MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.
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DOI：
10.1186/1471-2105-11-333
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发表时间：
2010-06-18
影响因子：
3
通讯作者：
Elofsson A
中科院分区：
文献类型：
--
作者：
Illergård K;Callegari S;Elofsson A
在水溶性蛋白质中，隐藏疏水残基和暴露极性和带电残基在能量上是有利的。与水溶性蛋白相比，跨膜蛋白面临三种不同的环境：膜内的疏水性脂质环境、膜外的亲水性水环境和富含磷脂头基的界面区域。因此，跨膜蛋白在不同区域暴露不同类型的残基在能量上是有利的。一组结构确定的跨膜蛋白的调查表明，溶剂暴露的残留物的组成显着不同的膜内外。相比之下，埋在蛋白质内部的残基显示出小得多的差异。然而，在所有区域中，暴露的残基比埋藏的残基保守性更低。此外，我们发现，目前最先进的表面积预测器对其中一个区域进行了优化，而在其他区域表现不佳。为了规避这一限制，我们开发了一个新的预测，MPRAP，在所有地区表现良好。此外，MPRAP在完整的膜蛋白上比专门的预测因子的组合表现得更好，并且在水溶性蛋白上可以接受。MPRAP的网络服务器可在http://mprap.cbr.su.se/上获得。通过在训练中包括完整的α-螺旋跨膜蛋白，MPRAP能够准确地预测膜内外的表面可及性。该预测器可以帮助预测3D结构，并识别错误的蛋白质结构。
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.
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影响因子：
2.9
作者：
Pollastri, G;Baldi, P;Casadio, R
通讯作者：
Casadio, R
影响因子：
5.6
作者：
Granseth, E;von Heijne, G;Elofsson, A
通讯作者：
Elofsson, A
影响因子：
5.8
作者：
Granseth, Erik;Viklund, Hakan;Elofsson, Arne
通讯作者：
Elofsson, Arne
DOI：
10.1016/0005-2795(75)90109-9
发表时间：
1975-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
MATTHEWS, BW
通讯作者：
MATTHEWS, BW
影响因子：
56.9
作者：
REES, DC;DEANTONIO, L;EISENBERG, D
通讯作者：
EISENBERG, D