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Int. J. Mol. Sci. 2011, 12(9), 5577-5591; doi:10.3390/ijms12095577
Article

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

Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ Nijmegen, The Netherlands
Received: 25 July 2011 / Revised: 22 August 2011 / Accepted: 22 August 2011 / Published: 30 August 2011
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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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.
Keywords: amphitropic proteins; Eisenberg plot; hydrophobic moment plot; Heliquest; lipid binding regions; protein-lipid interactions; transmembrane proteins amphitropic proteins; Eisenberg plot; hydrophobic moment plot; Heliquest; lipid binding regions; protein-lipid interactions; transmembrane proteins
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Keller, R.C. New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis. Int. J. Mol. Sci. 2011, 12, 5577-5591.

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