Synergistic role of DNA-binding protein and macromolecular crowding on DNA condensation. An experimental and theoretical approach

Ramisetty, Sravani Keerthi; Dias, Rita S.

doi:10.1016/j.molliq.2015.04.051

Cited by 8 publications

(5 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The dashed and solid black curves in the figure show that the size distribution of model DNA, in the absence and presence of neutral crowding agents (Φcrow= 0.06), respectively, nearly overlap. In fact, and as reported in our previous study [58], no DNA condensation was observed in the presence of neutral crowders up to a volume fraction Φcrow= 0.20. In addition, the radius of the crowders was changed to 4, 6, and 8 Å and no significant differences were found on the size distribution of the model DNA for volume fractions of 0.16 and 0.2 (not shown).…”

Section: Resultssupporting

confidence: 90%

“…Returning to the size distribution of DNA, it is also shown in Figure 3 that the presence of neutral crowding agents, up to Φcrow= 0.16, does not affect the conformational state of DNA in the presence of protein. However, it is interesting to note that calculations conducted with protein-to-DNA mixing ratios below charge neutrality show that crowding agents favor DNA condensation for systems with intermediate protein concentration and intermediate protein-protein association strength (εpp= 1 kT) [58].…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model

Dias

2019

Polymers

Self Cite

View full text Add to dashboard Cite

Bacterial cells do not have a nuclear membrane that encompasses and isolates the genetic material. In addition, they do not possess histone proteins, which are responsible for the first levels of genome condensation in eukaryotes. Instead, there is a number of more or less specific nucleoid-associated proteins that induce DNA bridging, wrapping and bending. Many of these proteins self-assemble into oligomers. The crowded environment of cells is also believed to contribute to DNA condensation due to excluded volume effects. Ribosomes are protein-RNA complexes found in large concentrations in the cytosol of cells. They are overall negatively charged and some DNA-binding proteins have been reported to also bind to ribosomes. Here the effect of protein self-association on DNA condensation and stability of DNA-protein complexes is explored using Monte Carlo simulations and a simple coarse-grained model. The DNA-binding proteins are described as positively charged dimers with the same linear charge density as the DNA, described using a bead and spring model. The crowding molecules are simply described as hard-spheres with varying charge density. It was found that applying a weak attractive potential between protein dimers leads to their association in the vicinity of the DNA (but not in its absence), which greatly enhances the condensation of the model DNA. The presence of neutral crowding agents does not affect the DNA conformation in the presence or absence of protein dimers. For weakly self-associating proteins, the presence of negatively charged crowding particles induces the dissociation of the DNA-protein complex due to the partition of the proteins between the DNA and the crowders. Protein dimers with stronger association potentials, on the other hand, stabilize the nucleoid, even in the presence of highly charged crowders. The interactions between protein dimers and crowding agents are not completely prevented and a few crowding molecules typically bind to the nucleoid.

show abstract

Section: Resultssupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model

Dias

2019

Polymers

Self Cite

View full text Add to dashboard Cite

show abstract

“…4 Entropic crowding, caused by the depletion effect of small neutral molecules like polyethylene glycol on the DNA as a polymer, has been shown to be necessary in explaining the formation of a compact nucleoid in vitro. [5][6][7][8] In vivo, os-motic shock and mechanical cell-size perturbations confirm this picture, 9 and show that a 30% increase in the crowders (ribosomes and proteins) concentration can lead to a 3-fold decrease in nucleoid size, while association of DNA-binding proteins also clearly plays a role in this process 10 .…”

Section: Introductionmentioning

confidence: 76%

A mean-field theory for predicting single polymer collapse induced by neutral crowders

Chaboche,

Campos-Villalobos,

Giunta

et al. 2023

Preprint

View full text Add to dashboard Cite

Crowding by macromolecules in the surrounding environment can collapse a single long polymer to globular form through depletion forces of entropic nature. For instance, the genomic DNA of the bacterium Escherichia coli can be compacted by crowding, and the current consensus is that crowding is needed in order to fold it into the "nucleoid", occupying a well defined region of the cell. Motivated by the biological importance of this problem, numerous theoretical and computational investigations have been conducted to ascertain the primary factors influencing the phases of polymer-crowder systems. Despite numerous candidate order parameters predicting this transition have been proposed, a singular quantitative description of the collapse transition in polymers driven by the presence of crowders is still elusive. Here, integrating results from molecular simulations of polymer chains in explicit crowders, we derive a unifying phenomenological model based on an effective monomer-monomer interaction potential. We demonstrate the predictive power of the new theory through an investigation of polymers with varying lengths, crowders of different sizes in a range spanning from low-density to high-density conditions. Finally, we address the role of jamming by crowders.

show abstract

“…4 Entropic crowding, caused by the depletion effect of small neutral molecules like polyethylene glycol on the DNA as a polymer, has been shown to be necessary in explaining the formation of a compact nucleoid in vitro . 5–8 In vivo , osmotic shock and mechanical cell-size perturbations confirm this picture, 9 and show that a 30% increase in the crowders (ribosomes and proteins) concentration can lead to a 3-fold decrease in nucleoid size, while association of DNA-binding proteins also clearly plays a role in this process. 10…”

Section: Introductionmentioning

confidence: 79%

A mean-field theory for predicting single polymer collapse induced by neutral crowders

Chaboche,

Campos-Villalobos,

Giunta

et al. 2024

Soft Matter

View full text Add to dashboard Cite

show abstract

Synergistic role of DNA-binding protein and macromolecular crowding on DNA condensation. An experimental and theoretical approach

Cited by 8 publications

References 52 publications

Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model

Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model

A mean-field theory for predicting single polymer collapse induced by neutral crowders

A mean-field theory for predicting single polymer collapse induced by neutral crowders

Contact Info

Product

Resources

About