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Topology independent structural matching discovers novel templates for protein interfaces
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0002-3772-8279
2018 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 17, p. 787-794Article in journal (Refereed) Published
Abstract [en]

Motivation: Protein-protein interactions (PPI) are essential for the function of the cellular machinery. The rapid growth of protein-protein complexes with known 3D structures offers a unique opportunity to study PPI to gain crucial insights into protein function and the causes of many diseases. In particular, it would be extremely useful to compare interaction surfaces of monomers, as this would enable the pinpointing of potential interaction surfaces based solely on the monomer structure, without the need to predict the complete complex structure. While there are many structural alignment algorithms for individual proteins, very few have been developed for protein interfaces, and none that can align only the interface residues to other interfaces or surfaces of interacting monomer subunits in a topology independent (non-sequential) manner. Results: We present InterComp, a method for topology and sequence-order independent structural comparisons. The method is general and can be applied to various structural comparison applications. By representing residues as independent points in space rather than as a sequence of residues, InterComp can be applied to a wide range of problems including interface-surface comparisons and interface-interface comparisons. We demonstrate a use-case by applying InterComp to find similar protein interfaces on the surface of proteins. We show that InterComp pinpoints the correct interface for almost half of the targets (283 of 586) when considering the top 10 hits, and for 24% of the top 1, even when no templates can be found with regular sequence-order dependent structural alignment methods.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2018. Vol. 34, no 17, p. 787-794
National Category
Biophysics
Identifiers
URN: urn:nbn:se:liu:diva-151793DOI: 10.1093/bioinformatics/bty587ISI: 000444317200024OAI: oai:DiVA.org:liu-151793DiVA, id: diva2:1253322
Conference
17th European Conference on Computational Biology (ECCB)
Note

Funding Agencies|Swedish Research Council [2012-5270, 2016-05369]; Swedish e-Science Research Center; Foundation Blanceflor Boncompagni Ludovisi, nee Bildt

Available from: 2018-10-04 Created: 2018-10-04 Last updated: 2019-03-06

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