biochem100bSolutionSet5

biochem100bSolutionSet5 - BMB100B Winter 2009 Rubin Problem...

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BMB100B Winter 2009 Rubin Problem Set #5 Due Tuesday, February 17 th 10:00 A.M. 1) Leupeptin is a common protease inhibitor. Here is its structure: Use the structure of trypsin bound to leupeptin (PDB ID: 1JRT) to answer the following: a) Explain the mechanism of leupeptin inhibition. Leupeptin is a peptide mimic that contains a C-terminal aldehyde instead of a carboxylic acid. The aldehyde carbonyl can still be attacked by the catalytic serine but there is nothing to eliminate from the resulting hemiacetal. While the hemiacetal can be readily hydrolyzed back to leupeptin + serine, the presence of leupeptin in the active site however blocks substrate from binding. Accordingly, leupeptin is a competitive inhibitor. Note in the structure 1JRT, the crystallographers luckily captured the hemiacetal state, which mimics the tetrahedral intermediate. b) Design a leupeptin analog that would inhibit chymotrypsin. The specificity difference between trypsin and chymotrypsin is most pronounced in the amino acid immediately preceding the “scissile” bond (peptide bond that is cleaved). The difference arises from different environments in the active site. Whereas trypsin prefers a basic residue, chymotrypsin prefers a bulky aromatic such as phenylalanine. Thus, replacing the C-terminal amino aldehyde arginine sidechain with a phenyl group would be a better inhibitor of chymotrypsin (smaller K I ). 2) In the absence of inhibitor, what effect on the catalytic activity of trypsin would you expect from the mutations below and why? Using the 1JRT trypsin structure (imagining no inhibitor) may help. a) D102N
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This note was uploaded on 01/15/2010 for the course BIO 31402 taught by Professor Lee during the Spring '09 term at UCSC.

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biochem100bSolutionSet5 - BMB100B Winter 2009 Rubin Problem...

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