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Structural disorder promotes assembly of protein complexes.

Hegyi H, Schad E, Tompa P - BMC Struct. Biol. (2007)

Bottom Line: Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes.The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2-4 components, and 9.6% for complexes of 11-100 components in yeast).Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. hegyi@enzim.hu

ABSTRACT

Background: The idea that the assembly of protein complexes is linked with protein disorder has been inferred from a few large complexes, such as the viral capsid or bacterial flagellar system, only. The relationship, which suggests that larger complexes have more disorder, has never been systematically tested. The recent high-throughput analyses of protein-protein interactions and protein complexes in the cell generated data that enable to address this issue by bioinformatic means.

Results: In this work we predicted structural disorder for both E. coli and S. cerevisiae, and correlated it with the size of complexes. Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes. The distribution of disorder has a median value of 10% in yeast for complexes of 2-4 components (6% in E. coli), but 18% for complexes in the size range of 11-100 proteins (12% in E. coli). The level of disorder as assessed for regions longer than 30 consecutive disordered residues shows an even stronger division between small and large complexes (median values about 4% for complexes of 2-4 components, but 12% for complexes of 11-100 components in yeast). The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2-4 components, and 9.6% for complexes of 11-100 components in yeast). Further analysis shows that this correlation is not directly linked with the increased disorder in hub proteins, but reflects a genuine systemic property of the proteins that make up the complexes.

Conclusion: Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.

Show MeSH
The maximum complex size each E. coli protein occurs in, as a function of its "hubness". Only those E. coli proteins are presented here that appear in both pairwise interactions and complexes in the IntAct database (852 proteins altogether). For each protein the size of the largest complex it appears in is presented as the function of the number of interacting partners in pairwise interactions. Data are presented on a log-log scale. The fitted curve represents a linear relationship but a negligible one, apparent from the very small value of R2, 0.02.
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Figure 6: The maximum complex size each E. coli protein occurs in, as a function of its "hubness". Only those E. coli proteins are presented here that appear in both pairwise interactions and complexes in the IntAct database (852 proteins altogether). For each protein the size of the largest complex it appears in is presented as the function of the number of interacting partners in pairwise interactions. Data are presented on a log-log scale. The fitted curve represents a linear relationship but a negligible one, apparent from the very small value of R2, 0.02.

Mentions: On the other hand, there was no significant relationship between the size of the complex a protein appears in and its "hubness" (i.e. the number of its partners in pair-wise experiments) for either E. coli or yeast (shown only for E. coli, Fig. 6). This shows that the larger complexes-greater disorder relationship and the more pair-wise interactions-greater disorder [8-11] are most certainly two distinct phenomena, not directly related to each other.


Structural disorder promotes assembly of protein complexes.

Hegyi H, Schad E, Tompa P - BMC Struct. Biol. (2007)

The maximum complex size each E. coli protein occurs in, as a function of its "hubness". Only those E. coli proteins are presented here that appear in both pairwise interactions and complexes in the IntAct database (852 proteins altogether). For each protein the size of the largest complex it appears in is presented as the function of the number of interacting partners in pairwise interactions. Data are presented on a log-log scale. The fitted curve represents a linear relationship but a negligible one, apparent from the very small value of R2, 0.02.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194777&req=5

Figure 6: The maximum complex size each E. coli protein occurs in, as a function of its "hubness". Only those E. coli proteins are presented here that appear in both pairwise interactions and complexes in the IntAct database (852 proteins altogether). For each protein the size of the largest complex it appears in is presented as the function of the number of interacting partners in pairwise interactions. Data are presented on a log-log scale. The fitted curve represents a linear relationship but a negligible one, apparent from the very small value of R2, 0.02.
Mentions: On the other hand, there was no significant relationship between the size of the complex a protein appears in and its "hubness" (i.e. the number of its partners in pair-wise experiments) for either E. coli or yeast (shown only for E. coli, Fig. 6). This shows that the larger complexes-greater disorder relationship and the more pair-wise interactions-greater disorder [8-11] are most certainly two distinct phenomena, not directly related to each other.

Bottom Line: Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes.The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2-4 components, and 9.6% for complexes of 11-100 components in yeast).Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. hegyi@enzim.hu

ABSTRACT

Background: The idea that the assembly of protein complexes is linked with protein disorder has been inferred from a few large complexes, such as the viral capsid or bacterial flagellar system, only. The relationship, which suggests that larger complexes have more disorder, has never been systematically tested. The recent high-throughput analyses of protein-protein interactions and protein complexes in the cell generated data that enable to address this issue by bioinformatic means.

Results: In this work we predicted structural disorder for both E. coli and S. cerevisiae, and correlated it with the size of complexes. Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes. The distribution of disorder has a median value of 10% in yeast for complexes of 2-4 components (6% in E. coli), but 18% for complexes in the size range of 11-100 proteins (12% in E. coli). The level of disorder as assessed for regions longer than 30 consecutive disordered residues shows an even stronger division between small and large complexes (median values about 4% for complexes of 2-4 components, but 12% for complexes of 11-100 components in yeast). The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2-4 components, and 9.6% for complexes of 11-100 components in yeast). Further analysis shows that this correlation is not directly linked with the increased disorder in hub proteins, but reflects a genuine systemic property of the proteins that make up the complexes.

Conclusion: Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.

Show MeSH