BMB170a_2011_PS2

# BMB170a_2011_PS2 - BMB170A 2011 Problem Set 2 Proteins II...

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1 BMB170A 2011 Due 10/25/2011 Problem Set 2: Proteins II 1. Protein Folding (30 points total) a. Levinthal’s Paradox (10 points): Calculate the time it would take for a typical 300 residue protein to sample all conformations available to it if: - The Φ and Ψ angles can only adopt two stable conformations each (a gross underestimate) - Each sidechain samples two χ 1 angles with no other adjustments (another gross underestimate). Assume all sidechains have identities where two χ 1 angles are possible. - Singles bonds are estimated to reorient to different conformations 10 13 times per second Compare this value to the age of the universe (13.75 ± 0.17 billion years) and to the actual amount of time proteins typically take to fold (10 -6 to 10 2 seconds). What does this tell us about how proteins fold? b. Inclusion Bodies (5 points): The following image is an electron micrograph of Escherichia coli cells taken by Scott Betts, formerly of the King Lab at MIT. The image clearly shows dark staining areas called inclusion bodies. Though the exact mechanism of their formation currently escapes explanation, these structures are seen as “graveyards” for unfolded or misfolded proteins and aggregates like discarded viral capsids and amyloids. Give three reasons why overexpression of an engineered protein in a foreign host might lead to the formation of inclusion bodies.

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2 c. Knots (5 points): Protein backbones exhibit a strong tendency against knots with only a handful showing knotted topologies (see http://knots.mit.edu/cgi-bin/knots/knotsubmit.pl?showlist=1& ). Why is this surprising with regard to entropy? Provide a possible explanation for why knotted topologies are more rare than expected. d. Chaperones (10 points): Group II chaperonins are homologues of group I chaperonins, such as GroEL from Escherichia coli. While group I chaperonins are found in prokaryotes and the cytosol of eukaryotic organelles, group II chaperonins reside in the cytosol of archaeal and eukaryotic cells. Recently, a series of crystal structures of a group II chaperonin in Methanococcus maripaludis was solved. The PDB ID code 3KFK corresponds to the open state of the protein and the ID code 3KFB corresponds to the closed state. Make two figures showing the hydrophilic and hydrophobic patches necessary for chaperonin function. You will be evaluated on the clarity of your figures (labeling, colors, easy of viewing, etc.). Use your figures to describe how this chaperonin helps proteins fold in the proper conformation. For guidance, see Pereira et al., Journal of Biological Chemistry, 2010.
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## This note was uploaded on 01/03/2012 for the course BI 170a taught by Professor List during the Fall '09 term at Caltech.

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BMB170a_2011_PS2 - BMB170A 2011 Problem Set 2 Proteins II...

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