Investigation of hydrophobic moment and hydrophobicity properties for transmembrane α-helices

Journal article


Wallace, J, Daman, OA, Harris, F and Phoenix, DA (2004). Investigation of hydrophobic moment and hydrophobicity properties for transmembrane α-helices. Theoretical Biology and Medical Modelling. 1 (5).
AuthorsWallace, J, Daman, OA, Harris, F and Phoenix, DA
Abstract

Integral membrane proteins are the primary targets of novel drugs but are largely without solved structures. As a consequence, hydrophobic moment plot methodology is often used to identify putative transmembrane α-helices of integral membrane proteins, based on their local maximum mean hydrophobic moment (〈μH〉) and the corresponding mean hydrophobicity (〈H〉). To calculate these properties, the methodology identifies an optimal eleven residue window (L = 11), assuming an amino acid angular frequency, θ, fixed at 100°. Using a data set of 403 transmembrane α-helix forming sequences, the relationship between 〈μH〉 and 〈H〉, and the effect of varying of L and / or θ on this relationship, was investigated. Confidence intervals for correlations between 〈μH〉 and 〈H〉 are established. It is shown, using bootstrapping procedures that the strongest statistically significant correlations exist for small windows where 7 ≤ L ≤ 16. Monte Carlo analysis suggests that this correlation is dependent upon amino acid residue primary structure, implying biological function and indicating that smaller values of L give better characterisation of transmembrane sequences using 〈μH〉. However, varying window size can also lead to different regions within a given sequence being identified as the optimal window for structure / function predictions. Furthermore, it is shown that optimal periodicity varies with window size; the optimum, based on 〈μH〉 over the range of window sizes, (7 ≤ L ≤ 16), was at θ = 102° for the transmembrane α-helix data set. © 2004 Wallace et al; licensee BioMed Central Ltd.

Keywordsamino acid; membrane protein; alpha helix; amino acid sequence; article; calculation; confidence interval; correlation analysis; hydrophobicity; methodology; Monte Carlo method; prediction; chemical phenomena; chemical structure; chemistry; human; protein secondary structure; Humans; Hydrophobic and Hydrophilic Interactions; Membrane Proteins; Models, Molecular; Protein Structure, Secondary; Humans; Membrane Proteins; Protein Structure, Secondary; Models, Molecular; Hydrophobic and Hydrophilic Interactions; Humans; Hydrophobic and Hydrophilic Interactions; Membrane Proteins; Models, Molecular; Protein Structure, Secondary; 06 Biological Sciences; Bioinformatics
Year2004
JournalTheoretical Biology and Medical Modelling
Journal citation1 (5)
PublisherBMC
ISSN1742-4682
Digital Object Identifier (DOI)doi:10.1186/1742-4682-1-5
Web address (URL)https://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-1-5
Publication dates
Print16 Aug 2004
Publication process dates
Deposited28 Sep 2018
Accepted16 Aug 2004
Publisher's version
License
CC BY 4.0
Permalink -

https://openresearch.lsbu.ac.uk/item/87qzv

  • 0
    total views
  • 6
    total downloads
  • 0
    views this month
  • 3
    downloads this month

