de.mpg.escidoc.pubman.appbase.FacesBean
English
 
Help Guide Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons45799

Zhu,  Hongbo
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons45521

Sommer,  Ingolf
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons44907

Lengauer,  Thomas
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons44341

Domingues,  Francisco S.
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

Locator
There are no locators available
Fulltext (public)
There are no public fulltexts available
Supplementary Material (public)
There is no public supplementary material available
Citation

Zhu, H., Sommer, I., Lengauer, T., & Domingues, F. S. (2008). Alignment of Non-Covalent Interactions at Protein-Protein Interfaces. PLoS ONE, 3(4), e1926.1-9. doi:10.1371/journal.pone.0001926.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000F-1AD3-1
Abstract
Background The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. Methodology/Principal Findings Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. Conclusions/Significance The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.