Hydrophobicity scale

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Hydrophobicity scales , hydrophobicity and hydropathy describe the extent of the hydrophobic effect on molecules in biochemistry . With increasing hydrophobicity they are called hydrophilic , amphiphilic or hydrophobic .

properties

The hydrophobicity of low molecular weight compounds ( small molecules ) is described by the octanol-water partition coefficient . The ranking of the values ​​describes the hydrophobicity as follows: from negative (hydrophilic), through zero (neutral), to positive (hydrophobic).

The respective hydrophobicity was also determined for nucleobases.

Hydrophobicity scales of proteins

In proteins both hydrophilic and hydrophobic are amino acids as polymer before. An accumulation of hydrophobic amino acids in a row indicates their occurrence inside a protein or a transmembrane domain . There are different scales for the hydrophobicity (also hydropathic index , hydrophobicity index ) of amino acids in proteins, which are referred to as hydropathic indices (in the singular: hydropathic index ) or hydrophobicity scales . In some scales, cysteine is defined as the most hydrophobic amino acid because these methods are based on the probabilities of the respective amino acids being on the surface of a protein and there are hardly any disulfide bridges on the protein surface. The different scales can be divided into five categories.

The JTT2 scale gives a ratio that results from the frequency with which the amino acid occurs in the transmembrane segments, divided by the frequency of the amino acid in a large amount of proteins. There is also the Gunnar von Heijne scale , the Kyte and Doolittle scale , the Wimley-White scale , the aWW scale , the Eisenberg consensus scale , and the Engelman-Steitz scale .

Eisenberg consensus scale (ECS)
R. K D. Q N E. H S. T P Y C. G A. M. W. L. V F. I.
-2.5 -1.5 -0.90 -0.85 -0.78 -0.74 -0.40 -0.18 -0.05 0.12 0.26 0.29 0.48 0.62 0.64 0.81 1.1 1.1 1.2 1.4
Kyte and Doolittle scale
R. K N D. Q E. H P Y W. S. T G A. M. C. F. L. V I.
-4.5 -3.9 -3.5 -3.5 -3.5 -3.5 -3.2 -1.6 -1.3 -0.9 -0.8 -0.7 -0.4 1.8 1.9 2.5 2.8 3.8 4.2 4.5


Individual evidence

  1. ^ PM Cullis, R. Wolfenden: Affinities of nucleic acid bases for solvent water. In: Biochemistry. Volume 20, Number 11, May 1981, pp. 3024-3028, ISSN  0006-2960 . PMID 7248264 .
  2. ↑ a b Kallol M. Biswas, Daniel R. DeVido, John G. Dorsey (2003) Journal of Chromatography A, 1000, 637-655.
  3. ↑ a b c d Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein . In: J. Mol. Biol. . 157, No. 1, May 1982, pp. 105-32. doi : 10.1016 / 0022-2836 (82) 90515-0 . PMID 7108955 .
  4. ↑ a b c Eisenberg D: Three-dimensional structure of membrane and surface proteins . In: Ann. Rev. Biochem. . 53, July 1984, pp. 595-623. doi : 10.1146 / annurev.bi.53.070184.003115 . PMID 6383201 .
  5. ^ GD Rose, R. Wolfenden: Hydrogen bonding, hydrophobicity, packing, and protein folding. In: Annual review of biophysics and biomolecular structure. Volume 22, 1993, pp. 381-415, ISSN  1056-8700 . doi: 10.1146 / annurev.bb.22.060193.002121 . PMID 8347995 .
  6. ^ J. Janin: Surface and inside volumes in globular proteins. In: Nature. Volume 277, Number 5696, February 1979, pp. 491-492, ISSN  0028-0836 . PMID 763335 .
  7. ↑ GD Rose, AR Geselowitz, GJ Lesser, RH Lee, MH Zehfus: Hydrophobicity of amino acid residues in globular proteins. In: Science. Volume 229, Number 4716, August 1985, pp. 834-838, ISSN  0036-8075 . PMID 4023714 .
  8. ^ R. Wolfenden, L. Andersson, PM Cullis, CC Southgate: Affinities of amino acid side chains for solvent water. In: Biochemistry. Volume 20, Number 4, February 1981, pp. 849-855, ISSN  0006-2960 . PMID 7213619 .
  9. ↑ D. Boyd, C. Schierle, J. Beckwith: How many membrane proteins are there? In: Protein science: a publication of the Protein Society. Volume 7, Number 1, January 1998, pp. 201-205, ISSN  0961-8368 . doi: 10.1002 / pro.5560070121 . PMID 9514275 . PMC 2143806 (free full text).
  10. ↑ G. von Heijne: Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. In: Journal of molecular biology. Volume 225, Number 2, May 1992, pp. 487-494, ISSN  0022-2836 . PMID 1593632 .
  11. ↑ WC Wimley, SH White: Experimentally determined hydrophobicity scale for proteins at membrane interfaces. In: Nature structural biology. Volume 3, Number 10, October 1996, pp. 842-848, ISSN  1072-8368 . PMID 8836100 .
  12. ^ S. Jayasinghe, K. Hristova, SH White: Energetics, stability, and prediction of transmembrane helices. In: Journal of molecular biology. Volume 312, Number 5, October 2001, pp. 927-934, ISSN  0022-2836 . doi: 10.1006 / jmbi.2001.5008 . PMID 11580239 .
  13. ^ David Eisenberg, Robert M. Weiss, Thomas C. Terwilliger, William Wilcox: Hydrophobic moments and protein structure. In: Faraday Symp. Chem. Soc. (1982), Vol. 17, pp. 109-120. doi: 10.1039 / FS9821700109 .
  14. ^ D. Eisenberg, E. Schwarz, M. Komaromy, R. Wall: Analysis of membrane and surface protein sequences with the hydrophobic moment plot. In: Journal of molecular biology. Volume 179, Number 1, October 1984, pp. 125-142, ISSN  0022-2836 . PMID 6502707 .
  15. ↑ DM Engelman, TA Steitz, A. Goldman: Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. In: Annual review of biophysics and biophysical chemistry. Volume 15, 1986, pp. 321-353, ISSN  0883-9182 . doi: 10.1146 / annurev.bb.15.060186.001541 . PMID 3521657 .