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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Hydrophobicity

  • Replacing the isoleucine at amino-acid position three of bacteriophage T4 lysozyme causes changes in the thermodynamic stability of the protein that are directly related to the hydrophobicity of the substituted residue [1].
  • The ability of TNBS to decrease mucosal hydrophobicity and induce colitis was attenuated if the hapten was coupled with dipalmitoylphosphatidylcholine [2].
  • These sequences, which resemble authentic presequences in their overall amino acid composition and degree of hydrophobicity, are rather frequent; greater than 2.7% of clones generated from E. coli DNA and greater than 5% of clones from the dihydrofolate reductase gene were functional in our screening system [3].
  • Difficulties in obtaining adequate quantities of virions retaining env, as well as the unstable nature and hydrophobicity of the oligomer, may account for the absence of previous biophysical studies to determine the oligomeric valency of membrane-associated env [4].
  • Mechanism of fusion of Sendai virus: role of hydrophobic interactions and mobility constraints of viral membrane proteins. Effects of polyethylene glycol [5].

High impact information on Hydrophobicity

  • The solution structure of a CUE domain of the yeast Cue2 protein in complex with ubiquitin reveals intermolecular interactions involving conserved hydrophobic surfaces, including the Leu8-Ile44-Val70 patch on ubiquitin [6].
  • Together with the TRAM protein, Sec61p provides a site in the membrane, at the interface of channel and lipid, through which a TM domain can dynamically equilibrate between the lipid and aqueous phases, depending on the hydrophobicity of the TM domain and the length of the polypeptide segment tethering it to the ribosome [7].
  • Peptide binding is mediated by electrostatic interactions with the EEVD motif, with the C-terminal aspartate acting as a two-carboxylate anchor, and by hydrophobic interactions with residues upstream of EEVD [8].
  • BID's activity is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, resulting in a change of cellular localization [9].
  • The tip of the FYVE domain has basic and hydrophobic surfaces positioned so that nonspecific interactions with the phospholipid bilayer can abet specific binding to phosphatidylinositol 3-phosphate [10].

Chemical compound and disease context of Hydrophobicity

  • We demonstrated that IgG exposure to pro-oxidative ferrous ions or to reactive oxygen species enhances paratope flexibility and hydrophobicity, leading to expansion of the spectrum of recognized antigens, regulation of cell proliferation, and protection in experimental sepsis [11].
  • The results indicate that signal peptide hydrophobicity can completely override possible requirements for negatively charged residues and strong beta-turn forming potential in the mature protein and that the polyleucine-containing signal peptide may act as a generic signal sequence for the transport of non-native proteins in E. coli [12].
  • Mannose resistant adhesion to HEp-2 cells was determined for 124 isolates of E coli and surface hydrophobicity was estimated by salt agglutination in 96 of these isolates [13].
  • RESULTS: Upon exposure, phage were inactivated (non-infective) at methanol, ethanol and 1-propanol concentrations inversely dependent upon alcohol hydrophobicity [14].
  • At the same time or later the backbone torsions rearrange due to local tendency of the proline ring to form a turn: this step depends on solvation forces and is helped by loose hydrophobic interactions [15].

Biological context of Hydrophobicity


Anatomical context of Hydrophobicity


Associations of Hydrophobicity with chemical compounds

  • Since disruption of homophilic interactions between the bound molecules required the presence of Triton X-100, hydrophobic interactions may occur after the initial ionic binding [25].
  • Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix [26].
  • The galactose moiety is oriented differently from ligands in the mannose-glucose specific legume lectins and is held by hydrophobic interactions with Ala88, Tyr106, Phe131, and Ala218 and by seven hydrogen bonds, four of which are to the conserved Asp89, Asn133, and NH of Gly107 [27].
  • In pressinoic acid, the Tyr2 side chain is in the expected "pressor conformation," that is, extended away from the ring system, and is stabilized through a hydrophobic interaction with the Phe3 side chain [28].
  • Experiments with the environment-sensitive fluorescent probe ANS (8-anilino-1-naphthalene-sulfonic acid) provided further evidence for a reversible structural transition at mildly acidic pH associated with an increase in exposed hydrophobicity in class II molecules [29].