Related outputs

Liposome Mediated-CYP1A1 Gene Silencing Nanomedicine Prepared Using Lipid Film-Coated Proliposomes as a Potential Treatment Strategy of Lung Cancer
Zhang, M, Wang, Q, Wan, K, Ahmed, W, Phoenix, D, Zhang, Z, Elrayess, MA, Elhissi, A and Sun, X (2019). Liposome Mediated-CYP1A1 Gene Silencing Nanomedicine Prepared Using Lipid Film-Coated Proliposomes as a Potential Treatment Strategy of Lung Cancer. International Journal of Pharmaceutics.
Biophysical investigation into the antibacterial action of modelin-5-NH2
Dennison, S, Hauß, T, Badiani, K, Harris, F and Phoenix, D (2019). Biophysical investigation into the antibacterial action of modelin-5-NH2. Soft Matter.
Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity
Manzo, G, Ferguson, PM, Gustilo, VB, Hind, CK, Clifford, M, Bui, TT, Drake, AF, Atkinson, RA, Sutton, JM, Batoni, G, Lorenz, CD, Phoenix, DA and Mason, AJ (2019). Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity. Scientific Reports. 9 (1), p. 1385.
Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities
Manzo, G., Ferguson, P.M., Hind, C.K., Clifford, M., Gustilo, V.B., Ali, H., Bansal, S.S., Bui, T.T., Drake, A.F., Atkinson, R.A., Sutton, J.M., Lorenz, C.D., Phoenix, D. and Mason, A.J. (2019). Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities. Scientific Reports. 9.
The effect of C-terminal amidation on the efficacy and selectivity of antimicrobial and anticancer peptides
Harris, F, Dennison, S, Bhatt, T, Singh, J and Phoenix, DA (2009). The effect of C-terminal amidation on the efficacy and selectivity of antimicrobial and anticancer peptides. Molecular and Cellular Biochemistry. 332 (43).
Anionic host defence peptides from the plant kingdom: their anticancer activity and mechanisms of action
Harris, F, Prabhu, S, R Dennison, S, J Snape, T, Lea, R, Mura, M and Phoenix, DA (2016). Anionic host defence peptides from the plant kingdom: their anticancer activity and mechanisms of action. Protein and peptide letters. 23 (8), pp. 676-687.
An Atlas of Anionic Antimicrobial Peptides from Amphibians
Dennison, SR, Harris, F, Mura, M and Phoenix, DA (2018). An Atlas of Anionic Antimicrobial Peptides from Amphibians. Current Protein & Peptide Science. 19 (8), pp. 823-838.
Bacterial resistance to host defence peptides
Phoenix, DA, Dennison, SR and Harris, F (2016). Bacterial resistance to host defence peptides. in: Host Defense Peptides and Their Potential as Therapeutic Agents Springer International Publishing. pp. 161-204
Prediction of Peptide and Protein Propensity for Amyloid Formation
Famlia, C, Dennison, SR, Quintas, A and Phoenix, DA (2015). Prediction of Peptide and Protein Propensity for Amyloid Formation. PLoS ONE. 10.
PH dependent antimicrobial peptides and proteins, their mechanisms of action and potential as therapeutic agents
Malik, E, Dennison, SR, Harris, F and Phoenix, DA (2016). PH dependent antimicrobial peptides and proteins, their mechanisms of action and potential as therapeutic agents. Pharmaceuticals. 9 (4).
Ethanol-based proliposome delivery systems of paclitaxel for in vitro application against brain cancer cells
Najlah, M, Jain, M, Wan, KW, Ahmed, W, Albed Alhnan, M, Phoenix, DA, Taylor, KMG and Elhissi, A (2016). Ethanol-based proliposome delivery systems of paclitaxel for in vitro application against brain cancer cells. Journal of Liposome Research.
The role of C-terminal amidation in the membrane interactions of the anionic antimicrobial peptide, maximin H5.
Dennison, SR, Mura, M, Harris, F, Morton, LH, Zvelindovsky, A and Phoenix, DA (2015). The role of C-terminal amidation in the membrane interactions of the anionic antimicrobial peptide, maximin H5. Biochim Biophys Acta. 1848 (5), pp. 1111 - 1118.
Low pH enhances the action of maximin H5 against Staphylococcus aureus and helps mediate lysylated phosphatidylglycerol induced resistance
Dennison, S, Morton, L, Harris, F and Phoenix, DA (2016). Low pH enhances the action of maximin H5 against Staphylococcus aureus and helps mediate lysylated phosphatidylglycerol induced resistance. Biochemistry. 55 (27), pp. 3735-3751.
Investigations into the potential anticancer activity of Maximin H5
Dennison, SR, Harris, F and Phoenix, DA (2017). Investigations into the potential anticancer activity of Maximin H5. Biochimie. 137 (June), pp. 29-34.
The effect of amidation on the behaviour of antimicrobial peptides
Mura, M, Wang, J, Zhou, Y, Pinna, M, Zvelindovsky, A, Dennison, SR and Phoenix, DA (2016). The effect of amidation on the behaviour of antimicrobial peptides. European Biophysics Journal. 45 (3), pp. 195-207.