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DNABinding_WJA-1 - Transcription Factors DNA binding...

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Transcription Factors DNA binding proteins Structural domains/motifs Transcription factors Predicting protein function from AA sequence Visual Molecular Dynamics (VMD) Upcoming assignment…
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Structural Domains and Motifs Domain: compact region of protein structure that is capable of folding on its own, and is often made up of a continuous AA sequence. Motif: typically smaller, not capable of folding on its own, but when detected in a protein it can be a good indicator of structure and/or function
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Structural Domains: What do these proteins have in common? hemoglobin cytochrome c myoglobin
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Structural Domains: What do these proteins have in common? hemoglobin cytochrome c myoglobin They all have a heme-binding domain!
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Structural Motifs: What do these proteins have in common? trypsin chymotrypsin
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Structural Motifs: What do these proteins have in common? trypsin chymotrypsin They both have the catalytic triad motif!
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What kind of structural domain / motif would a transcription factor have? Think about the function
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What kind of structural domain / motif would a transcription factor have? DNA Binding motifs 1. Helix-turn-helix (HTH) 2. Zinc finger (Zn-finger) 3. Leucine zipper (bZIP) These 3 types of domains are found in 80% of DNA binding proteins Mostly contact the major groove of DNA
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DNA-binding motif structural characteristics Charge? Residues? Cofactors? Secondary structure?
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#1 - The Helix-Turn-Helix Motif First identified in prokaryotic proteins Example: E. coli Lac repressor All bind as dimers to dyad- symmetric sites on DNA (specific sites) All contain two alpha helices separated by a loop with a beta turn The C-terminal helix fits in major groove of DNA; N-
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