Gene context of Hydrophobicity


Analytical, diagnostic and therapeutic context of Hydrophobicity


  1. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3. Matsumura, M., Becktel, W.J., Matthews, B.W. Nature (1988) [Pubmed]
  2. Molecular association of trinitrobenzenesulfonic acid and surface phospholipids in the development of colitis in rats. Tatsumi, Y., Lichtenberger, L.M. Gastroenterology (1996) [Pubmed]
  3. Sequences from a prokaryotic genome or the mouse dihydrofolate reductase gene can restore the import of a truncated precursor protein into yeast mitochondria. Baker, A., Schatz, G. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  4. Oligomeric structure of virion-associated and soluble forms of the simian immunodeficiency virus envelope protein in the prefusion activated conformation. Center, R.J., Schuck, P., Leapman, R.D., Arthur, L.O., Earl, P.L., Moss, B., Lebowitz, J. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  5. Mechanism of fusion of Sendai virus: role of hydrophobic interactions and mobility constraints of viral membrane proteins. Effects of polyethylene glycol. Hoekstra, D., Klappe, K., Hoff, H., Nir, S. J. Biol. Chem. (1989) [Pubmed]
  6. Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding. Kang, R.S., Daniels, C.M., Francis, S.A., Shih, S.C., Salerno, W.J., Hicke, L., Radhakrishnan, I. Cell (2003) [Pubmed]
  7. The Sec61p complex mediates the integration of a membrane protein by allowing lipid partitioning of the transmembrane domain. Heinrich, S.U., Mothes, W., Brunner, J., Rapoport, T.A. Cell (2000) [Pubmed]
  8. Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Scheufler, C., Brinker, A., Bourenkov, G., Pegoraro, S., Moroder, L., Bartunik, H., Hartl, F.U., Moarefi, I. Cell (2000) [Pubmed]
  9. Solution structure of the proapoptotic molecule BID: a structural basis for apoptotic agonists and antagonists. McDonnell, J.M., Fushman, D., Milliman, C.L., Korsmeyer, S.J., Cowburn, D. Cell (1999) [Pubmed]
  10. Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p. Misra, S., Hurley, J.H. Cell (1999) [Pubmed]
  11. Ferrous ions and reactive oxygen species increase antigen-binding and anti-inflammatory activities of immunoglobulin G. Dimitrov, J.D., Ivanovska, N.D., Lacroix-Desmazes, S., Doltchinkova, V.R., Kaveri, S.V., Vassilev, T.L. J. Biol. Chem. (2006) [Pubmed]
  12. Transport of an export-defective protein by a highly hydrophobic signal peptide. Rusch, S.L., Kendall, D.A. J. Biol. Chem. (1994) [Pubmed]
  13. Adhesive and hydrophobic properties of Escherichia coli from the rectal mucosa of patients with ulcerative colitis. Hartley, M.G., Hudson, M.J., Swarbrick, E.T., Gent, A.E., Hellier, M.D., Grace, R.H. Gut (1993) [Pubmed]
  14. Filamentous bacteriophage stability in non-aqueous media. Olofsson, L., Ankarloo, J., Andersson, P.O., Nicholls, I.A. Chem. Biol. (2001) [Pubmed]
  15. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. Mohanty, D., Elber, R., Thirumalai, D., Beglov, D., Roux, B. J. Mol. Biol. (1997) [Pubmed]
  16. Gastric mucosal hydrophobicity in duodenal ulceration: role of Helicobacter pylori infection density and mucus lipids. Asante, M., Ahmed, H., Patel, P., Davis, T., Finlayson, C., Mendall, M., Northfield, T. Gastroenterology (1997) [Pubmed]
  17. SEC62 encodes a putative membrane protein required for protein translocation into the yeast endoplasmic reticulum. Deshaies, R.J., Schekman, R. J. Cell Biol. (1989) [Pubmed]
  18. Deciphering the structural framework of glycine receptor anchoring by gephyrin. Kim, E.Y., Schrader, N., Smolinsky, B., Bedet, C., Vannier, C., Schwarz, G., Schindelin, H. EMBO J. (2006) [Pubmed]
