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Helix kinks are equally prevalent in soluble and membrane proteins.

Wilman HR, Shi J, Deane CM - Proteins (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.

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Hydrophobicities, solvent accessible surface areas, and membrane contacts. (a) Helical wheel diagram showing the average hydrophobicity of residues around membrane kinks. K indicates the kink residue (position 0 in Fig. 2). (b) Wheel diagram for soluble kinks. K indicates the kink residue. (c) Average percentage of residues in contact with the membrane in membrane kinks. (d) Average solvent accessible percentage of residues in soluble kinks. Bars show 2 s.d. from 50 samples. See Figure S5 in the Supporting Information for the analogous figure based on the MC-Helan analysis. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]
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fig04: Hydrophobicities, solvent accessible surface areas, and membrane contacts. (a) Helical wheel diagram showing the average hydrophobicity of residues around membrane kinks. K indicates the kink residue (position 0 in Fig. 2). (b) Wheel diagram for soluble kinks. K indicates the kink residue. (c) Average percentage of residues in contact with the membrane in membrane kinks. (d) Average solvent accessible percentage of residues in soluble kinks. Bars show 2 s.d. from 50 samples. See Figure S5 in the Supporting Information for the analogous figure based on the MC-Helan analysis. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

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.


Helix kinks are equally prevalent in soluble and membrane proteins.

Wilman HR, Shi J, Deane CM - Proteins (2014)

Hydrophobicities, solvent accessible surface areas, and membrane contacts. (a) Helical wheel diagram showing the average hydrophobicity of residues around membrane kinks. K indicates the kink residue (position 0 in Fig. 2). (b) Wheel diagram for soluble kinks. K indicates the kink residue. (c) Average percentage of residues in contact with the membrane in membrane kinks. (d) Average solvent accessible percentage of residues in soluble kinks. Bars show 2 s.d. from 50 samples. See Figure S5 in the Supporting Information for the analogous figure based on the MC-Helan analysis. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4285789&req=5

fig04: Hydrophobicities, solvent accessible surface areas, and membrane contacts. (a) Helical wheel diagram showing the average hydrophobicity of residues around membrane kinks. K indicates the kink residue (position 0 in Fig. 2). (b) Wheel diagram for soluble kinks. K indicates the kink residue. (c) Average percentage of residues in contact with the membrane in membrane kinks. (d) Average solvent accessible percentage of residues in soluble kinks. Bars show 2 s.d. from 50 samples. See Figure S5 in the Supporting Information for the analogous figure based on the MC-Helan analysis. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.

Show MeSH