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Tools for Predicting Binding and Insertion of CPPs into Lipid Bilayers

  • Paulo F. Almeida
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 683)

Abstract

The ability to predict properties such as peptide binding and insertion into membranes is an important and time-saving asset in the design of new cell-penetrating peptides (CPPs). Methods to predict those properties are described here, which make use of calculations performed with the Wimley–White hydrophobicity scales. In addition, electrostatic effects can be estimated in a way that provides acceptably close approximations in many cases. Finally, an estimate of the probability of insertion is also discussed. These procedures are illustrated by comparing the calculations with experiments on a few CPPs.

Key words

Binding thermodynamics Membrane insertion Interfacial hydrophobicity scale Octanol hydrophobicity scale Protein transduction domains Amphipathic peptides 

Notes

Acknowledgments

This work was supported by National Institutes of Health grant No. GM072507. I thank Steve White and Bill Wimley for their comments on the manuscript.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Paulo F. Almeida
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of North Carolina WilmingtonWilmingtonUSA

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