Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes.

Journal of Structural Biology
Saliha Ece Acuner OzbabacanAttila Gursoy

Abstract

Apoptosis is a matter of life and death for cells and both inhibited and enhanced apoptosis may be involved in the pathogenesis of human diseases. The structures of protein-protein complexes in the apoptosis signaling pathway are important as the structural pathway helps in understanding the mechanism of the regulation and information transfer, and in identifying targets for drug design. Here, we aim to predict the structures toward a more informative pathway than currently available. Based on the 3D structures of complexes in the target pathway and a protein-protein interaction modeling tool which allows accurate and proteome-scale applications, we modeled the structures of 29 interactions, 21 of which were previously unknown. Next, 27 interactions which were not listed in the KEGG apoptosis pathway were predicted and subsequently validated by the experimental data in the literature. Additional interactions are also predicted. The multi-partner hub proteins are analyzed and interactions that can and cannot co-exist are identified. Overall, our results enrich the understanding of the pathway with interactions and provide structural details for the human apoptosis pathway. They also illustrate that computational modeling of prot...Continue Reading

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Citations

Aug 21, 2013·Trends in Molecular Medicine·Ruth NussinovCarla Mattos
Apr 18, 2013·Journal of Proteome Research·Guray KuzuOzlem Keskin
May 3, 2013·Genome Medicine·Uros Kuzmanov, Andrew Emili
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Jun 9, 2015·Structure·Serena MuratciogluRuth Nussinov
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Aug 19, 2015·Biophysical Journal·Serena MuratciogluAttila Gursoy
Aug 16, 2015·Biophysical Journal·Emine Guven-MaiorovRuth Nussinov
May 9, 2013·Seminars in Cancer Biology·Chung-Jung Tsai, Ruth Nussinov
May 29, 2013·Seminars in Cancer Biology·Emine Guven MaiorovRuth Nussinov
Jan 22, 2014·Molecular & Cellular Proteomics : MCP·Guray KuzuAttila Gursoy
Oct 4, 2014·Oncotarget·Ruth NussinovChung-Jung Tsai
Aug 18, 2017·BMC Biophysics·H Billur EnginHannah Carter

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