Problem 15
When a vertebrate dies, its muscles stiffen as they are deprived of ATP, a state called rigor mortis. Using your knowledge of the catalytic cycle of myosin in muscle contraction, explain the molecular basis of the rigor state.
Problem 17
To fully appreciate how proteins function in a cell, it is helpful to have a threedimensional view of how proteins interact with other cellular components. Fortunately, this is possible using online protein databases and three- dimensional molecular viewing utilities such as JSmol, a free and user- friendly molecular viewer that is compatible with most browsers and operating systems. In this exercise, examine the interactions between the enzyme lysozyme and the Fab portion of the antilysozyme antibody. Use the PDB identifier 1FDL to explore the structure of the IgG1 Fab fragment-lysozyme complex (antibody- antigen complex). To answer the questions, use the information on the Structure Summary page at the Protein Data Bank (www.rcsb.org), and view the structure using JSmol or a similar viewer. a. Which chains in the three-dimensional model correspond to the antibody fragment, and which correspond to the antigen, lysozyme? b. What type of secondary structure predominates in this Fab fragment? c. How many amino acid residues are in the heavy and light chains of the Fab fragment? In lysozyme? Estimate the percentage of the lysozyme that interacts with the antigen- binding site of the antibody fragment. d. Identify the specific amino acid residues in lysozyme and in the variable regions of the Fab heavy and light chains that are situated at the antigen- antibody interface. Are the residues contiguous in the primary sequence of the polypeptide chains?
