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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

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Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

Sections in Voet to Study or Read

StudyRead

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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.


Table 8 6 hydropathy scale for amino acid side chains
Table 8-6 Hydropathy Scale for Amino Acid Side Chains.

Values below line

are NEGATIVE!!

Page 263


Figure 8 60 hydropathic index plot for bovine chymotrypsinogen
Figure 8-60 Hydropathic index plot for bovine chymotrypsinogen.

Page 263


Figure 8 46abc schematic diagrams of supersecondary structures
Figure 8-46abc Schematic diagrams of supersecondary structures

Page 249


Figure 8 46d schematic diagrams of supersecondary structures
Figure 8-46d Schematic diagrams of supersecondary structures.

Page 249


Figure 8 47a x ray structures of 4 helix bundle proteins a e coli cytochrome b 562
Figure 8-47a X-Ray structures of 4-helix bundle proteins.(a) E. coli cytochrome b562.

Page 250



Figure 8 25 the microscopic organization of hair
Figure 8-25 The microscopic organization of hair.

Page 232


Figure 8 26 the structure of a keratin
Figure 8-26 The structure of a keratin.

Page 232


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

Exploring collagen

http://www.rcsb.org/pdb/molecules/pdb4_1.html


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240
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


Figure 8 29 the triple helix of collagen
Figure 8-29 The triple helix of collagen.

Page 235


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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.


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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.

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Figure 8 31 electron micrograph of collagen fibrils from skin
Figure 8-31 Electron micrograph of collagen fibrils from skin.

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Figure 8 32 banded appearance of collagen fibrils
Figure 8-32 Banded appearance of collagen fibrils.

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Figure 8 33 a biosynthetic pathway for cross linking lys hyl and his side chains in collagen
Figure 8-33 A biosynthetic pathway for cross-linking Lys, Hyl, and His side chains in collagen.

Page 238


Figure 8 34 distorted structure in abnormal collagen
Figure 8-34 Distorted structure in abnormal collagen.

Page 239



Figure 8 35 x ray diffraction photograph of a single crystal of sperm whale myoglobin
Figure 8-35 X-Ray diffraction photograph of a single crystal of sperm whale myoglobin.

Page 240


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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



Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

Cut-away view

surface

Stryer Fig. 3.45 Mb yellow = hydrophobic, blue=charged,

white=others




Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Figure 9 1

Chapter 9!!!

Figure 9-1

Page 277


Figure 9 2 reductive denaturation and oxidative renaturation of rnase a
Figure 9-2 Reductive denaturation and oxidative renaturation of RNase A.

Page 277


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240
Figure 9-3 Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein.

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Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

Figure 9-14b Reactions catalyzed by protein disulfide isomerase (PDI). (b) The oxidized PDI-dependent synthesis of disulfide bonds in proteins.

Page 288


Figure 9 4 primary structure of porcine proinsulin
Figure 9-4 Primary structure of porcine proinsulin.

Page 278


H bond fun fact
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)


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

Many

conformational

states

Fewer

conformational

states

A “single”

conformational state


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

High energy

Many

conformational

states

Fewer

conformational

states

A “single”

conformational state

Low energy


Figure 9 11c folding funnels c classic folding landscape
Figure 9-11c Folding funnels. (c) Classic folding landscape.

Page 285


Figure 9 11d folding funnels d rugged energy surface
Figure 9-11d Folding funnels. (d) Rugged energy surface.

Page 285


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

“Ideal”

“Real” ?


Figure 9 12 polypeptide backbone and disulfide bonds of native bpti
Figure 9-12 Polypeptide backbone and disulfide bonds of native BPTI.

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Figure 9 13 renaturation of bpti
Figure 9-13 Renaturation of BPTI.

Page 287


Figure 9 26 secondary structure prediction
Figure 9-26 Secondary structure prediction.

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Figure 9 28 conformational fluctuations in myoglobin
Figure 9-28 Conformational fluctuations in myoglobin.

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Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240
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
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
Figure 9-32bc Amyloid fibrils. (b) and (c) Model and isolated b sheet.

Page 307


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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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Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240

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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Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240
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 prp c
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 prp sc
Figure 9-35b Prion protein conformations. (b) A plausible model for the structure of PrPSc.


Figure 9 36 molecular formula for iron protoporphyrin ix heme
Figure 9-36 Molecular formula for iron-protoporphyrin IX (heme).

Page 313


Figure 9 37 primary structures of some representative c type cytochromes
Figure 9-37 Primary structures of some representative c-type cytochromes.

Page 313


Sections in voet to study or read study read ch 8 pp 219 233 collagen pp 233 240
Figure 9-38 Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37.

Page 314