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Inferring physical protein contacts from large-scale purification data of protein complexes.

Schelhorn SE, Mestre J, Albrecht M, Zotenko E - Mol. Cell Proteomics (2011)

Bottom Line: Our results show that raw purification data can indeed be exploited to determine high-confidence physical protein contacts within protein complexes.In contrast to previous findings, we observe that physical contacts inferred from purification experiments of protein complexes can be qualitatively comparable to binary protein interactions measured by experimental high-throughput assays such as yeast two-hybrid.This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Informatics, Saarbr├╝cken, Germany. sven@mpi-inf.mpg.de

ABSTRACT
Recent large-scale data sets of protein complex purifications have provided unprecedented insights into the organization of cellular protein complexes. Several computational methods have been developed to detect co-complexed proteins in these data sets. Their common aim is the identification of biologically relevant protein complexes. However, much less is known about the network of direct physical protein contacts within the detected protein complexes. Therefore, our work investigates whether direct physical contacts can be computationally derived by combining raw data of large-scale protein complex purifications. We assess four established scoring schemes and introduce a new scoring approach that is specifically devised to infer direct physical protein contacts from protein complex purifications. The physical contacts identified by the five methods are comprehensively benchmarked against different reference sets that provide evidence for true physical contacts. Our results show that raw purification data can indeed be exploited to determine high-confidence physical protein contacts within protein complexes. In particular, our new method outperforms competing approaches at discovering physical contacts involving proteins that have been screened multiple times in purification experiments. It also excels in the analysis of recent protein purification screens of molecular chaperones and protein kinases. In contrast to previous findings, we observe that physical contacts inferred from purification experiments of protein complexes can be qualitatively comparable to binary protein interactions measured by experimental high-throughput assays such as yeast two-hybrid. This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens.

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A, Box plots showing the frequency distribution of chaperone-proteins and nonchaperone proteins in the Large-Scale data set, in their roles as bait or prey within purifications. Frequencies on the abscissa are scaled logarithmically. Boxes represent 50% of the data of a given distribution, whereas bold vertical lines denote the median. B, Assessment of inferred and experimentally obtained physical contacts involving molecular chaperones against the Chaperone reference set of experimentally confirmed binary chaperone interactions. The BGS reference set does not contain a sufficient number of chaperone interactions to allow validation.
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Figure 4: A, Box plots showing the frequency distribution of chaperone-proteins and nonchaperone proteins in the Large-Scale data set, in their roles as bait or prey within purifications. Frequencies on the abscissa are scaled logarithmically. Boxes represent 50% of the data of a given distribution, whereas bold vertical lines denote the median. B, Assessment of inferred and experimentally obtained physical contacts involving molecular chaperones against the Chaperone reference set of experimentally confirmed binary chaperone interactions. The BGS reference set does not contain a sufficient number of chaperone interactions to allow validation.

Mentions: Although the ISA method performs consistently well in the assessment against experimentally determined physical contacts, its performance difference to the original SA method appears to be only minor. However, one of the main improvements of our novel method ISA is the enhanced model that takes full advantage of additional evidence contained in repeated observations, depends on the presence of repeated purifications of the same bait protein in the experimental data. A closer analysis of the purifications in the Large-Scale data reveals that proteins were used as baits at a median number of only one time (see bait frequency distribution of nonchaperone proteins in Fig. 4A). Additionally, although both the Gavin and the Krogan experiments were performed on a genomic scale, only 1102 of the overall 2,830 distinct bait proteins in the Large-Scale data set were used as baits in both experiments. Therefore, the combination of the two experimental data sets resulted in relatively few repeated purifications.


Inferring physical protein contacts from large-scale purification data of protein complexes.

Schelhorn SE, Mestre J, Albrecht M, Zotenko E - Mol. Cell Proteomics (2011)

A, Box plots showing the frequency distribution of chaperone-proteins and nonchaperone proteins in the Large-Scale data set, in their roles as bait or prey within purifications. Frequencies on the abscissa are scaled logarithmically. Boxes represent 50% of the data of a given distribution, whereas bold vertical lines denote the median. B, Assessment of inferred and experimentally obtained physical contacts involving molecular chaperones against the Chaperone reference set of experimentally confirmed binary chaperone interactions. The BGS reference set does not contain a sufficient number of chaperone interactions to allow validation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108834&req=5

Figure 4: A, Box plots showing the frequency distribution of chaperone-proteins and nonchaperone proteins in the Large-Scale data set, in their roles as bait or prey within purifications. Frequencies on the abscissa are scaled logarithmically. Boxes represent 50% of the data of a given distribution, whereas bold vertical lines denote the median. B, Assessment of inferred and experimentally obtained physical contacts involving molecular chaperones against the Chaperone reference set of experimentally confirmed binary chaperone interactions. The BGS reference set does not contain a sufficient number of chaperone interactions to allow validation.
Mentions: Although the ISA method performs consistently well in the assessment against experimentally determined physical contacts, its performance difference to the original SA method appears to be only minor. However, one of the main improvements of our novel method ISA is the enhanced model that takes full advantage of additional evidence contained in repeated observations, depends on the presence of repeated purifications of the same bait protein in the experimental data. A closer analysis of the purifications in the Large-Scale data reveals that proteins were used as baits at a median number of only one time (see bait frequency distribution of nonchaperone proteins in Fig. 4A). Additionally, although both the Gavin and the Krogan experiments were performed on a genomic scale, only 1102 of the overall 2,830 distinct bait proteins in the Large-Scale data set were used as baits in both experiments. Therefore, the combination of the two experimental data sets resulted in relatively few repeated purifications.

Bottom Line: Our results show that raw purification data can indeed be exploited to determine high-confidence physical protein contacts within protein complexes.In contrast to previous findings, we observe that physical contacts inferred from purification experiments of protein complexes can be qualitatively comparable to binary protein interactions measured by experimental high-throughput assays such as yeast two-hybrid.This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Informatics, Saarbr├╝cken, Germany. sven@mpi-inf.mpg.de

ABSTRACT
Recent large-scale data sets of protein complex purifications have provided unprecedented insights into the organization of cellular protein complexes. Several computational methods have been developed to detect co-complexed proteins in these data sets. Their common aim is the identification of biologically relevant protein complexes. However, much less is known about the network of direct physical protein contacts within the detected protein complexes. Therefore, our work investigates whether direct physical contacts can be computationally derived by combining raw data of large-scale protein complex purifications. We assess four established scoring schemes and introduce a new scoring approach that is specifically devised to infer direct physical protein contacts from protein complex purifications. The physical contacts identified by the five methods are comprehensively benchmarked against different reference sets that provide evidence for true physical contacts. Our results show that raw purification data can indeed be exploited to determine high-confidence physical protein contacts within protein complexes. In particular, our new method outperforms competing approaches at discovering physical contacts involving proteins that have been screened multiple times in purification experiments. It also excels in the analysis of recent protein purification screens of molecular chaperones and protein kinases. In contrast to previous findings, we observe that physical contacts inferred from purification experiments of protein complexes can be qualitatively comparable to binary protein interactions measured by experimental high-throughput assays such as yeast two-hybrid. This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens.

Show MeSH