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Cited by 66Protein Structure and DynamicsMachine Learning in BioinformaticsLipid Membrane Structure and Behavior

The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.

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

Open access
Phoenix, David A., Harris, Frederick·2002·Molecular Membrane Biology
DOI 10.1080/09687680110103631
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Abstract

Amphiphilic alpha-helices play a major role in membrane dependent processes and are manifested in the primary structure of a protein by the periodic appearance of hydrophobic residues. Based on these periodic sequences, the hydrophobic moment was introduced, , which essentially treats the hydrophobicity of amino acid residues as a two-dimensional vector sum and provides a measure of amphiphilicity within regular repeat structures. To identify putative amphiphilic alpha-helix forming sequences, hydrophobic moment analysis assumes an amino acid residue periodicity of 100 and scans protein primary structures to find the 11-residue window with maximal . Taken with the window's mean hydrophobicity, , hydrophobic moment plot analysis uses the coordinate pair, [ , ] to classify alpha-helices as either surface active, globular or transmembrane. More recently, this latter analysis has been extended to recognize candidate oblique orientated alpha-helices. Here, the hydrophobic moment is reviewed and data to query the logic of using a fixed window length and a fixed residue angular periodicity in hydrophobic moment analysis are provided. In addition, problems associated with the use of such analysis to predict alpha-helix structure/function relationships are considered.

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Crossref · 10.1080/09687680110103631

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  • The average global charge of sequences from the long-term case is 3.11 pKa.

    “The average global charge of peptides representing the overall charge of amino-acid residues in each sequence36 of the generation set from the mixed case is 2.32 pKa while the sequences from the short-term and long-term cases show 3.89 pKa and 3.11 pKa, respectively (see Fig. 5d).”

    From Experimental demonstration of highly reliable dynamic memristor for artificial neuron and neuromorphic computing (2022) · cites this paper as [36]

    The Hydrophobicity scale and Window size sections discuss hydrophobicity and hydrophobic-moment analysis, not the global charge of peptide sequences. Searches for global or net charge, pKa, the long-term case, and 3.11 found no passage supporting the stated average; no page numbers were available in our copy. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • The average global charge of sequences from the short-term case is 3.89 pKa.

    “The average global charge of peptides representing the overall charge of amino-acid residues in each sequence36 of the generation set from the mixed case is 2.32 pKa while the sequences from the short-term and long-term cases show 3.89 pKa and 3.11 pKa, respectively (see Fig. 5d).”

    From Experimental demonstration of highly reliable dynamic memristor for artificial neuron and neuromorphic computing (2022) · cites this paper as [36]

    The Introduction and Hydrophobicity scale sections discuss hydrophobicity and amphiphilicity, not average global charge. A search of our copy for “3.89 pKa,” “short-term case,” and global charge found no passage reporting the claimed value; page numbers were unavailable. (LLM, conf=0.74)

    Experimental — accuracy not yet measured

  • The average global charge of peptides in the generation set from the mixed case is 2.32 pKa.

    “The average global charge of peptides representing the overall charge of amino-acid residues in each sequence36 of the generation set from the mixed case is 2.32 pKa while the sequences from the short-term and long-term cases show 3.89 pKa and 3.11 pKa, respectively (see Fig. 5d).”

    From Experimental demonstration of highly reliable dynamic memristor for artificial neuron and neuromorphic computing (2022) · cites this paper as [36]

    The review’s Surface active α-helices section discusses the distribution of charged residues, but it does not report an average global charge for a mixed-case peptide generation set. Searches for “2.32 pKa” and the short-term and long-term charge values found no matching result in our copy. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Citations

Cites

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Research works printed but not linked: 12

  1. [1]1. Anantharamaiah, G. M., Jones, M. K. and Segrest, J. P., 1993, An atlas of the amphipathic helical domains of human exchangeable plasma apolipoproteins . In The Amphipathic Helix, R. M. Epand, ed. (Florida: CRC Press), pp. 109 ± 142.
  2. [14]14. Cornut, I., Thiaudiere, E. and Dufourcq, J., 1993, The amphipathic helix in cytotoxic peptides. In The Amphipathic Helix, R. M. Epand, ed. (Florida: CRC Press), pp. 333 ± 346.
  3. [25]25. 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.
  4. [28]28. Harris, F. and Phoenix, D. A., 1998, Membrane binding of Escherichia coli penicillin-binding protein 4 is predominantly electrostatic and occurs at a specific binding site. Protein and Peptide Letters, 5, 63 ± 66.
  5. [35]35. 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.
  6. [52]52. Phoenix, D. A. and Harris, F., 1995, The membrane interactiv e properties of the low molecular weight penicillin-binding proteins. Biochemical Society Transactions, 23, 976 ± 980.
  7. [59]59. Rahman, 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.
  8. [65]65. Segrest, J. P., Jones, M. K., De Loof, H., Brouillette, C. G., Venkatacha- lapathi, 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.
  9. [67]67. Segrest, J. P., Venkatachalapathi, Y. V., Srinivas, S. K., Gupta, K. B., De Loof, 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. Balaram and S. Ramaseshan, eds (Bangalore: Indian Academy of Sciences), pp. 597 ± 635.
  10. [73]73. Taylor, J. W., 1993, Amphiphilic helices in neuropeptides. In The Amphipathic Helix, R. M. Epand, ed. (Florida: CRC Press), pp. 221 ± 254.
  11. [75]75. Tomich, J., 1993, Amphipathic helices in channel forming structures. In The Amphipathic Helix, R. M. Epand, ed. (Florida: CRC Press), pp. 221 ± 254.
  12. [79]79. Tytler, E. M., Segrest, J. P., E pand, R. M., Song-Qing, N., Epand, R. F., Mishra, V. K., Venkatachapalapathi, Y. V. and Ananthara- maiah, G. M., 1993, Reciprocal effects of apolipoprotein and lytic peptide analogues on membranes. Journal of Biological Chem- istry, 268, 22112 ± 22118.

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Metadata

Authors
Phoenix, D. A., & Harris, F.
Affiliations
University of Lancashire (GB)
ORCID
Phoenix, David A.
Venue
Molecular Membrane Biology
Publisher
Informa UK Limited
Published
2002-01
Volume
19
Issue
1
Pages
1-10
ISSN
  • 0968-7688 (ISSN-L)
  • 1464-5203
DOI
10.1080/09687680110103631
OpenAlex
W2127045036
Cited by
66
References
63
Citations by year
2025: 1 · 2024: 5 · 2023: 3 · 2022: 5 · 2021: 8 · 2020: 2 · 2019: 4 · 2018: 2 · 2017: 2 · 2016: 2 · 2015: 1 · 2014: 2 · 2013: 7
FWCI
1.27
Type
journal article
Language
en
Open access
Locations
  • Molecular Membrane Biology (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
Keywords
hydrophobic moment, transmembrane helices, helix prediction, membrane proteins, protein primary structure
MeSH terms
Amino Acid Sequence, Animals, Fourier Analysis, Membrane Proteins, Molecular Sequence Data, Periodicity, Surface Properties, Protein Structure, Secondary, Protein Interaction Mapping, Hydrophobic and Hydrophilic Interactions

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