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Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240 PowerPoint PPT Presentation


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Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240 Mb pp. 240-248pp. 248-256 Bioinfo pp. 256-258Stability pp. 258-262 Hydropathy pp. 263-266Symmetry pp. 266-end Ch 9: pp. 276-278pp. 278-283 Folding pp. 283-290Chaperones pp. 290-306

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Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240

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Sections in Voet to Study or Read

StudyRead

Ch 8: pp. 219-233Collagen pp. 233-240

Mb pp. 240-248pp. 248-256

Bioinfo pp. 256-258Stability pp. 258-262

Hydropathy pp. 263-266Symmetry pp. 266-end

Ch 9: pp. 276-278pp. 278-283

Folding pp. 283-290Chaperones pp. 290-306

Prions pp. 306-312Evolution pp. 312-end

Suggested Problems Ch 9: 3, 4, 6, 12, 14


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 8-6Hydropathy Scale for Amino Acid Side Chains.

Values below line

are NEGATIVE!!

Page 263


Figure 8-60Hydropathic index plot for bovine chymotrypsinogen.

Page 263


Figure 8-46abcSchematic diagrams of supersecondary structures

Page 249


Figure 8-46dSchematic diagrams of supersecondary structures.

Page 249


Figure 8-47aX-Ray structures of 4-helix bundle proteins.(a) E. coli cytochrome b562.

Page 250


Fibrous Proteins


Figure 8-25The microscopic organization of hair.

Page 232


Figure 8-26The structure of a keratin.

Page 232


Figure 8-27aThe two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the a helices.

Page 233


Figure 8-27bThe 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


Exploring collagen

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


Figure 8-28The amino acid sequence at the C-terminal end of the triple helical region of the bovine a1(I) collagen chain.

Page 234


Figure 8-29The triple helix of collagen.

Page 235


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.


Figure 8-30bX-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


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


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

Page 237


Figure 8-32Banded appearance of collagen fibrils.

Page 237


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

Page 238


Figure 8-34Distorted structure in abnormal collagen.

Page 239


Globular Proteins


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

Page 240


Figure 8-39aRepresentations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound heme are drawn in stick form.

Page 244


Figure 8-39bRepresentations 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


Figure 8-39cRepresentations 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


Figure 8-43aThe 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


Mb


Cut-away view

surface

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

white=others


Stryer Fig. 3.46 Porin


Porin


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


Chapter 9!!!

Figure 9-1

Page 277


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

Page 277


Figure 9-3Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein.

Page 278


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

Page 288


Figure 9-4Primary structure of porcine proinsulin.

Page 278


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)


Many

conformational

states

Fewer

conformational

states

A “single”

conformational state


High energy

Many

conformational

states

Fewer

conformational

states

A “single”

conformational state

Low energy


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

Page 285


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

Page 285


“Ideal”

“Real” ?


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

Page 286


Figure 9-13Renaturation of BPTI.

Page 287


Figure 9-26Secondary structure prediction.

Page 301


Figure 9-28Conformational fluctuations in myoglobin.

Page 303


Figure 9-30aThe internal motions of myoglobin as determined by a molecular dynamics simulation. (a) The Ca backbone and the heme group.

Page 305


Figure 9-30bThe internal motions of myoglobin as determined by a molecular dynamics simulation. (b) An a helix.

Page 305


Figure 9-32aAmyloid fibrils. (a) An electron micrograph of amyloid fibrils of the protein PrP 27-30.

Page 307


Figure 9-32bcAmyloid fibrils. (b) and (c) Model and isolated b sheet.

Page 307


Figure 9-34aEvidence that the scrapie agent is a protein.(a) Scrapie agent is inactivated by treatment with diethylpyrocarbonate, which reacts with His side chains.

Page 310


Figure 9-34bEvidence that the scrapie agent is a protein.(b) Scrapie agent is unaffected by treatment with hydroxylamine, which reacts with cystosine residues.

Page 310


Figure 9-34cEvidence that the scrapie agent is a protein.(c) Hydroxylamine rescues diethylpyrocarbonate-inactivated scrapie reagent.

Page 310


Figure 9-35aPrion protein conformations. (a) The NMR structure of human prion protein (PrPC).

Page 311


Figure 9-35bPrion protein conformations. (b) A plausible model for the structure of PrPSc.


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

Page 313


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

Page 313


Figure 9-38Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37.

Page 314


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