Description of recent theoretical research in the study of self-organization of cytoplasmic matter via cytoskeletal transport

Ideas in theoretical physics of biological systems

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.

In the area of nanopore technology, detection methods are based on the recorded electrical signal induced by ionic transport through the nanopore.This signal also is often used to determine the nanopore diameter. Thus fundamental understanding of ionic transport at the nanoscale is essential, because ions do not in general exhibit bulk-like behavior. Indeed, at low salt concentration, the conductance-concentration relation does not follow a bulk-like linear law. In addition, for small nanopores, surface effects can prevail over bulk transport. In order to illustrate this phenomenon, we have tailored high aspect ratio (conical and cylindrical), putatively uncharged nanopores using tracketching on PET Film and atomic layer deposition technique. Starting from experimental results, we will discuss different approaches to fitting the data, including a simple phenomenological model, commonly used to determine nanopore diameter, and a more sophisticated mesoscopic model based on the space charge model. Application of the mesoscopic model leads us to conclude that, surprisingly, a weak surface charge density is needed to fit the transport model to the experimental data. To go further, molecular dynamic simulations were also performed on a system modeled to resemble as closely as possible the experimental one. From different nanopore geometries and the adsorption of hydrophibic polypeptides, we will attempt to explain the origin of the weak surfacecharge.