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| a-b barrels (the TIM fold) |
-8 stranded parallel b barrel concentric with 8 outer a helices
-loop region of the C terminal side of b strands is active site |
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mcs5109 Wed, 12 Nov 2008 03:42:56 GMT |
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| b barrels |
-Diverse group
-4 to over 10 antiparallel strands
-typically 2 b sheets that pack against each other
-twist-like barrel |
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mcs5109 Wed, 12 Nov 2008 03:40:56 GMT |
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| globin fold |
-in myoglobin, hemoglobin
-bundle of 8 a helices
-helices forms a pocket for the active site
-heme for oxygen binding
-Protects heme from contacting other heme |
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mcs5109 Wed, 12 Nov 2008 03:40:56 GMT |
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| Four helix bundles |
-simplest
-4 a helices in a bundle
-residues contacting each other in the bundle are hydrophobic |
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mcs5109 Wed, 12 Nov 2008 03:40:56 GMT |
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| a-a motifs |
-Four helix bundles
-globin fold |
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mcs5109 Wed, 12 Nov 2008 03:37:17 GMT |
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| b-a-b motif |
-parallel b-sheets connected by a-helix
-common
-helix packs against B sheet to shield its hydrophobic residues
-loop regions vary in length
-loop connecting C end of B sheet to a-helix is often binding site or active site
-right handed |
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mcs5109 Wed, 12 Nov 2008 03:37:17 GMT |
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| Hairpin b motifs |
-2adjacent antiparallel strands joined by a loop (2-5 aas)
-hairpin or a b-b unit |
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mcs5109 Wed, 12 Nov 2008 03:37:17 GMT |
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| Supersecondary structure |
-Building blocks for proteins:
bab motif
b hairpin motif
aa motif
Greek key motif |
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mcs5109 Wed, 12 Nov 2008 03:37:17 GMT |
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| domains |
-globular structures
-a polypeptide usually wanders back and forth within domain.
-Neighboring domains typically connected by one or two segments.
-Domains often have specific function (ex: binding site for NAD) |
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mcs5109 Wed, 12 Nov 2008 03:28:00 GMT |
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| Side chain location trends |
-tendency to hide hydrophobic residues
-When in interior, always hydrogen bonded.
-H bond ‘neutralizes’ charge so that it can go to interior |
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mcs5109 Wed, 12 Nov 2008 03:27:59 GMT |
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| tertiary structure |
-folding of secondary structure with the side chains spatially oriented |
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mcs5109 Wed, 12 Nov 2008 03:24:42 GMT |
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| how to read 2-D NMR |
-off diagonal peaks arise from interaction of two protons that are < 5 Angstroms apart
-molecule to be assembled in space.
-Inter-proton distance not precise |
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mcs5109 Wed, 12 Nov 2008 03:24:42 GMT |
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| 2D-NMR |
-Nuclear magnetic resonance
-monitor protons
-apply large external magnetic field
-separates nuclear spin energies
-flips spin from lower to higher energy state |
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mcs5109 Wed, 12 Nov 2008 03:24:42 GMT |
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| protein crystals |
-protein crystals mostly water (60%)
-jello-like matrix limits resolution
-Leu, Ile and Thr can't be distinguished, so primary structure needed
-catalytically active--> shows protein is native |
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mcs5109 Wed, 12 Nov 2008 03:18:23 GMT |
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| X-ray crystallography |
-X-rays are approximately 1.5 Angstroms (covalent bonds are 1.5 A)
-need crystal lattice
-electron density affects intensity
-produces electron density map
-atoms are fitted to map |
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mcs5109 Wed, 12 Nov 2008 03:18:23 GMT |
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| Globular proteins |
-spherical
-structures studied via X-ray and NMR studies |
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mcs5109 Wed, 12 Nov 2008 03:18:23 GMT |
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