ProblemSet2-4 - Bioc100B Winter 2010 Seth Rubin Problem Set#2 Due Tuesday January 19th 10:00 A.M 1 Go to the Protein Data Bank and download the

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Bioc100B Winter 2010 Seth Rubin Problem Set #2 Due Tuesday, January 19 th 10:00 A.M. 1) Go to the Protein Data Bank and download the structure of the cAMP response element binding (CREB) protein (PDB ID: 1DH3). CREB is a transcription factor whose function is abnormal in several diseases including the neurological disorder Huntington’s disease. This structure is solved in the presence of DNA, but here we are interested in the protein itself. a) Is the structure a homodimer or heterodimer? b) Draw a helical wheel diagram for ~4-5 turns of each helix. Begin with V308 and include the remaining sequence to the C-terminus for each. c) Are the helices parallel or antiparallel? Would the opposite structure be stable? Refer to your helical wheel diagram in your argument. 2) In class, we noted that the specificity of a protein for a particular ligand in a mixture of ligands depends on the relative affinities of the protein for each ligand. In this problem, you will explore how it can also depend on the relative concentrations of ligands. a)
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This note was uploaded on 03/16/2010 for the course BIOC 100B taught by Professor Sethrubin during the Winter '10 term at University of California, Santa Cruz.

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ProblemSet2-4 - Bioc100B Winter 2010 Seth Rubin Problem Set#2 Due Tuesday January 19th 10:00 A.M 1 Go to the Protein Data Bank and download the

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