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handout3_filled - Structural Biochemistry TA Phu Tran...

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Structural Biochemistry Dr. Lukas Buehler TA Phu Tran pdtran@ucsd.edu Sections A03 W 1 - 3 pm Solis 111 OH after class by appointment Handout 3 DNA-Binding Proteins DNA-binding proteins bind, sometimes with specificity, to DNA. They usually bind to the minor groove, the major groove, or both. The minor groove of B-DNA is 5Ǻ wide, 8Ǻ deep, and is too narrow for an _ alpha helix _. The minor groove of B-DNA can be recognized by _ beta sheets _ of TATA box-binding proteins. The major groove of B-DNA is 12Ǻ wide, 8Ǻ deep, and can bind _ alpha helices _. DNA-binding proteins can recognize the specificity of the bases (ACGT) by the characteristics of the exposed groups on the major and minor grooves. There are four classifications of groups that DNA-Binding proteins can recognize: H-Bond donor, acceptor, methyl group, and hydrogen group (Me and H groups have VdW interactions). These groups are differently exposed on A=T pairs and G= C pairs compared to T=A pairs and C= G pairs. This specificity of binding is important when the DNA-binding protein involved is a restriction enzyme (example: EcoR1) that cuts after specific nucleotides, or when the DNA-binding protein is a transcription factor that starts transcription of the DNA. Some DNA-binding protein motifs: Helix-turn-helix, _ Leucine _ zipper, Zinc finger. The helix-turn-helix motif is actually a homodimer made of _ two _ identical subunits. The helices have to recognize and bind to each other (through the _ oligomerization domain _) as well as to the DNA. An example of an HTH protein is the lac- repressor tetramer (from two HTH dimers) which is active when no _ lactose _ is available in the environment for a certain bacteria (ex. E. coli). This lac-repressor represses lac operons by tightly binding to the DNA gene sequence so that that sequence is
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handout3_filled - Structural Biochemistry TA Phu Tran...

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