The uniform arrangement of the backbone carbonyl oxygens and amide nitrogens in an ? helix gives the helix a net dipole, so that it carries a partial positive charge at the amino end and a partial negative charge at the carboxyl end. Where would you expect the ends of ? helices to be located in ? protein? Why?
Comparison of a homeodomain protein from yeast and Drosophila shows that only 17 of 60 amino acids are identical. How is it possible for a protein to change over 70% of its amino acids and still fold in the same way? Can you mention one example?
In 1968 Cyrus Levinthal pointed out a complication in protein folding that is widely known as the Levinthal paradox. He argued that because there are astronomical numbers of conformations open to a protein in the denatured state, it would take a very long time for a protein to search through all the possibilities to find the correct one, even if it tested each possible conformation exceedingly rapidly. Yet denatured proteins typically take less than a second to fold inside the cell or in the test tube. How do you suppose that proteins manage to fold so quickly?
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