biochem100BSolutionSet1-1 - BMB100B Winter 2009 Rubin...

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BMB100B Winter 2009 Rubin Solution Set #1 1) Explain the following generalities regarding amino acid types in alpha helices. a) Prolines are rarely found in the middle of helical sequences. The unique ring structure of proline places restrictions on the phi dihedral angle that is less favorable for an alpha helix (~-70 to -75 deg). In addition, because of the substituted amide, there is no backbone hydrogen for proline to donate. Proline is sometimes found at the beginning of an alpha helix, where there is no requirement for a hydrogen bond donor. b) Glycines are rarely found in the middle of helical sequences. Glycine contains two C α hydrogens, and there are considerably less restrictions on its phi and psi angles, i.e. there are fewer conformations with steric hindrance between the side chain and the peptide backbone. One reason why amino acids adopt helical conformations is this dihedral angle restriction. On the other hand, it is energetically more favorable (from the entropy contribution) for glycine to be in less structured regions of proteins (e.g. loops), in which it can adopt many conformations. c) Negative charged amino acids are commonly found at the beginning of helices. The backbone carbonyl dipoles in a helix are all oriented the in the same direction. This results in an electric dipole, in which the positive end is coincident with the N-terminal end of the helix. Negative charges at the N-terminal end interact favorably with the dipole moment. d) Polyalanine has a high propensity to form an alpha helix, while polyphenylalanine does not. Both amino acids can adopt backbone conformations that are consistent with and favor helical formation. However, because alpha helices are densely packed structures, the bulky phenylalanine sidechain would be sterically unfavorable in polyphenylalanine. e) Polyglutamate only forms an alpha helix at very low pH. Glutamate can form a helical backbone conformation and the sidechain is not bulky. However, at high pH the high density of negative charge in a helical polyglutamate structure would be energetically unfavorable from the repulsive electrostatics. At low pH, the glutamate sidechain is electrically neutral so there
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This note was uploaded on 01/15/2010 for the course BIO 31459 taught by Professor Zuo during the Spring '09 term at UCSC.

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biochem100BSolutionSet1-1 - BMB100B Winter 2009 Rubin...

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