Role of protein-protein interactions on organization and dynamics of a model chromatin.

The three-dimensional organization of chromatin is influenced by chromatin-binding proteins through both specific and non-specific interactions. However, the roles of chromatin sequence and the interactions between binding proteins in shaping chromatin structure remain elusive. By employing a simple polymer-based model of chromatin that explicitly considers sequence-dependent protein binding and protein-protein interactions, we elucidate a mechanism for chromatin organization. We find that tuning protein-protein interactions and protein concentration is sufficient to either promote or inhibit chromatin compartmentalization. Moreover, chromatin sequence and protein-protein attraction strongly affect the structural and dynamic exponents that describe the spatiotemporal organization of chromatin. Strikingly, our model's predictions for the exponents governing chromatin structure and dynamics successfully capture experimental observations, in sharp contrast to previous chromatin models. Overall, our findings have the potential to reinterpret data obtained from various chromosome conformation capture technologies, laying the groundwork for advancing our understanding of chromatin organization.

Dissecting the complexity of biomolecular condensates.

Biomolecular condensates comprise a diverse and ubiquitous class of membraneless organelles. Condensate assembly is often described by liquid-liquid phase separation. While this process explains many key features, it cannot account for the compositional or architectural complexity that condensates display in cells. Recent work has begun to dissect the rich network of intermolecular interactions that give rise to biomolecular condensates. Here, we review the latest results from theory, simulations and experiments, and discuss what they reveal about the structure-function relationship of condensates.

Confinement and crowding control the morphology and dynamics of a model bacterial chromosome.

Motivated by recent experiments probing the shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like sub-volume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion until finally saturating, its morphology gradually opening up while displaying a changing number of helical turns. For shorter cells, the chromosome extension varies non-monotonically with cell size, which we show is associated with a radial to longitudinal spatial reordering of the crowders. Confinement and crowders constrain chain dynamics leading to anomalous diffusion. While the scaling exponent for the mean squared displacement of center of mass grows and saturates with cell length, that of individual loci displays a broad distribution with a sharp maximum.

Physicochemical Response of Gelatin in a Coulombic Soup of Monovalent Salt: A Molecular Simulation and Experimental Study.

The effect of salt on the static properties of aqueous solution of gelatin is studied by molecular dynamics simulation at pH = 1.2, 7, and 10. At the isoelectric point (pH = 7), a monotonic increase in size of the polymer is obtained with the addition of sodium chloride ions. In the positive polyelectrolyte regime (pH = 1.2), collapse of gelatin is observed with increase in salt concentration. In the negative polyelectrolyte regime, we observe an interesting collapse-reexpansion behavior. This is due to the screening of repulsion between the excess charges followed by the screening of attraction of oppositely charged ions as the salt concentration is increased. This mechanism is very different from the charge inversion mechanism which causes the reexpansion in the presence of multivalent ions. The location of salt concentration corresponding to the minimum size of the chain is comparable to the theoretical estimate. The shift in the peak of radial distribution function calculated between monomers and salt ions confirms this spatial reorganization. The predictions from the simulation are verified by dynamic light scattering(DLS) and small-angle X-ray scattering (SAXS) experiments. The size of the hydrodynamic "clusters" obtained from DLS confirms the simulation predictions. Persistence length of the gelatin is calculated from SAXS to get single chain statistics, which also agrees well with the simulation results.

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome.

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome.