Crowding-Regulated Binding of Divalent Biomolecules

Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds

Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.

Conformational and static properties of tagged chains in solvents: effect of chain connectivity in solvent molecules

Polymer chains immersed in different solvent molecules exhibit diverse properties due to multiple spatiotemporal scales and complex interactions. Using molecular dynamics simulations, we study the conformational and static properties of tagged chains in different solvent molecules. Two types of solvent molecules were examined: one type consisted of chain molecules connected by bonds, while the other type consisted of individual bead molecules without any bonds. The only difference between the two solvent molecules lies in the chain connectivity. Our results show a compression of the tagged chains with the addition of bead or chain molecules. Chain molecule confinement induces a stronger compression compared to bead molecule confinement. In chain solvent molecules, the tagged chain's radius of gyration reached a minimum at a monomer volume fraction of ∼0.3. Notably, the probability distributions of chain size remain unchanged at different solvent densities, irrespective of whether the solvent consists of beads or polymers. Furthermore, as solvent density increases, a crossover from a unimodal to a bimodal distribution of bond angles is observed, indicating the presence of both compressed and expanded regions within the chain. The effective monomer-solvent interaction is obtained by calculating the partial radial distribution function and the potential of the mean force. In chain solvents, the correlation hole effect results in a reduced number of nearest neighbors around tagged monomers compared to bead solvents. The calculation of pore size distribution reveals that the solvent nonhomogeneity induced by chain connectivity leads to a broader distribution of pore sizes and larger pore dimensions at low volume fractions. These findings provide a deeper understanding of the conformational behavior of polymer chains in different solvent environments.

Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding

Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.