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. / <p>authorCount :3</p>
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:su-49473 |
| Date | January 2010 |
| Creators | Illergård, Kristoffer, Callegari, Simone, Elofsson, Arne |
| Publisher | Stockholms universitet, Institutionen för biokemi och biofysik, Stockholms universitet, Institutionen för biokemi och biofysik, Stockholms universitet, Institutionen för biokemi och biofysik |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Article in journal, info:eu-repo/semantics/article, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | BMC Bioinformatics, 1471-2105, 2010, 11, s. 333-, info:eu-repo/grantAgreement/EC/FP7/512092 |
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