Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences
| العنوان: | Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences |
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| المؤلفون: | Hadeer Elhabashy, Debora S. Marks, Oliver Kohlbacher, Rohan Maddamsetti, Anna G. Green, Kelly P Brock |
| المصدر: | Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021) Nature Communications |
| بيانات النشر: | Nature Portfolio, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | 0301 basic medicine, Proteome, Science, General Physics and Astronomy, Computational biology, Plasma protein binding, Protein function predictions, Genome, Molecular Docking Simulation, Article, General Biochemistry, Genetics and Molecular Biology, Protein–protein interaction, Evolution, Molecular, 03 medical and health sciences, Residue (chemistry), 0302 clinical medicine, Protein structure, Bacterial Proteins, Protein Interaction Mapping, Escherichia coli, Amino Acids, Multidisciplinary, Base Sequence, Chemistry, Membrane Proteins, Protein sequence analyses, General Chemistry, Eukaryotic Cells, 030104 developmental biology, Structural biology, Protein structure predictions, Genome, Bacterial, 030217 neurology & neurosurgery, Protein Binding |
| الوصف: | Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion have solved structures. Recently, sequence coevolution-based approaches have led to a breakthrough in predicting monomer protein structures and protein interaction interfaces. Here, we address the challenges of large-scale interaction prediction at residue resolution with a fast alignment concatenation method and a probabilistic score for the interaction of residues. Importantly, this method (EVcomplex2) is able to assess the likelihood of a protein interaction, as we show here applied to large-scale experimental datasets where the pairwise interactions are unknown. We predict 504 interactions de novo in the E. coli membrane proteome, including 243 that are newly discovered. While EVcomplex2 does not require available structures, coevolving residue pairs can be used to produce structural models of protein interactions, as done here for membrane complexes including the Flagellar Hook-Filament Junction and the Tol/Pal complex. Our understanding of the residue-level details of protein interactions remains incomplete. Here, the authors show sequence coevolution can be used to infer interacting proteins with residue-level details, including predicting 467 interactions de novo in the Escherichia coli cell envelope proteome. |
| اللغة: | English |
| تدمد: | 2041-1723 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db3262e3e344cec78e3857cd1034e28e https://doaj.org/article/1f5d36246a5a4cf98d205592e87dd62a |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....db3262e3e344cec78e3857cd1034e28e |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 20411723 |
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