Advanced search
Publication Cover
Molecular Membrane Biology Volume 19, 2002 - Issue 1
Journal homepage
2,376
Views
46
CrossRef citations to date
0
Altmetric
Research Article

The hydrophobic moment and its use in the classification of amphiphilic structures (Review)

David A. Phoenix Centre for Forensic Science, University of Central Lancashire, Preston, Lancashire PR1 2HE, UK
&
Frederick Harris Centre for Forensic Science, University of Central Lancashire, Preston, Lancashire PR1 2HE, UK
Pages 1-10 | Published online: 09 Jul 2009

  • Anantharamaiah, G. M., Jones, M. K. and Segnest J. P., 1993, An alias of the amphpathic helical domains of human exchangeable plasma apolipoproteins. In The Amphphipathic Helix, R. M Epand, ed. (Florida: CRC Press), pp. 109-142.
  • Auger, I. E., 1993, Computational techniques to predict amphipathic helical segments. In The Amphipathic Helix, R. M Epand, ed. (Florida: CRC Press), pp. 7-19.
  • Bechinger, B., 2000, Biophysical investigations of membrane perturbations by polypeptides using solid-state NMR spectroscopy. Molecular Membrane Biology, 17, 135-142.
  • Biggins, P. C. and Sansom, S. P., 1999, Interactions of a-helices with lipid bilayers: a review of emulation studies. Biophysical Chemistry, 76, 161-183.
  • Boggs, J. M, Jo, E., Polozov, I. V., Epand, R. F., Anantharamaiah, G. M, Blazyk, J. and Epand, R. M, 2001, Effect of magainin, class L, and class A amphipathic peptides on fatty acid spin labels in lipid bilayers. Biochimica et Biophysica Acta, 1511, 28-41.
  • Bowie, J. U., 1997, Helix packing in membrane proteins. Journal of Molecular Biology, 272, 780-789.
  • Bradshaw, J. P., Darkes, M J., Harroun, T. A., Katsaras, J. and Epand, R. M, 2000a, Oblique membrane insertion of viral fusion peptides probed by neutron diffraction. Biochemistry, 39, 6581-6585.
  • Bradshaw, J. P., Darkes, M. J. M., Katsaras, J. and Epand, R. M., 2000b, Neutron diffraction studies of vrai fusion peptides. Physica B, 276, 495-498.
  • Brandenburg, K., Harris, F., Phoenix, D. A. and Seydel, U, 2001, An FTIR investigation into the lipid interactions of peptides corresponding to the C-terminal anchoring regions of Escherichia coli penicilin-binding proteins 4 and 5. Membrane and Cell Biology, in press.
  • Brasseur, R., 2000, Tilted peptides: a motif for membrane destabilisation (Hypothesis). Molecular Membrane Biology, 17, 31-40.
  • Brasseur, R., Pillot, T., Uns, L, Vandekerckhove, J. and Rosseneu, M., 1997, Peptides in membranes: tipping the balance of stability. Trends in Biochemical Sciences, 22, 167-171.
  • Broome-Smith, J. K., Ionnidis, I., Edelman, A. and Spratt, B. G., 1988, Nucleotide sequences of the penicilin-binding protein 5 and 6 genes of Escherichia coli. Nucleic Acids Research, 16, 1617.
  • Clothia, C. and Finkelstein, A. V., 1990, The classification and origins of protein folding patterns. Annual Review of Biochemistry, 59, 1007-1039.
  • Cornette, J. L, Cease, K. B., Mergelit, H., Spouge, J. L, Berzofsky, J. A. and De Lisi, C. D., 1987, Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. Journal of Molecular Biology, 195, 659-685.
  • Comut I., Thiaudiere, E. and Dufoureq, J., 1993, The amphipathic helix in cytotoxic peptides. In The Amphipathic Helix, R. M Epand, ed. (Florida: CRC Press), pp. 333-346.
  • Decout, A., Labeur, C., Vanloo, B., Goethals, M., Vandekerckhove, J., Brasseu, R. and Rosseneu, M., 1999, Contribution of the hydrophobicity gradient to the secondary structure and activity of fusogenic peptides. Molecular Membrane Biology, 16, 237-246.
  • Dempsey, C. E., 1990, The actions of melittins on membranes. Biochimica et Biophysics Acta, 1027, 143-161.
  • Eddy, R., Krogh, A., Mitchison, G. and Durbin, R., 1998, Biological Sequence Analysis: Prababilistic Models of Proteins and Nucleic Acids (Cambridge: Cambridge University Press).
  • Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R., 1984b, Analysis of membrane and surface protein sequences with the hydrophobe moment plot. Journal of Molecular Biology, 179, 125-142.
  • Eisenberg, D., Weiss, R. M. and Terwiliger, T. C., 1982b, The helical hydrophobe moment a measure of the amphiphilicity of a helix. Nature, 299, 371-374.
