homework6 - Biophysical Chemistry I, Fall 2010 Homework...

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Biophysical Chemistry I, Fall 2010 Homework Assignment #6, due Nov. 23 As you have learned, proteins interact with small molecules, either as substrates or co-factors (which are often involved in chemical reactions) or as structural components (such as metal ions), or just as external agents that promote crystallization. In this assignment, you will use the “Ligand Explorer” component of RCSB to learn one way to study these interactions. 1. Go to http://www.rcsb.org , as usual, and navigate to PDB ID 3MI4, which is for a version of trypsin. Write a short paragraph about the biological function of this protein. 2. Scroll down to “ligand chemical components”, where you should see that there are four ligands (non-protein components) in this structure. One of the ligands (benzamidine) has a binding afFnity listed of 31-39000 nM. Draw the conventional (two-dimensional) chemical structure of benzamidine; deFne what is meant by the binding afFnity, and write down its relation to the binding free energy. What is the numerical value of the
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This note was uploaded on 01/15/2012 for the course CHE 543 taught by Professor Staff during the Fall '10 term at Syracuse.

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