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365 S2011 L12 - Visualizing protein structures Proteins are...

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1 Visualizing protein structures Proteins are complicated so visualization is tailored to what you want to show 1. Ball and stick details but is cluttered 2. Space filling only shows outside 3. Artistic renditions give overview but are imprecise
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2 Jack bean Concanavalin A Triose phosphate isomerase
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3 Stick model
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4 > 60,000 structure have been solved What have we learned? 1 Side chain location varies with polarity 2 Helices and β -strands/sheets combine in a variety of ways 3 Large proteins contain domains
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5 Side chain location varies with polarity Non-polar residues — in the center (V, L, I, M, F) Charged polar residues — mostly on the surface (R, H, K, D, E) Uncharged polar residues — mostly on the outside (S, T, N, Q, Y) (the center they form hydrogen bonds with other polar side chains)
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8 Side chain localization in elements of secondary structure
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9 Super secondary structures Assemblies of secondary structural elements seen in many unrelated proteins βαβ motifs β hairpin αα motif β barrel
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11 4 helix bundle β sandwich
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12
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13 Domains 1. Large proteins fold into separate globular clusters called domains (60-200 aa, 25Å) 2. Two or more
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