Lecture3

Lecture3 - Proteins binding to DNA...

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1 Proteins binding to DNA Sequence-specific DNA binding proteins restriction endonucleases transcription factors (also recombination enzymes) Non-specific DNA binding proteins DNA topology DNA packaging proteins
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2 EcoRI restriction enzyme partial unwinding: opening major groove, facilitate base interactions
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3 EcoRV restriction enzyme: bending DNA
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4 HTH motif protein structure module 5’-TGTACTAGTTAACTAGTAC-3’ 3’-ACATGATCAATTGATCATG-5’ two helices at 120° interactions with base pairs and  sugar phosphate backbone via   H-bonds   salt-bridges   van der Waals contacts protein dimer- DNA palindrome bacteriophage repressor protein
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5
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6 HTH: helix  α 2 and  α 3
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7 E.coli trp repressor protein:  dimeric TF: HTH  but no direct basepair H-bonds  but all interactions via bridging water
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8 E.coli met repressor protein:  two-stranded anti-parallel beta sheets
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9 zinc finger motif
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10 gal4 DNA binding domain: yeast TF with Zn finger
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11 zif268 protein: 3 zinc finger protein scaffold for TF engineering
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12 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. AP-1: mammalian TF leucine zipper basic domain bZIP
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13 Leucine-zipper
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14 bZIP: yeast GCN4 bZIP: human Max
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15 Rel - homology domain (RHD) G.Ghosh, UCSD
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16 Protein-binding to DNA can alter the DNA structure TBP binds DNA, bends it and helps to initiate transcription
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17 packaging DNA: eukaryotic chromosomes made up from nucleosomes
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18
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Lecture3 - Proteins binding to DNA...

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