ProblemSet3 - BIOC100A Problem Set # 3 1. The toxic...

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Unformatted text preview: BIOC100A Problem Set # 3 1. The toxic proteins found in snake and scorpion venom are often small, but very stable proteins. Secondary structure prediction for these proteins often suggest only small helices or beta sheets, with most of the protein being predicted to be "coil", which means lacking in secondary structure. Another feature of these proteins is they have a high percentage of cysteine residues, and some of them have associated zinc ions. Discuss the how these proteins likely maintain their folded structure and compare that to our understanding of how larger globular proteins maintain their folded structure. 2. In contrast to globular proteins and regions exposed to the cytosol, the integral membrane portions of membrane proteins contain very few residues not ordered into secondary structure elements such as beta sheet and alpha helix. Why is satisfying backbone hydrogen bonds by forming secondary structure elements more important for protein folding in the membrane than in solution? 3. A folded protein structure contains 6 ion pairs between lysine and glutamate. There are no other possible ion pairs in the protein. A chemical cross-linker forms a covalent bond between ion paired lysine and glutamate side chains. By analogy to the Anfinsen experiment the following experiments are done: A) folded protein -> unfold with urea -> remove urea to refold -> add cross-linker ->remove excess cross-linker->measure activity B) folded protein -> unfold with urea -> add cross-linker -> remove excess cross-linker -> remove urea to refold->measure activity The cross-linker does not by itself alter the activity of the protein when the correct ion pairs are formed. A protein with incorrect ion pairs cross-linked would be inactive. The activity measured at the beginning and end of experiment (A) is 100%. What percentage of the activity do you expect to observe at the end of experiment (B)? Assume that all unfolded conformations are equally likely. 4. Why is the sequence similarity generally higher when comparing two globins from mammals than when comparing a globin from a mammal and a globin from a plant? 5. The diagram below shows the size distribution for globular proteins produced by the bacterium E. coli. Explain why the distribution of protein sizes has the periodicity that is seen in the diagram and estimate a value for x. 6. The BLOSUM scoring matrix gives a measure of how conservative a mutation is. For substitutions of aspartic acid (ASP, D), which of the following orderings correctly places the amino acids from most conservative to least conservative: A) K,L,A,C,E,S B) E,S,K,A,C,L C) L,C,A,K,S,E D) A,C,E,K,L,S 7. Amino acids on the surface of proteins are (more likely /less likely) to change over evolution. Explain you answer. The domains in multi-domain proteins often interact by interactions between ____________ of amino acids located __________________ of the domains. Based on your answers, explain why arrangements of domains in proteins relative to each are more likely to change than the fold of the domains themselves. 8. Switching between your thermodynamic and kinetic hats, provide reasoning for why prion p roteins do not normally fold into their apparently most stable (the pathogenic) state. 9. This is the sequence of the human insulin gene: MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSL QPLALEGSLQKRGIVEQCCTSICSLYQLENYCN This is the sequence of the duck insulin protein: AANQHLCGSHLVEALYLVCGERGFFYSPKTXXDVEQPLVNGPLHGEVGELPFQHEEYQXX GIVEQCCENPCSLYQLENYCN a. Try to align the proteins by hand (it is best to use Courier font for alignment). What percent of duck amino acids are identical to human? What percent are similar? How many gaps do you need to introduce for the alignment? b. Compare your results with the NCBI BLAST alignment server: http://blast.ncbi.nlm.nih.gov/ Choose protein alignment and past the two sequences into the subject and query boxes. Click the Alignment Parameters arrow at the bottom of the page and play with the scoring parameters. Click BLAST and the alignment will display in a new window. Do the different scoring matrixes change the results? 10. Visit the protein data bank (www.pdb.org). For each of proteins listed below (search by the identifier code indicated), note the following characteristics of the protein. You can use the JMol viewer in the webpage to examine the structure (right-click to get the menu that lets you change the view) or download the structure (Download Files, choose Biological Assembly) and examine it with PyMol or RasMol (a) What is the oligomeric state of the protein? (b) Identify the number of domains in a monomer. (c) Classify the type of domain structure of each domain. (β-barrel, helical bundle, α-β, etc.) (d) Indicate whether the β-strands are parallel or antiparallel. (d) For proteins that have multiple α-helices, what approximate angles are made between the different pairs of adjacent α-helices? Green fluorescent protein (1EMA) HIV protease (1HVR) HSP90 chaperone complex (2CG9) Potassium channel Kir2.2 (3JYC) Triose phosphate isomerase (2JK2) Lysozyme (1LYD) Immunoglobin (1IGT) ...
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This note was uploaded on 01/17/2011 for the course BIOC 100A taught by Professor Harrynoller during the Fall '10 term at University of California, Santa Cruz.

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