Unique Physicochemical Patterns of Residues in Protein–Protein
Interfaces
Tamas Lazar
Mainak Guharoy
Eva Schad
Peter Tompa
10.1021/acs.jcim.8b00270.s001
https://acs.figshare.com/articles/journal_contribution/Unique_Physicochemical_Patterns_of_Residues_in_Protein_Protein_Interfaces/7160732
Protein–protein
interactions can be characterized by high-resolution structures of
complexes, from which diverse features of the interfaces can be derived.
For the majority of protein–protein interactions identified,
however, there is no information on the structure of the complex or
the interface involved in the interaction. Understanding what surface
properties drive certain interactions is crucial in the functional
evaluation of protein complexes. Here we show that the local patterning
of the physicochemical properties of amino acids within surface patches
is characteristic of interfaces. To describe this feature in a quantitative
manner, we have defined a statistical potential, iPat, as a measure
of surface patterning. iPat, which does not take evolutionary conservation
or knowledge of the interaction partner into consideration, represents
a function principally different from algorithms that consider intermolecular
contacts. We assess its suitability for characterizing protein and
peptide interfaces, and we demonstrate that iPat is uniquely descriptive
for interfaces of proteins that undergo large conformational changes
or that are involved in the binding of intrinsically disordered protein
(IDP) partners. We suggest that as a stand-alone propensity or in
combination with other features, iPat represents a new feature in
analyzing the functional binding specificity of protein–protein
interactions that has better predictive potential than other simple
1D features, such as hydrophobicity or stickiness.
2018-09-13 00:00:00
1 D features
iPat
binding specificity
peptide interfaces
protein complexes
surface patterning
surface properties drive
IDP
surface patches
interaction partner
physicochemical properties