  • Eisenberg, D., Webs, R. M, Terwilliger, T. C. and Wilcox, W., 1982a, Hydrophobie moment and protein structure. Faraday Symposia of the Chemical Society, 17, 109-120.
  • Eisenberg, D., Wesson, M and Wilcox, W., 1984a, Hydrophobe moments as tools for analysing protein sequences and structures. In Prediction of protein structure and principles of protein conformation G. Fasman, ed. (New York: Plenum Press), pp. 635-646.
  • Eisenberg, D., Wilcox, W. and McLachian, A. D., 1986, Hydrophobicity and amphiphilicity in protein structure. Journal of Cellular Biochemistry, 31, 11-17.
  • Epand, R. M, Shai, Y. C., Segrest J. P. and Anantharamaiah, G. M., 1995, Mechanisms far the modulation of membrane bilayer properties by amphipathic helical peptides. Biopolymers, 37, 319-338.
  • Fujii, G., 1999, To fuse or not to fuse: the effects of electrostatic interactions, hydrophobe forces and structural amphiphilicity on protein-mediated membrane destabilisation. Advanced Drug Delivery Reviews, 38, 257-277.
  • Harris, F., 1998, Investigations into the membrane interactive properties of the Escherichia coli low molecular mass PBP's. PhD Thesis, University of Central Lancashire, Preston, UK.
  • Harris, F. and Phoenix, D. A., 1997a, An investigation into the surface activities of C-terminal homologues of the Escherichia cou low molecular mass penicilin-binding proteins 4, 5 and 6. Biochemie, 79, 171-174.
  • Harris, F. and Phoenix, D. A., 1997b, The Escherichia coli low molecular mass penicilin-briding proteins and a putative membrane bound protein complex. Membrane and Cell Biology, 14, 481-485.
  • Harris, F. and Phoenix, D. A., 1998, Membrane binding of Escherichia coli penicilin-briding protein 4 is predominantly electrostatic and occurs at a specific binding site. Protein and Peptide Letters, 5, 63-66.
  • Harris, F., Daman, A., Wallace, J. and Phoenix, D. A., 2001a. Hydrophobie moment and hydrophobicity distributional properties and classification for membrane interacting transmembrane sequences. Protein Science, 10 (suppl), 341,.
  • Harris, F., Daman, A., Wallace, J. and Phoenix, D. A., 2001b, Distributional properties of uncleaved and stop-transfer trans-membrane sequences. Protein Science, 10 (suppl), 340.
  • Harris, F., Demel, R. A., Phoenix, D. A. and De Kruijff, B., 1998, An investigation into the lipid interactions of peptides corresponding to the C-terminal anchoring domains of Escherichia coli penicillin-binding proteins 4, 5 and 6. Biochimica et Biophysica Acta, 1415, 10-22.
  • Harris, F., Wallace, J. and Phoenix, D. A., 2000, Use of hydrophobic moment plot methodology to aid the identification of oblique orientated a-helices. Molecular Membrane Biology, 17, 201-207.
  • Harris, F., Wallace, J. and Phoenix, D. A., 2001c, Oblique orientated a-helix formation in the C-terminal regions of the Escherichia coli low molecular mass PBP's. Biochemical Society Abstracts, 29, 74.
  • Hashemzadeh-Bonehi, L, Jacob, J. P., Misopoulos, C. and Broome-Smith, J. K., 1998, Determinants of membrane protein topology and membrane anchoring. In Protein targeting and translocation. D. A. Phoenix, ed. (London: Portland Press), pp. 49-66.
  • Hristova, K., Wimley, W. C., Mishra, V. K., Ananatharamaiah, G. M, Segrest J. P. and White, S. H., 1999, An amphipathic a-helix at a membrane interface: a structural study using a novel X-ray diffraction method. Journal of Molecular Biology, 290, 99-117.
  • Huang, P. and Loew, G. H., 1995, Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular-dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 12, 937-956.
  • Johnson, J. E. and Cornell, R. B., 1999, Amphitropic proteins: regulation by reversible membrane interactions (review). Molecular Membrane Biology, 16, 217-235.
  • Karle, I. L, Flippenanderson, J. L, Uma, K., Balaram, H. and Balaram, P., 1989, Alpha-helix and mixed 310/alpha-helix in co-crystallized conformers of BOC-AIB-VAL-AIB-AIB-VAL-VAL-VAL-AIB-VAL-AIB-OME. Proceedings of the National Academy of Sciences (USA), 86, 765-769.
  • Kiefer, D. and Kuhn, A., 1998, Insertion of single- and multi-spanning proteins into the bacterial cytoplasme membrane. In Proton targeting and translocation, D. A. Phoenix, ed. (London: Portland Press), pp. 67-84.
