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@article{976927,
author = {Sehnal, David and Svobodová Vařeková, Radka and Huber, Heinrich J. and Geidl, Stanislav and Ionescu, CrinaandMaria and Wimmerová, Michaela and Koča, Jaroslav},
article_number = {2},
doi = {http://dx.doi.org/10.1021/ci200444d},
keywords = {protein structural motifs; superimposition; comparison; lectins; apoptosis},
language = {eng},
issn = {1549-9596},
journal = {Journal of Chemical Information and Modeling},
title = {SiteBinder: An improved approach for comparing multiple protein structural motifs},
volume = {52},
year = {2012}
}
TY - JOUR
ID - 976927
AU - Sehnal, David - Svobodová Vařeková, Radka - Huber, Heinrich J. - Geidl, Stanislav - Ionescu, Crina-Maria - Wimmerová, Michaela - Koča, Jaroslav
PY - 2012
TI - SiteBinder: An improved approach for comparing multiple protein structural motifs
JF - Journal of Chemical Information and Modeling
VL - 52
IS - 2
SP - 343–359
EP - 343–359
SN - 15499596
KW - protein structural motifs
KW - superimposition
KW - comparison
KW - lectins
KW - apoptosis
N2 - There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.
ER -
SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J. HUBER, Stanislav GEIDL, Crina-Maria IONESCU, Michaela WIMMEROVÁ and Jaroslav KOČA. SiteBinder: An improved approach for comparing multiple protein structural motifs. \textit{Journal of Chemical Information and Modeling}. vol.~52, No~2, p.~343–359. ISSN~1549-9596. doi:10.1021/ci200444d. 2012.
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