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Bioinformatics Advance Access published online on June 10, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn255
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon

Yungki Park and Volkhard Helms *

Center for Bioinformatics, Saarland University, Germany.

*To whom correspondence should be addressed. Volkhard Helms, E-mail: volkhard.helms{at}bioinformatik.uni-saarland.de


  Abstract

Summary: To be fully functional, membrane proteins should not only fold, but also get inserted into the membrane, which is mediated by the Sec61 translocon. Recent experimental studies have attempted to elucidate how the Sec61 translocon accomplishes this delicate task by measuring the translocon-mediated membrane insertion free energies of 357 systematically designed peptides. On the basis of this data set, we have developed MINS2, a novel sequence-based computational method for predicting the membrane insertion free energies of protein sequences. A benchmark analysis of MINS2 shows that MINS2 significantly outperforms previously proposed methods. Importantly, the application of MINS2 to known membrane protein structures shows that a better prediction of membrane insertion free energies does not lead to a better prediction of transmembrane segments of polytopic membrane proteins.

Availability: A web server for MINS2 is publicly available at http://service.bioinformatik.uni-saarland.de/mins.

Contact: volkhard.helms{at}bioinformatik.uni-saarland.de

Associate Editor: Prof. Anna Tramontano

Received on April 25, 2008; revised on June 2, 2008; accepted on June 2, 2008

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