  • Kyte, J. and Dolittle, R. F., 1982, A simple method for displaying the hydropathic character of a prater. Journal of Molecular Biology, 157, 105-132.
  • Manly, B. F. J., 1991, Randomisation and Mante Carlo methods in Biology (London: Chapman and HaII).
  • Martin, I., Ruysschaert, J.-M and Epand, R. E., 1999, Rote of the N-terminal peptides of vrai envelope proteins in membrane fusion. Advanced Drug Delivery Reviews, 38, 233-255.
  • McLachlen, A. D., 1993, Multichannel Fourier analysis of patterns in protein sequences. Journal of Physical Chemistry, 97, 3000-3006.
  • McLachlan, A. D. and Stewart M, 1976, The 14-fold periodicity in a-tropomysin and the interaction with actin. Journal of Molecular Biology, 103, 271-298.
  • Mishra, V. K. and Palgunachari, M N., 1996, Interaction of model class A (1), class A (2) and class Y amphipathic helical peptides with membranes. Biochemistry, 35, 11210-11220.
  • Manne, M, Nilsson, I., Johansson, M, Elhmed, N. and von Heijne, G., 1998, Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. Journal of Molecular Biology, 284, 1177-1183.
  • Mart, H., Terpstra, P. and Keck, W., 1991, Penicilin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicilin-interacting proteins. FEMS Letters, 78, 213-220.
  • Oren, Z. and Shai, Y., 1998, Made of action of linear amphiphiic a-helical antimicrobial peptides. Biopolymers, 47, 451-463.
  • Pecheur, E. I., Sainte Marie, J., Bienvenue, A. and Hoekstra, D., 1999, Peptides and membrane fusion: towards an understanding of the molecular mechanism of protein induced fusion. Journal of Membrane Biology, 167, 1-17.
  • Peuvot, J., Schank, A., Lins, L. and Brasseur, R., 1999, Are the fusion processes involved in birth, life and death of the cell depending on tilted insertion of peptides into membranes? Journal of Theoretical Biology, 198, 173-181.
  • Pewsey, A. R., Phoenix, D. A. and Roberts, M G., 1996, Mante Carlo analysis of potential C-terminal membrane interactive a-helices. Protein and Peptide Letters, 3, 185-192.
  • Phoenix, D. A. and Harris, F., 1995, The membrane interactive properties of the low molecular weight penicilin-binding proteins. Biochemical Society Transactions, 23, 976-980.
  • Phoenix, D. A. and Harris, F., 1998, Amphiphilic a-helices and lipid interactions. In Protein targeting and transliocation, D. A. Phoenix, ed. (London: Portland Press), pp. 19-36.
  • Phoenix, D. A., Stanworth, A. and Harris, F., 1998, The Hydrophobie moment plot and its efficacy in the prediction and classification of membrane interactive proteins and peptides. Membrane and Cell Biology, 12, 101-110.
  • Plank, C., Zauner, W. and Wagner, E., 1999, Application of membrane-active peptides for drug and gene delivery across cellular membranes. Advanced Drug Delivery Reviews, 34, 21-35.
  • Polverini, E., Casadio, R., Neyroz, P. and Masotti, L, 1998, Conformational changes of neuromedin B and Delta sleep-inducing peptide induced by their interaction with lipid membranes as revealed by spectroscopic techniques and molecular dynamic simulation. Archives of Biochemisty and Biophysics, 2, 225-235.
  • Polverini, E., Neyroz, P. Fariselli, P., Casadio, R. and Masotti, L, 1995, The effect of membranes on the conformation of neuromeclin-C. Biochemistry and Biophysical Research Communications, 214, 663-668.
  • Polzov, I. V., Polzova, A. I., Mishra, V. K., Anantharamaiah, G. M., Segrest J. P. and Epand, R. M, 1998, studies of kinetics and equilibrium membrane binding of class A and class L model amphipathic peptides. Biochimica et Biophysica Acta, 1368, 343-354.
  • Polzov, I. V., Polova, A. I., Tytler, E. M, Anantharamaiah, G. M., Segrest J. P. Woolley, G. A. and Epand, R. M., 1997, Role of lipids in the permeabilization of membranes by class L amphipathic helical peptides. Biochemisty, 36, 9237-9245.
  • Rahmen, M, Lins, L, Thomas-Soumarmon A, and Brasseur, R., 1997, Are amphipathic assymetric peptides ubiquitous structures for membrane destabilisation? Journal of Molecular Modeling, 3, 203-215.
  • Roberts, M G., Phoenix, D. A. and Pewsey, A. R. 1997, An algorithm for the detection of surface-active a-helices with the potential to anchor proteins at the membrane interface. CABIOS, 13, 99-106.
