Dataset Information

Local network patterns in protein-protein interfaces.

ABSTRACT: Protein-protein interfaces hold the key to understanding protein-protein interactions. In this paper we investigated local interaction network patterns beyond pair-wise contact sites by considering interfaces as contact networks among residues. A contact site was defined as any residue on the surface of one protein which was in contact with a residue on the surface of another protein. We labeled the sub-graphs of these contact networks by their amino acid types. The observed distributions of these labeled sub-graphs were compared with the corresponding background distributions and the results suggested that there were preferred chemical patterns of closely packed residues at the interface. These preferred patterns point to biological constraints on physical proximity between those residues on one protein which were involved in binding to residues which were close on the interacting partner. Interaction interfaces were far from random and contain information beyond pairs and triangles. To illustrate the possible application of the local network patterns observed, we introduced a signature method, called iScore, based on these local patterns to assess interface predictions. On our data sets iScore achieved 83.6% specificity with 82% sensitivity.

SUBMITTER: Luo Q

PROVIDER: S-EPMC3592891 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Local network patterns in protein-protein interfaces.

Luo Qiang Q Hamer Rebecca R Reinert Gesine G Deane Charlotte M CM

PloS one 20130308 3

Protein-protein interfaces hold the key to understanding protein-protein interactions. In this paper we investigated local interaction network patterns beyond pair-wise contact sites by considering interfaces as contact networks among residues. A contact site was defined as any residue on the surface of one protein which was in contact with a residue on the surface of another protein. We labeled the sub-graphs of these contact networks by their amino acid types. The observed distributions of the ...[more]

PMID: 23520460

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Project description:Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual ?-strands (?-interfaces), but are otherwise unrelated. The results show that the ?-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the ?-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular ?-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular ?-strands, of intramolecular ?-strands and of ?-strands forming ?-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the ?-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a ?-interface formation. Such ?-strands could be considered as 'assemblons', independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development.

Dataset Information

Local network patterns in protein-protein interfaces.

Publications

Local network patterns in protein-protein interfaces.

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