Practical tool for making an Eisenberg plot.

Rob C A Keller

Overview

The use of the so-called hydrophobic moment plot (or Eisenberg plot) add to protein or peptide sequence analysis. Water solubility, binding affinity to membranes can be predicted based on physicochemical properties like net charge, mean hydrophobicity.

Summary

In combination with the earlier described Heliquest approach to determine possible lipid binding regions: a novel approach is described to predict potential lipid binding regions in proteins and/or peptides. The 'traditional' use of the Eisenberg plot can now be performed as well using the user-friendly and reproducable tool as described in this study.

Author Comments

Dr. rob keller, PhD
Dr. rob keller, PhD
Charlemagne College
Researcher/educator
biochemistry
Nijmegen | Netherlands
Too often results of the Eisenberg plot can be found in the literature that seems to be influenced by the personal interpretation of researchers/groups and/or their software specialists of the original papers of Eisenberg et al. This study uses an approach that is checked for reproducability of the original approach.Dr. rob keller, PhD

Resources

Eisenberg plot
https://www.researchgate.net/figure/Eisenberg-plot-as-obtained-by-Heliquest-generated-data-based-on-the-original-databases-of_fig1_51733310

New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis.

Authors:
Dr. rob keller, PhD
Dr. rob keller, PhD
Charlemagne College
Researcher/educator
biochemistry
Nijmegen | Netherlands

Int J Mol Sci 2011 30;12(9):5577-91. Epub 2011 Aug 30.

Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ Nijmegen, The Netherlands; E-Mail: ; Tel.: +0031-243820460;

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.

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Source
http://dx.doi.org/10.3390/ijms12095577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189734PMC
February 2015
201 Reads
7 Citations
4.183 Impact Factor

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