BIBC 100 Problem Set #1 4/11/08 1) Go to the PDB website (Protein Data Bank), and retrieve PDB ID “2cpl”. See the “Images and Visualization” box to the right. The programs KiNG, Jmol, Webmol, etc. allow you to look at the structure of this protein and manipulate it in various ways. You will have to experiment with the various programs and see what they do. I find KiNG and Webmol to be the easiest to understand; Jmol isn’t too bad either. All require Java – I ran these programs in the Safari browser, with the Mac OS X operating system. I expect this exercise to take you about 2 hours to complete. What is this protein? What does it do? Is this protein made up of a single amino acid chain, or multiple chains? How long are the chain(s)? Describe the secondary structural composition and any major folds/motifs you see in this protein. What secondary structural element is made up of amino acids 30 to 42 in this protein? What is the identity of amino acid 30? What atom is the carbonyl oxygen of amino acid 30 hydrogen-bonded to? 2) For the small peptide DENSRREETSCW, what is the overall charge of the peptide at pH 7.4? 3) The molecular mass of serine is 105 Da, and thus the molecular mass of three individual molecules of serine is 315 Da. However, a tripeptide composed of three serine residues has a molecular mass of 279 Da. Why does the peptide have this smaller mass?4) What would be the approximate molecular weight of a 600 a.a. protein? (Hint: see the discussion of the range of sizes of peptides and proteins in Chapter 3) 5) Plot the following 10-residue peptide as an alpha-helix on the helical wheel (see slide 12, Lecture 3, from B and T figure 2-4). Make sure to mark the details such as N-terminus, C-terminus, the distance/angle between each residue, hydrophobic region/polar region. N-Terminus –M-T-R-A-A-S-L-I-Q-S – C-Terminus 6) Go to the NCBI website, and BLAST (protein BLAST) this sequence: MAPWMHLLTVLALIALWGPNSVQAYSSQHLCGSQLVEALFMTCGRSGFYRPHDKKELEDLQVEQAELGLDAGGLQPSALDMILQKRGIVDQCCNNICTYNQLQNYCNVP What is this protein? What type of organism has this protein? An “E-value or Expect value” is a statistical measure of similarity between proteins. One of your BLAST hits has an expect value of 2e-27 (very similar). The BLAST program shows an alignment between your query sequence and this protein. How many amino acids are identical to one another in the alignment? How many are similar to one
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