New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis

Abstract

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.

Comparison between the behavior of different hydrophobic peptides allowing membrane anchoring of proteins

“…The Heliquest lipid-binding feature can however be combined with the Eisenberg plot approach [68][69][70] to generate a useful graphical representation of the mean hydrophobic moment as a function of the mean hydrophobicity [71]. It uses the Fauchere and Pliska scale [72] instead of the normalized scale of Eisenberg [69], thereby providing a user-friendly approach [71].…”

“…It uses the Fauchere and Pliska scale [72] instead of the normalized scale of Eisenberg [69], thereby providing a user-friendly approach [71]. The mean hydrophobicity corresponds to a measure of the overall hydrophobicity of the amino acid sequence whereas the mean hydrophobic moment is a measure of the way polar and non-polar amino acids are distributed in the same amino acid sequence [71]. This plot provides interesting information on whether the peptide sequences correspond to globular, surface seeking or transmembrane segments [68][69][70][71].…”

“…The mean hydrophobicity corresponds to a measure of the overall hydrophobicity of the amino acid sequence whereas the mean hydrophobic moment is a measure of the way polar and non-polar amino acids are distributed in the same amino acid sequence [71]. This plot provides interesting information on whether the peptide sequences correspond to globular, surface seeking or transmembrane segments [68][69][70][71]. The plot has been divided in three different regions (globular, surface seeking and transmembrane) on the basis of protein databases.…”

Interactions of Lipid Membranes with Fibrillar Protein Aggregates

“…To verify this idea, we employed the online server HeliQuest to obtain the mean hydrophobicity (<H>), hydrophobic moment (μH), net charge (z) and, eventually, lipid discrimination factor (D) characterizing lipid binding affinity of a given polypeptide fragment (Gautier et al 2008;Keller 2011). HeliQuest analysis of 1-83/G26R/W@8 sequence showed that this peptide contains four most probable membrane-binding regions, namely R10-R27, K23-K40, L44-R61, and S52-Q69, with the strongest lipid-binding potential in L44-R61.…”

Estudos biofísicos e de atividade de peptídeos correspondentes ao N-terminal das toxinas esticolisinais I e II - contribuição para a elucidação do mecanismo de ação

“…Valores de <H> e <μH> calculados para N-TOAC-StII 11-30 indicam maior tendência de inserção das regiões entre 14-24 e 13-29 da hélice em pH 3,0 em relação ao pH 7,0 (<H> = 0,522 e <μH> = 0,727 para hélice entre 14-24 em pH 7,0 e <H> = 0,522 e <μH> = 0,727 em pH 3,0) (Eisenberg et al, 1982, Eisenberg et al, 1984, Keller, 2011. Considerando o peptídeo como quase que completamente helicoidal, de modo que a mobilidade de TOAC é influenciada pela mobilidade do restante da hélice, a maior inserção em pH 3,0 corrobora maior imobilização de TOAC nos espectros nessa condição.…”