MINS2: revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon.
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 signi.cantly 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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Center for Bioinformatics, Saarland University, Germany.
Yungki
Y
Park
Volkhard
V
Helms
D000595:Amino Acid Sequence; D001665:Binding Sites; D002462:Cell Membrane / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D011485:Protein Binding; D000069816:SEC Translocation Channels; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D008565:Membrane Proteins; D000069816:SEC Translocation Channels