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The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

Bilayers of amphiphiles can organize into spherical vesicles, nanotubes, planar, undulating, and helical nanoribbons, and scroll-like cochleates. These bilayer-related architectures interconvert under suitable conditions. Here, a charged, chiral amphiphile (palmitoyl-lysine, C16-K1) is used to elucidate the pathway for planar nanoribbon to cochleate transition induced by salt (NaCl) concentration. In situ small- and wide-angle X-ray scattering (SAXS/WAXS), atomic force and cryogenic transmission electron microscopies (AFM and cryo-TEM) tracked these transformations over angstrom to micrometer length scales. AFM reveals that the large length (L) to width (W) ratio nanoribbons (L/W > 10) convert to sheets (L/W → 1) before rolling into cochleates. A theoretical model based on electrostatic and surface energies shows that the nanoribbons convert to sheets via a first-order transition, at a critical Debye length, with 2 shallow minima of the order of thermal energy at L/W >> 1 and at L/W = 1. SAXS shows that interbilayer spacing (D) in the cochleates scales linearly with the Debye length, and ranges from 13 to 35 nm for NaCl concentrations from 100 to 5 mM. Theoretical arguments that include electrostatic and elastic energies explain the membrane rolling and the bilayer separation-Debye length relationship. These models suggest that the salt-induced ribbon to cochleate transition should be common to all charged bilayers possessing an intrinsic curvature, which in the present case originates from molecular chirality. Our studies show how electrostatic interactions can be tuned to attain and control cochleate structures, which have potential for encapsulating, and releasing macromolecules in a size-selective manner. [ABSTRACT FROM AUTHOR]

Membraneless organelles are aggregates of disordered proteins that form spontaneously to promote specific cellular functions in vivo. The possibility of synthesizing membraneless organelles out of cells will therefore enable fabrication of protein-based materials with functions inherent to biological matter. Since random copolymers contain various compositions and sequences of solvophobic and solvophilic groups, they are expected to function in nonbiological media similarly to a set of disordered proteins in membraneless organelles. Interestingly, the internal environment of these organelles has been noted to behave more like an organic solvent than like water. Therefore, an adsorbed layer of random copolymers that mimics the function of disordered proteins could, in principle, protect and enhance the proteins' enzymatic activity even in organic solvents, which are ideal when the products and/or the reactants have limited solubility in aqueous media. Here, we demonstrate via multiscale simulations that random copolymers efficiently incorporate proteins into different solvents with the potential to optimize their enzymatic activity. We investigate the key factors that govern the ability of random copolymers to encapsulate proteins, including the adsorption energy, copolymer average composition, and solvent selectivity. The adsorbed polymer chains have remarkably similar sequences, indicating that the proteins are able to select certain sequences that best reduce their exposure to the solvent. We also find that the protein surface coverage decreases when the fluctuation in the average distance between the protein adsorption sites increases. The results herein set the stage for computational design of random copolymers for stabilizing and delivering proteins across multiple media. [ABSTRACT FROM AUTHOR]

Controlling interactions between proteins and nanoparticles in electrolyte solutions is crucial for advancing biological sciences and biotechnology. The assembly of charged nanoparticles (NPs) and proteins in aqueous solutions can be directed by modifying the salt concentration. High concentrations of monovalent salt can induce the solubilization or crystallization of NPs and proteins. By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic correlations in the electrolyte, NPs pairs at high monovalent salt concentrations interact via remarkably strong long-range attractions or repulsions, which can be split into three regimes depending on the surface charge densities of the NPs. NPs with zero-to-low surface charge densities interact via a long-range attraction that is stronger and has a similar range to the depletion attraction induced by polymers with radius of gyrations comparable to the NP diameter. On the other hand, moderately charged NPs with smooth surfaces as well as DNA-functionalized NPs with no possibility of hybridization between them interact via a strong repulsion of range and strength larger than the repulsion predicted by models that neglect ionic correlations, including the Derjaguin-Landau-Vervey-Overbeek (DLVO) model. Interactions between strongly charged NPs (>2 e/nm²), both types smooth and DNA-functionalized NPs, show an attractive potential well at intermediate-to-high salt concentrations, which demonstrates that electrolytes can induce aggregation of strongly charged NPs. Our work provides an improved understanding of the role of ionic correlations in NP assembly and design rules to utilize the salting-out process to crystallize NPs. [ABSTRACT FROM AUTHOR]