Name
Title | ||
|---|---|---|
MPRAP: An accessibility predictor for a-helical transmem-brane proteins that performs well inside and outside the membrane |
Abstract | ||
|---|---|---|
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.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/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. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1186/1471-2105-11-333 | BMC Bioinformatics |
Keywords | Field | DocType |
membrane proteins,protein structure,water,protein folding,microarrays,surface area,membrane protein,algorithms,bioinformatics,protein conformation,natural sciences,transmembrane protein,water soluble | Water environment,Phospholipid,Protein folding,Membrane protein,Biology,Cell membrane,Transmembrane protein,Membrane,Bioinformatics,Protein structure | Journal |
Volume | Issue | ISSN |
11 | 1 | 1471-2105 |
Citations | PageRank | References |
19 | 0.71 | 7 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kristoffer Illergård | 1 | 19 | 0.71 |
| Simone Callegari | 2 | 19 | 1.05 |
| Arne Elofsson | 3 | 633 | 56.98 |