  • Schiffer, M and Edmundson, A. B., 1967, Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophysical Journal, 7, 121-135.
  • Segrest, J. P., De Loaf, K, Dohlman, J. G., Brouillette, C. G. and Anantharamaiah, G. M, 1990, Amphipathic helix motif: classes and properties. Proteins: Structure Function and Genetics, 8, 103-117.
  • Segrest J. P, Harvey S. C. and Zannis, V., 2000, Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications. Trends in Cardiovascular Medicine, 10, 246-252.
  • Segrest, J. P., Jackson, R. L, Morrisett, J. D. and Gotto, A. M. Jr, 1974, A molecular theory of lipid-protein interactions in the plasma lipoproteins. FEBS Letters, 38, 247-253.
  • Segrest J. P., Jones, M K., De Loaf, K, Brauillette, C. G., Venkatachalapathi, Y. V. and Anantharamaiah, G. M, 1992a, Amphipathic helix in exchangeable apolipoproteins: a review of secondary structure and function. Journal of Lipid Research, 33, 141-166.
  • Segrest, J. P., Jones, M. K., Klon, A. E., Sheldahl, C. J., Helinger, M., De Loot H. and Harvey, S. C., 1999, A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein.-Journal of Biological Chemistry, 274, 31755-31758.
  • Segrest, J. P., Venkatachalapathi, Y. V., Srinivas, S. K., Gupta, K. B., De Loot H. and Anatharamaiah, G. M., 1992b, Role of basic amino acid residues in the amphipathic helix: the snorkel hypothesis. In Molecular conformation and biological interactions, P. Balaramand S. Ramaseshan, eds (Bangalore: Indian Academy of Sciences), pp. 597-635.
  • Siligardi, G., Harris, F. and Phoenix, D. A., 1997, a-helical conformation in the C-termral anchoring darners of Escherichia coli penicillin-binding proteins 4, 5 and 6. Biochimica et Biophysica Acta, 1329, 278-284.
  • Siligardi, G., Samori, B., Melandri, S., Visconti, M. and Drake, A., 1994, Correlations between biological activities and conformation properties for human, salmon, eel, porcine calcitonins and elactonin elucidated by CD spectroscopy. European Journal of Biochemistry, 221, 1117-1125.
  • Sonnhammer, E. L. L, von Heijne, G. and Krogh, A., 1998, A Markov model for predicting transmembrane helices in protein sequences. In Proceedings for the sixth International Conference on Intelligent Systems for Molecular Biology, J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff and Christoph Sensen, eds (California: AAAI Press), pp. 175-182.
  • Spruijt, R. B., Wolfs, C. J. A. M, Verver, J. W. V. and Hemmings, M. A., 1996, Accessibility and environment probing using cysteineresidues introduced along the putative transmembrane domain of the major coat protein of bacteriophage Ml 3. Biochemistry, 35, 10383-10391.
  • Stopar, D., Spruijt, R. B., Wolfe, C. J. A. M. and Hemmings, M. A., 1996, Local dynamics of the Ml 3 major coat protein in different membrane-mimicking systems. Biochemistry, 35, 15467-15473.
  • Taylor, J. W., 1993, Amphiphilic helices in neuropeptides. In The Amphipathic Helix, R. M Epand, ed. (Florida: CRC Press), pp. 221-254.
  • Tieleman, D. P. and Sansom, M S. P., 2001, Molecular dynamics simulations of antimicrobial peptides: from membrane binding to trans-membrane channels. International Journal of Quantum Chemistry, 83, 166-179.
  • Tomich, J., 1993, Amphipathic helices in channel forming structures. In The Amphipathic Helix, R. M Epand, ed. (Florida: CRC Press), pp. 221-254.
  • Tossi, A., Sandri, L and Giangaspero, A., 2000, Amphipathic, alpha-helical antimicrobial peptides. Biopolymers, 55, 4-30.
  • Trinquier, G. and Sanejouand, Y. H., 1998, Which effective property of amino acids is best preserved by the genetic code? Protein Engineering, 11, 153-169.
  • Tytler, E. M. Anantharamaiah, G. M, Waker, D. E. and Mistry, M J., 1995, Molecular-basis for prokaryotic specificity of magainin-induced lysis Biochemistry, 34, 4393-4401.
  • Tytler, E. M, Segrest J. P., Epand, R. M, Song-Qing, M, Epand, R. F., Mishra, V. K., Venkatachapalapathi, Y. V. and Anantharamaiah, G. M., 1993, Reciprocal effects of apolpoprotein and lytic peptide analogues on membranes. Journal of Biological Chemistry, 268, 22112-22118.
  • Ubarretxena-Belandia, l. and Engelman, D. M., 2001, Helical membrane proteins diversity of functions in the context of simple architecture. Current Opinion in Structural Biology, 11, 370-376.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.