homework2

homework2 - http://en.wikipedia.org/wiki/FASTA . Convert...

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Biophysical Chemistry I, Fall 2010 Homework Assignment #2, due Sept. 21 1. Download the 1ZNF entry from the PDB. If you examine the ±le in a text editor, you will see that there are 37 copies of the structure, iden- ti±ed by cards with the word “MODEL” in the ±rst ±ve characters (i.e. “MODEL 1” through “MODEL 37”). For this assignment, please work only with MODEL 1. Click on the “molecule of the month fea- tures”, and read about this structure. Write a short summary (3-4 sentences) about the biological signi±cance of zinc ±ngers. 2. Make a list of the backbone hydrogen bonds in the structure (MODEL 1 only). These will be C=O. ..H-N units where (for the purposes of this assignment) the distance between O and H is less than 2.3 Å. Make a table showing the donor residue (the one with the NH group), the acceptor residue (with the C=O group) and the N. ..O and H. ..O distances. Identify hydrogen bonds that correspond to an α -helix, a 3 10 helix, or to a β structure. 3. Read the brief introduction to sequence similarity searches in Wikipedia:
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Unformatted text preview: http://en.wikipedia.org/wiki/FASTA . Convert the 1ZNF sequence to FASTA format (see http://en.wikipedia.org/wiki/FASTA_format ). (You should ignore the blocking groups ACE and NH2 at the beginning and the end of the struture.) Submit your FASTA format as the answer to this question. 4. Go to advanced search at the PDB web site, choose the query type Sequence (blast/fasta) and enter your FASTA format sequence for this zinc nger; leave other parameters at their defaults. Submit the search to nd other structures in the PDB with similar amino acid sequences. Report the PDB code and title of the ve top hits. 5. The rst hit should be to 1ZNF itself. Click on the display full align-ment tab to verify that you have an exact match. For the second hit, show the sequence alignment, and discuss the extent to which the amino acid sequence of the second hit resembles and differs from that of 1ZNF itself. 1...
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