mb pp.
240-248 pp. 248-256 Bioinfo pp.
256-258 Stability pp. 258-262 Hydropathy pp.
263-266 Symmetry pp. 266-end Ch 9 pp.
276-278 pp. 278-283 Folding pp.
283-290 Chaperones pp. 290-306 Prions pp.
306-312 Evolution pp. 312-end
Suggested Problems Ch 9 3, 4, 6, 12, 14
2
Protein Explorer http//molvis.sdsc.edu/protexpl/
frntdoor.htm Do the 1 hour tour at this site.
http//molvis.sdsc.edu/protexpl/qtour.htm It may
take longer than 1 h.
3
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4
Table 8-6 Hydropathy Scale for Amino Acid Side
Chains.
Values below line are NEGATIVE!!
Page 263
5
Figure 8-60 Hydropathic index plot for bovine
chymotrypsinogen.
Page 263
6
Figure 8-46abc Schematic diagrams of
supersecondary structures
Page 249
7
Figure 8-46d Schematic diagrams of supersecondary
structures.
Page 249
8
Figure 8-47a X-Ray structures of 4-helix bundle
proteins.(a) E. coli cytochrome b562.
Page 250
9
Fibrous Proteins
10
Figure 8-25 The microscopic organization of hair.
Page 232
11
Figure 8-26 The structure of a keratin.
Page 232
12
Figure 8-27a The two-stranded coiled coil. (a)
View down the coil axis showing the interactions
between the nonpolar edges of the a helices.
Page 233
13
Figure 8-27b The two-stranded coiled coil. (b)
Side view in which the polypeptide back bone is
represented by skeletal (left) and space-filling
(right) forms.
Page 233
14
Exploring collagen
http//www.rcsb.org/pdb/molecules/pdb4_1.html
15
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16
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17
Figure 8-28 The amino acid sequence at the
C-terminal end of the triple helical region of
the bovine a1(I) collagen chain.
Page 234
18
Figure 8-29 The triple helix of collagen.
Page 235
19
Figure 8-30a X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (a) Ball
and stick representation.
20
Figure 8-30b X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (b) View
along helix axis.
Page 235
21
Figure 8-30c X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (c) A
schematic diagram.
Page 236
22
Figure 8-31 Electron micrograph of collagen
fibrils from skin.
Page 237
23
Figure 8-32 Banded appearance of collagen fibrils.
Page 237
24
Figure 8-33 A biosynthetic pathway for
cross-linking Lys, Hyl, and His side chains in
collagen.
Page 238
25
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26
Figure 8-34 Distorted structure in abnormal
collagen.
Page 239
27
Globular Proteins
28
Figure 8-35 X-Ray diffraction photograph of a
single crystal of sperm whale myoglobin.
Page 240
29
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.
Page 244
30
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.
Page 244
31
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.
Page 244
32
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.
Page 247
33
Mb
34
Cut-away view
surface
Stryer Fig. 3.45 Mb yellow hydrophobic,
bluecharged, whiteothers
35
Stryer Fig. 3.46 Porin
36
Porin
37
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
38
Figure 9-1
Chapter 9!!!
Page 277
39
Figure 9-2 Reductive denaturation and oxidative
renaturation of RNase A.
Page 277
40
Figure 9-3 Plausible mechanism for the thiol- or
enzyme-catalyzed disulfide interchange reaction
in a protein.
Page 278
41
Figure 9-14b Reactions catalyzed by protein
disulfide isomerase (PDI). (b) The oxidized
PDI-dependent synthesis of disulfide bonds in
proteins.
Page 288
42
Figure 9-4 Primary structure of porcine
proinsulin.
Page 278
43
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44
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)

45
Many conformational states
Fewer conformational states
A single conformational state
46
High energy
Many conformational states
Fewer conformational states
A single conformational state
Low energy
47
Figure 9-11c Folding funnels. (c) Classic
folding landscape.
Page 285
48
Figure 9-11d Folding funnels. (d) Rugged energy
surface.
Page 285
49
Ideal
Real ?
50
Figure 9-12 Polypeptide backbone and disulfide
bonds of native BPTI.
Page 286
51
Figure 9-13 Renaturation of BPTI.
Page 287
52
Figure 9-26 Secondary structure prediction.
Page 301
53
Figure 9-28 Conformational fluctuations in
myoglobin.
Page 303
54
Figure 9-30a The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(a) The Ca backbone and the heme group.
Page 305
55
Figure 9-30b The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(b) An a helix.
Page 305
56
Figure 9-32a Amyloid fibrils. (a) An electron
micrograph of amyloid fibrils of the protein PrP
27-30.
Page 307
57
Figure 9-32bc Amyloid fibrils. (b) and (c) Model
and isolated b sheet.
Page 307
58
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.
Page 310
59
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.
Page 310
60
Figure 9-34c Evidence that the scrapie agent is a
protein.(c) Hydroxylamine rescues
diethylpyrocarbonate-inactivated scrapie reagent.
Page 310
61
Figure 9-35a Prion protein conformations. (a) The
NMR structure of human prion protein (PrPC).
Page 311
62
Figure 9-35b Prion protein conformations. (b) A
plausible model for the structure of PrPSc.
63
Figure 9-36 Molecular formula for
iron-protoporphyrin IX (heme).
Page 313
64
Figure 9-37 Primary structures of some
representative c-type cytochromes.
Page 313
65
Figure 9-38 Three-dimensional structures of the
c-type cytochromes whose primary structures are
displayed in Fig. 9-37.
Page 314
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