MPRAP: An accessibility predictor for a-helical transmem-brane proteins that performs well inside and outside the membrane
2010 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 11, 333- p.Article in journal (Refereed) Published
Background: In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct environments; a hydrophobic lipid environment inside the membrane, a hydrophilic water environment outside the membrane and an interface region rich in phospholipid head-groups. Therefore, it is energetically favorable for transmembrane proteins to expose different types of residues in the different regions. Results: Investigations of a set of structurally determined transmembrane proteins showed that the composition of solvent exposed residues differs significantly inside and outside the membrane. In contrast, residues buried within the interior of a protein show a much smaller difference. However, in all regions exposed residues are less conserved than buried residues. Further, we found that current state-of-the-art predictors for surface area are optimized for one of the regions and perform badly in the other regions. To circumvent this limitation we developed a new predictor, MPRAP, that performs well in all regions. In addition, MPRAP performs better on complete membrane proteins than a combination of specialized predictors and acceptably on water-soluble proteins. A web-server of MPRAP is available at http://mprap.cbr.su.se/ Conclusion: By including complete a-helical transmembrane proteins in the training MPRAP is able to predict surface accessibility accurately both inside and outside the membrane. This predictor can aid in the prediction of 3D-structure, and in the identification of erroneous protein structures.
Place, publisher, year, edition, pages
2010. Vol. 11, 333- p.
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:su:diva-49473DOI: 10.1186/1471-2105-11-333ISI: 000280332100001OAI: oai:DiVA.org:su-49473DiVA: diva2:377960
FunderEU, FP7, Seventh Framework Programme, 512092Swedish Foundation for Strategic Research
authorCount :32010-12-152010-12-142014-11-10Bibliographically approved