Helix kinks are equally prevalent in soluble and membrane proteins.
Bottom Line: We compare length-matched sets of soluble and membrane helices, and find that the frequency of kinks, the role of Proline, the patterns of other amino acid around kinks (allowing for the expected differences in amino acid distributions between the two types of protein), and the effects of hydrogen bonds are the same for the two types of helices.However, there are a sizeable proportion of kinked helices that do not contain a Proline in either their sequence or sequence homolog.Moreover, we observe that in soluble proteins, kinked helices have a structural preference in that they typically point into the solvent.
Affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.Show MeSH
Mentions: The amino acid propensities around kinks in Figure 3 show a periodic pattern. Hydrophobic residues are more frequently observed in positions on the inside of kinks (−4,0,+4), while charged and polar residues are less frequent at these positions. The mean hydrophobicity of each position in membrane and soluble kinks are shown in Figure 4. The hydrophobicities are calculated from the sequence profiles, derived from the homologous sequences. There is a clear pattern in the hydrophobicity of soluble kinks, with more hydrophobic residues on the inside of kinks, and more hydrophilic residues on the outside of kinks. This pattern is repeated in the fraction of residues which are solvent accessible, with residues on the outside of kinks being more solvent accessible than those the inside [Fig. 4(d)]. This indicates that soluble kinks point into the aqueous environment, meaning that the residues on the outside of the kink will be in the solvent (Fig. 2). The solvent accessible surface areas are calculated only from the structures.
Affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.