SolutionSet2-2

SolutionSet2-2 - Bioc100B Winter 2010 Seth Rubin Solution...

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Bioc100B Winter 2010 Seth Rubin Solution Set #2 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? Homodimer. Same polypeptide chain. 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. The helices are parallel as the direction from their N-term to C-term is the same. The anti-parallel structure would likely not be as stable. In the antiparallel structure, one of the helices would have the amino acids swapped between positions A&G, B&F, and C&E. Although, the leucine interactions would be intact (leucines at the D positions), many of the electrostatic interactions between the G and E positions would be broken. 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) Consider a protein P and two ligands L 1 and L 2 . P can bind either ligand, but not both simultaneously. Derive algebraic expressions for the concentration of P bound to L 1 and L 2 ([P-L 1 ] and [P-L 2 ]) as a function of total protein and ligand concentrations and the dissociation constants ([P] t , [L 1 ] t , [L 2 ], K d1 , and K d2 ). Assume that the concentration of each ligand is much greater than protein so that you can take [L]=[L] t .
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Bioc100B Winter 2010 Seth Rubin b) Calculate [P-L 1 ] and [P-L 2 ] for the following three situations: [P] t [L 1 ] t K d1 [L 2 ] t K d2 1 nM 1 μ M 1 μ M 1 μ M 10 μ M 1 nM 1 μ M 1 μ M 10 μ M 10 μ M 1 nM 0.1 μ M 1 μ M 1 μ M 10 μ M c) What can you conclude about the effect on ligand preference of [L] and K d ?
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Bioc100B Winter 2010 Seth Rubin
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SolutionSet2-2 - Bioc100B Winter 2010 Seth Rubin Solution...

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