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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.
