Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials

Karin Noy*, Nir Kalisman, Chen Keasar

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Background. The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution. Results. We tested the new approach on four families of short β-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82). Conclusion. Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries.

Original languageAmerican English
Article number27
JournalBMC Structural Biology
Volume8
DOIs
StatePublished - 2008
Externally publishedYes

Bibliographical note

Funding Information:
CK is a Ralph Selig Career Development Chair in information theory. NK was supported by the Kreitman Foundation Fellowship. Henrik Kibak and Tamar Keasar are gratefully acknowledged for useful discussions and critical review of the manuscript. Finally, the anonymous reviewers are gratefully acknowledged for valuable suggestions and feedback. This research was supported by THE ISRAEL SCIENCE FOUNDATION (grant No. 289/ 06).

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