Hydrophobicity Plots


Hydrophobicity plots are used to identify sequences of amino acids in proteins that form transmembrane helices – parts of the protein that span the lipid membrane. This information can be used to aid determination of the structure of membrane proteins.

Keywords: membrane proteins; computer prediction; α helices; hydrophobicity; amphipathic

Figure 1.

Transmembrane α helices. Schematic diagrams of (a) a single‐pass membrane protein; and (b) a multipass membrane protein. The transmembrane helices are shown as cylinders and the lipid bilayer as a horizontal grey band.

Figure 2.

Hydrophobicity profile for human aquaporin‐1. Positive peaks of hydrophobicity correspond to potential membrane‐spanning helices. The horizontal black lines indicate the approximate positions of the six transmembrane helices H1 to H6. The profile was calculated using the scale of Kyte and Doolittle , with a 17‐residue rectangular window.

Figure 3.

Pore formation by a bundle of amphipathic α helices. (a) An amphipathic α helix that forms part of the lining of the central pore of the bacterial mechanosensitive channel Mscl (pdb code 1MSL). The polar surface is shaded dark grey. (b) Idealized representation of an amphipathic α helix, the polar face indicated by the grey surface. (c) Idealized representation of pore formation by a bundle of five amphipathic helices. The foremost helix has been removed to reveal the inside of the pore lined by the polar side‐chains.



Biggin PC and Sansom MSP (1998) Interactions of α‐helices with lipid bilayers: a review of simulation studies. Biophysical Chemistry 76: 161–183.

Chang G, Spencer RH, Lee AT, Barclay MT and Rees DC (1998) Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive channel. Science 282: 2220–2226.

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von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive inside rule. Journal of Molecular Biology 225: 487–494.

Further Reading

Cserzo M, Wallin E, Simon I, von Heijne G and Elofsson A (1997) Prediction of transmembrane alpha‐helices in prokaryotic membrane proteins: the Dense Alignment Surface method. Protein Engineering 10(6): 673–676. [http://www.biokemi.su.se/∼server/DAS] [“DAS” – Transmembrane Prediction server.]

Hofmann K and Stoffel W (1993) TMbase – A database of membrane spanning proteins segments. Biological Chemistry 347: 166. [http://www.ch.embnet.org/software/TMPRED‐form.html] [TMpred – Prediction of Transmembrane Regions and Orientation.]

Jones DT, Taylor WR and Thornton JM (1994) A model recognition approach to the prediction of all‐helical membrane protein structure and topology. Biochemistry 33: 3038–3049. [http://globin.bio.warwick.ac.uk/∼jones/memsat.html] [MEMSAT – MEMbrane protein Structure And Topology.]

Mitaku S and Hirokawa T (1999) Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length. Protein Engineering 12(11): 953–957. [http://azusa.proteome.bio.tuat.ac.jp/sosui] [SOSUI – Classification and Secondary Structure Prediction of Membrane Proteins.]

Rost B (1996) PHD: predicting one‐dimensional protein structure by profile based neural networks. Methods in Enzymology 266: 525–539. [http://www.embl‐heidelberg.de/predictprotein/predictprotein.html] [The PredictProtein server.]

Sonnhammer ELL, von Heijne G and Anders Krogh (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In: Glasgow J, Littlejohn T, Major F et al. (eds) Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pp. 175–182. Menlo Park, CA: AAAI Press. [http://www.cbs.dtu.dk/services/TMHMM‐1.0] [Prediction of transmembrane helices in proteins – TMHMM.]

von Heijne G (1992) Membrane protein structure prediction, hydrophobicity analysis and the positive‐inside rule. Journal of Molecular Biology 225: 487–494. [http://www.biokemi.su.se/∼server/toppred2] [TopPred 2 Topology prediction of membrane proteins.]

White SN (1994) Membrane Protein Structure: Experimental Approaches. New York: Oxford University Press.

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How to Cite close
Sansom, Mark SP(Apr 2001) Hydrophobicity Plots. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003042]