A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins

被引:58
作者
Beuming, T
Weinstein, H
机构
[1] CUNY Mt Sinai Sch Med, Dept Physiol & Biophys, New York, NY 10029 USA
[2] Cornell Univ, Weill Med Coll, Dept Physiol & Biophys, New York, NY 10021 USA
[3] Cornell Univ, Weill Med Coll, Inst Computat Biomed, New York, NY 10021 USA
关键词
D O I
10.1093/bioinformatics/bth143
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: The dearth of structural data on alpha-helical membrane proteins (MPs) has hampered thus far the development of reliable knowledge-based potentials that can be used for automatic prediction of transmembrane (TM) protein structure. While algorithms for identifying TM segments are available, modeling of the TM domains of alpha-helical MPs involves assembling the segments into a bundle. This requires the correct assignment of the buried and lipid-exposed faces of the TM domains. Results: A recent increase in the number of crystal structures of alpha-helical MPs has enabled an analysis of the lipid-exposed surfaces and the interiors of such molecules on the basis of structure, rather than sequence alone. Together with a conservation criterion that is based on previous observations that conserved residues are mostly found in the interior of MPs, the bias of certain residue types to be preferably buried or exposed is proposed as a criterion for predicting the lipid-exposed and interior faces of TMs. Applications to known structures demonstrates 80% accuracy of this prediction algorithm.
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页码:1822 / 1835
页数:14
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