Polypeptides, amphipathic helices

CI2 (Figure 19.2) is a 64-residue polypeptide inhibitor of serine proteases.23 It has a binding loop (Met-40, which binds in the primary site of chymotrypsin or subtilisin), a single a helix running from residues 12 to 24, and a mixed parallel and antiparallel /3 sheet. The strands and the amphipathic helix interact to form... 

Helixes are often amphipathic one side has hydrophobic residues that bind to h>drophobic areas in the protein the other has hydrophilic residues that interact w ith water (Figure 1.5). The alignment of dipoles of the polypeptide backbone nearly parallel to the axis of an a helix causes a net dipole moment with its positive pole at the N-terminus and negative pole at the C-terminus16 (Figure 1.6). 

Kojima, S., Kuriki, Y., Yoshida, T., Yazaki, K., and Miura, K. (1997). Fibril formation by an amphipathic alpha-helix-forming polypeptide produced by gene engineering. Proc. Japan Acad. B Phys. Biol. Sci. 73, 7—11. 

Basic Helix-Loop-Helix (bHLH) Proteins The DNA-binding domain of another class of dimeric transcription factors contains a structural motif very similar to the basic-zipper motif except that a nonhelical loop of the polypeptide chain separates two a-helical regions in each monomer (Figure 1 l-22b). Termed a basic helix-loop-helix (bHLH), this motif was predicted from the amino acid sequences of these proteins, which contain an N-terminal a helix with basic residues that interact with DNA, a middle loop region, and a C-termlnal region with hydrophobic amino acids spaced at intervals characteristic of an amphipathic a helix. As with basic-zipper proteins, different bHLH proteins can form heterodimers. 

While lipoproteins are the products of many different genes, the major apolipoproteins share properties distinguishing them from most lipid-free and membrane-associated proteins. For example, apolipoproteins consist of a single polypeptide chain that has relatively little tertiary structure. Most apolipoproteins contain stretches of amphipathic alpha-helix, whose hydrophobic face can be turned to the lipid surface of the particle. The apolipoproteins are flexible, as is reflected in their unusually small free energy of unfolding. As these apolipoproteins expand and contract at the cell surface, different protein domains are exposed that are detectable with monoclonal antibodies. These properties reflect the role of apolipoproteins at the surface of lipoprotein particles whose size changes as they circulate. 

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