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Peptides
Volume 26, Issue 2, February 2005, Pages 197-206
 
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doi:10.1016/j.peptides.2004.09.020    How to Cite or Link Using DOI (Opens New Window)
Copyright © 2004 Elsevier Inc. All rights reserved.

Protegrin structure–activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity

Nathan Ostberg and Yiannis KaznessisCorresponding Author Contact Information, E-mail The Corresponding Author

Department of Chemical Engineering and Materials Science, and Digital Technology Center, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA

Received 30 July 2004; 
revised 24 September 2004; 
accepted 28 September 2004. 
Available online 19 November 2004.

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Abstract

The protegrin family of antimicrobial peptides is among the shortest in sequence length while remaining very active against a variety of microorganisms. The major goal of this study is to characterize easily calculated molecular properties, which quantitatively show high correlation with antibacterial activity. The peptides studied have high sequence similarity but vary in activity over more than an order of magnitude. Hence, sequence analysis alone cannot be used to predict activity for these peptides. We calculate structural properties of 62 protegrin and protegrin-analogue peptides and correlate them to experimental activities against six microbe species, as well as hemolytic and cytotoxic activities. Natural protegrins structures were compared with synthetic derivatives using homology modeling, and property descriptors were calculated to determine the characteristics that confer their antimicrobial activity. A structure–activity relationship study of all these peptides provides information about the structural properties that affect activity against different microbial species.

Keywords: Antimicrobial peptide; Homology modeling; Structure–activity relationships

Article Outline

1. Introduction
1.1. Antimicrobial peptides
1.2. Protegrins
2. Materials and methods
2.1. Protegrin sequences
2.2. Homology modeling
2.3. Structural properties
2.4. Correlating properties with activity
2.5. Cytotoxicity versus hemolysis
3. Results
3.1. Activity correlations between species
3.2. Property–activity pairwise correlations
3.3. Property–activity models
3.4. Cytotoxicity versus hemolysis
4. Discussion
4.1. E. coli QSARs
4.2. Which hydrophobic moment to use?
4.3. Concluding remarks
Acknowledgements
Appendix A. QSAR models for each species
References





Peptides
Volume 26, Issue 2, February 2005, Pages 197-206
 
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