Quantifying the distribution of protein oligomerization degree reflects cellular information capacity

Abstract

The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Protein homo-oligomerization, which is correlated with cooperativity in biology, is one means of scaling the complexity of protein networks. It can play critical roles in determining the sensitivity of genetic regulatory circuits and metabolic pathways. Therefore, understanding the roles of oligomerization may lead to new approaches of probing biological functions. Here, we analyzed the frequency of protein oligomerization degree in the cell proteome of nine different organisms, and then, we asked whether there are design trade-offs between protein oligomerization, information precision and energy costs of protein synthesis. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks. These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems.

Protein quaternary structures in solution are a mixture of multiple forms

“…While some proteins exhibit several oligomeric forms [8][9][10] , for most proteins only one possible assembly is indicated. A recent study showed that in E.coli about a quarter of proteins with known structure are monomeric, close to half are dimeric and the rest have higher oligomeric states 11 . However, that study, as well as many others, rely on the quaternary state that is indicated in UniProt or the PDB.…”

Artificial Hsp100-mediated systems for re-localizing protein aggregates

“…S5B). In addition, the IGs were enriched for proteins that form homo oligomers (p < 0.0001, chi-square test, 2.7 fold enrichment, table S2), according to calculations based on the Uniprot database and a recent genome-wide oligomerization estimation ( 54 ). Hetero-oligomerization is probably also a driving force for the IGs, but to our knowledge, no comparative study has been performed.…”

Comprehensive genomic survey, structural classification and expression analysis of C2H2-type zinc finger factor in wheat (Triticum aestivum L.)

“…And the C 2 H 2 domains of Traes_3AS_BE15533CD.1 /2 (Z1;D)-C 2 H 2 domains are completely different from its variant Traes_3AS_BE15533CD.3 (M3-C 2 H 2 domain). Undoubtedly, different splice variants of a TaC 2 H 2 -ZF gene have different number or type C 2 H 2 domains, may perform different functions [ 26 ]. For the detailed information of the classified C 2 H 2 -ZFPs in T. aestivum , see Additional file 1 : Table S1.…”