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Proteins Domains, Motifs, and Quaternary Structure
Petsko & Ringe 1-5 to 1-18Voet-Voet Chapter 8-1 to 8-3
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How does the location of a Glu residue on a single α-helix would
affect its pKa?
NH2
COOH
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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 α helix are projected down the helix axis onto a plane.
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Figure 8-43b The H helix of sperm whale myoglobin.(b) A skeletal model, viewed as in Part a.
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Figure 8-43c The H helix of sperm whale myoglobin.(c) A space-filling model, viewed from the bottom of the page in Parts a and b and colored as in Part b.
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Figure 8-16b β pleated sheets. (b) The parallel β pleated sheets.
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Figure 8-16a β pleated sheets. (a) The antiparallel βpleated sheets.
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Voet
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Figure 8-17 A two-stranded β antiparallel pleated sheet drawn to emphasize its pleated appearance.
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Side chainsalternate indirection
7 Angstrom
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Voet
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Figure 8-47b X-Ray structures of 4-helix bundle proteins.(b) Human growth hormone.
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Figure 8-48 The immunoglobulin fold.
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Figure 8-49 Retinol binding protein.
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Figure 8-52 left The X-ray structure of the 247-residue enzyme triose phosphate isomerase (TIM) from chicken muscle.
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Figure 8-54b X-Ray structures of open β sheet-containing enzymes. (b) Porcine adenylate kinase (195 residues).
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Pore-forming toxins (PFT)
Water-soluble forms
of bacterial pore forming
toxins
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Staphylococcal α-HemolysinThe paradigm for β-barrel pore forming toxins
7 monomers Diameter ~ 16 Å
Song et al 1996
How does an amphipathicβ-hairpin fold into a soluble protein?
α-HemolysinSong et al 1996
Luk-FOlson et al 1999
Soluble monomer
Membrane-bound
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Perfringolysin O
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Four – helix bundle
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Quiz
• An oligomeric protein in a dilute buffer at pH 7 dissociates to its component subunits when exposed to the following agents. 1) 6M guanidinium chloride, b) 20% ethanol, c) 2M NaCl, d) temperatures below 0 oC, e) 2-mercaptoethanol, f) pH 3, g) 0.01 M SDS.
• Which of these observations would not support the contention that the quaternary structure of the protein is stabilized exclusively by hydrophobic interactions?
Main chain torsion angles
ϕ, phi: C(-1)-N─CA-C
α α α α
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Main chain torsion angles
ψ, psi: N-CA─C-N(+1)
α α α α
Figure 8-4 The torsional degrees of freedom of the main chain
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phi
psi
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