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Handout%2010 - BIBC100 Handout 10 DNA binding proteins DNA...

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BIBC100 Michelle Fung [email protected] OH: Wed 12-2p Muir Bio 3105 Handout 10 DNA binding proteins - DNA o Anti-parallel o G C. A=T. o Held together by _________ and ____________________ (ex: Van der waals) o Wrapped up in double helix – major groove/minor groove - Transcription – highly regulated process o Gene regulatory proteins bind a short, well-defined DNA sequence o More proteins interact with the ___________ groove - Why? More variability in the atoms/groups that are exposed in this groove of DNA, therefore the proteins can form more specific interactions o DNA and DNA binding proteins – form highly specific and STRONG interactions o Most common residues (of DNA binding proteins) that stick out to bind to DNA – ____, _____, _____, _____, _____ - Motifs seen in DNA binding proteins: 1) ______________ – 2 short α -helices (each about 7-9 aa) separated by a β - turn ___-term helix – recognition helix – fits into _______ groove Binds as ________________ – greatly increases binding affinity (increasing binding strength) These are part of a special class of HTH called homeodomain proteins (proteins that bind DNA in specific manner) – highly conserved o Yeast vs. Drosophila – only 17/60 aa identical, but their structures are practically identical! 2) _________________ – found in many eukaryotic DNA binding proteins Zinc coordinated in center (w/4 aa attached) – helps stabilize structure
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BIBC100 Michelle Fung [email protected] OH: Wed 12-2p Muir Bio 3105 Can have a number of these motifs in a row – greatly increases specificity binding 3) __________________ – 2 amphipathic α -helices – dimerizes to form short coiled-coil High concentration of _____ and ____ in DNA binding region – Why? o ______________________________ Every 7 th residue in Leu zipper region is Leu coiled-coil o Note: also seen in HA (viral protein) - Often, certain AA’s (of DNA binding protein) binds certain bases (of DNA) – but not absolute p53 – Tumor Suppressor - Pathway: DNA damage activation of protein kinase phosphorylation of p53
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