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          Institute: MPI für Informatik     Collection: Computational Biology and Applied Algorithmics     Display Documents

ID: 428290.0, MPI für Informatik / Computational Biology and Applied Algorithmics
Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
Authors:Zhu, Hongbo; Sommer, Ingolf; Lengauer, Thomas; Domingues, Francisco S.
Date of Publication (YYYY-MM-DD):2008
Title of Journal:PLoS ONE
Issue / Number:4
Start Page:e1926.1
End Page:9
Copyright:Copyright: © 2008 Zhu et al. This is an open-access article distributed under
the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Audience:Experts Only
Intended Educational Use:No
Abstract / Description: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.

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.
Last Change of the Resource (YYYY-MM-DD):2009-03-31
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Thomas Lengauer
Affiliations:MPI f�r Informatik/Computational Biology and Applied Algorithmics
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