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Unique physicochemical patterns of residues in protein-protein interfaces. / Lazar, Tamas; Guha Roy, Mainak; Schad, Eva; Tompa, Peter.

In: Journal of Chemical Information and Modeling, Vol. 58, No. 10, 22.10.2018, p. 2164-2173.

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Lazar, T, Guha Roy, M, Schad, E & Tompa, P 2018, 'Unique physicochemical patterns of residues in protein-protein interfaces', Journal of Chemical Information and Modeling, vol. 58, no. 10, pp. 2164-2173. https://doi.org/10.1021/acs.jcim.8b00270

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Author

Lazar, Tamas ; Guha Roy, Mainak ; Schad, Eva ; Tompa, Peter. / Unique physicochemical patterns of residues in protein-protein interfaces. In: Journal of Chemical Information and Modeling. 2018 ; Vol. 58, No. 10. pp. 2164-2173.

BibTeX

@article{fa26ebf946ed4bf2b95a0926a4839502,
title = "Unique physicochemical patterns of residues in protein-protein interfaces",
abstract = "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.",
author = "Tamas Lazar and {Guha Roy}, Mainak and Eva Schad and Peter Tompa",
year = "2018",
month = "10",
day = "22",
doi = "10.1021/acs.jcim.8b00270",
language = "English",
volume = "58",
pages = "2164--2173",
journal = "Journal of Chemical Information and Modeling",
issn = "1549-9596",
publisher = "American Chemical Society",
number = "10",

}

RIS

TY - JOUR

T1 - Unique physicochemical patterns of residues in protein-protein interfaces

AU - Lazar, Tamas

AU - Guha Roy, Mainak

AU - Schad, Eva

AU - Tompa, Peter

PY - 2018/10/22

Y1 - 2018/10/22

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85054605550&partnerID=8YFLogxK

U2 - 10.1021/acs.jcim.8b00270

DO - 10.1021/acs.jcim.8b00270

M3 - Article

VL - 58

SP - 2164

EP - 2173

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

SN - 1549-9596

IS - 10

ER -

ID: 39451686