  19. Paralemmin, a prenyl-palmitoyl-anchored phosphoprotein abundant in neurons and implicated in plasma membrane dynamics and cell process formation. Kutzleb, C., Sanders, G., Yamamoto, R., Wang, X., Lichte, B., Petrasch-Parwez, E., Kilimann, M.W. J. Cell Biol. (1998) [Pubmed]
  20. Some considerations of receptor specificity. Burgen, A.S. Trends Pharmacol. Sci. (1989) [Pubmed]
  21. Prevention of cholesterol gallstone disease by FXR agonists in a mouse model. Moschetta, A., Bookout, A.L., Mangelsdorf, D.J. Nat. Med. (2004) [Pubmed]
  22. Deranged hydrophobic barrier of the rat gastroduodenal mucosa after parenteral nonsteroidal anti-inflammatory drugs. Lugea, A., Antolín, M., Mourelle, M., Guarner, F., Malagelada, J.R. Gastroenterology (1997) [Pubmed]
  23. Effect of 16,16-dimethyl prostaglandin E2 on the surface hydrophobicity of aspirin-treated canine gastric mucosa. Lichtenberger, L.M., Richards, J.E., Hills, B.A. Gastroenterology (1985) [Pubmed]
  24. Luminal surface hydrophobicity of canine gastric mucosa is dependent on a surface mucous gel. Goddard, P.J., Kao, Y.C., Lichtenberger, L.M. Gastroenterology (1990) [Pubmed]
  25. Identification of an octapeptide involved in homophilic interaction of the cell adhesion molecule gp80 of dictyostelium discoideum. Kamboj, R.K., Gariepy, J., Siu, C.H. Cell (1989) [Pubmed]
  26. Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Müller, C.W., Herrmann, B.G. Nature (1997) [Pubmed]
  27. Structure of a legume lectin with an ordered N-linked carbohydrate in complex with lactose. Shaanan, B., Lis, H., Sharon, N. Science (1991) [Pubmed]
  28. Structure of pressinoic acid: the cyclic moiety of vasopressin. Langs, D.A., Smith, G.D., Stezowski, J.J., Hughes, R.E. Science (1986) [Pubmed]
  29. A structural transition in class II major histocompatibility complex proteins at mildly acidic pH. Runnels, H.A., Moore, J.C., Jensen, P.E. J. Exp. Med. (1996) [Pubmed]
  30. Crystal structure at 1.7 A resolution of VEGF in complex with domain 2 of the Flt-1 receptor. Wiesmann, C., Fuh, G., Christinger, H.W., Eigenbrot, C., Wells, J.A., de Vos, A.M. Cell (1997) [Pubmed]
  31. Crystal structure of PU.1/IRF-4/DNA ternary complex. Escalante, C.R., Brass, A.L., Pongubala, J.M., Shatova, E., Shen, L., Singh, H., Aggarwal, A.K. Mol. Cell (2002) [Pubmed]
  32. Structural basis for recruitment of human flap endonuclease 1 to PCNA. Sakurai, S., Kitano, K., Yamaguchi, H., Hamada, K., Okada, K., Fukuda, K., Uchida, M., Ohtsuka, E., Morioka, H., Hakoshima, T. EMBO J. (2005) [Pubmed]
  33. Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization. Turnbull, A.P., Kümmel, D., Prinz, B., Holz, C., Schultchen, J., Lang, C., Niesen, F.H., Hofmann, K.P., Delbrück, H., Behlke, J., Müller, E.C., Jarosch, E., Sommer, T., Heinemann, U. EMBO J. (2005) [Pubmed]
  34. The VASP tetramerization domain is a right-handed coiled coil based on a 15-residue repeat. Kühnel, K., Jarchau, T., Wolf, E., Schlichting, I., Walter, U., Wittinghofer, A., Strelkov, S.V. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  35. Temperature effects in hydrophobic interaction chromatography. Haidacher, D., Vailaya, A., Horváth, C. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  36. Determinant for beta-subunit regulation in high-conductance voltage-activated and Ca(2+)-sensitive K+ channels: an additional transmembrane region at the N terminus. Wallner, M., Meera, P., Toro, L. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  37. Partial purification and characterization of a protease from human plasma cleaving von Willebrand factor to fragments produced by in vivo proteolysis. Furlan, M., Robles, R., Lämie, B. Blood (1996) [Pubmed]
  38. Interactions of thrombospondin with sulfated glycolipids and proteoglycans of human melanoma cells. Roberts, D.D. Cancer Res. (1988) [Pubmed]
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