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K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.

Ding D, Li L, Shu C, Sun X - Front Microbiol (2016)

Bottom Line: We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network.Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET.Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China; Department of Mathematics and Computer Science, Chizhou CollegeChizhou, China.

ABSTRACT
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

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Related in: MedlinePlus

Ratio of DR_100 of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9) to the average DR_100 of the other proteins in the corresponding shells.
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Figure 5: Ratio of DR_100 of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9) to the average DR_100 of the other proteins in the corresponding shells.

Mentions: To assess this, we analyzed the protein disordered regions in these 18 periplasmic c-type cytochromes and computed their DR_100. All of the 18 c-type cytochromes had a high level of disordered content compared with the average DR_100 of the other proteins in the corresponding shells (Figure 5). Although protein disordered regions can fluctuate rapidly through a range of conformations, such conformational flexibility of disordered protein regions are quickly lost upon binding, which will reduce the overall free energy of binding and lead to weaker and more transient interactions (van der Lee et al., 2014).


K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.

Ding D, Li L, Shu C, Sun X - Front Microbiol (2016)

Ratio of DR_100 of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9) to the average DR_100 of the other proteins in the corresponding shells.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837345&req=5

Figure 5: Ratio of DR_100 of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9) to the average DR_100 of the other proteins in the corresponding shells.
Mentions: To assess this, we analyzed the protein disordered regions in these 18 periplasmic c-type cytochromes and computed their DR_100. All of the 18 c-type cytochromes had a high level of disordered content compared with the average DR_100 of the other proteins in the corresponding shells (Figure 5). Although protein disordered regions can fluctuate rapidly through a range of conformations, such conformational flexibility of disordered protein regions are quickly lost upon binding, which will reduce the overall free energy of binding and lead to weaker and more transient interactions (van der Lee et al., 2014).

Bottom Line: We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network.Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET.Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China; Department of Mathematics and Computer Science, Chizhou CollegeChizhou, China.

ABSTRACT
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

No MeSH data available.


Related in: MedlinePlus