Prediction of membrane-protein topology from first principles
2008 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 20, 7177-7781 p.Article in journal (Refereed) Published
The current best membrane-protein topology-prediction methods are typically based on sequence statistics and contain hundreds of parameters that are optimized on known topologies of membrane proteins. However, because the insertion of transmembrane helices into the membrane is the outcome of molecular interactions among protein, lipids and water, it should be possible to predict topology by methods based directly on physical data, as proposed >20 years ago by Kyte and Doolittle. Here, we present two simple topology-prediction methods using a recently published experimental scale of position-specific amino acid contributions to the free energy of membrane insertion that perform on a par with the current best statistics-based topology predictors. This result suggests that prediction of membrane-protein topology and structure directly from first principles is an attainable goal, given the recently improved understanding of peptide recognition by the translocon.
Place, publisher, year, edition, pages
2008. Vol. 105, no 20, 7177-7781 p.
bioinformatics, membrane insertion, topology prediction, translocon, biological hydrophobicity scale
Bioinformatics and Systems Biology
IdentifiersURN: urn:nbn:se:kth:diva-82618DOI: 10.1073/pnas.0711151105ISI: 000256162900015PubMedID: 18477697OAI: oai:DiVA.org:kth-82618DiVA: diva2:498477
QC 201202172012-02-122012-02-122012-02-17Bibliographically approved