Protein-ligand dissociation rate constant from all-atom simulation

Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom Molecular Dynamics (MD) simulations. Random Acceleration MD (τ-RAMD) was used where a random artificial force applied to the ligand facilitates its dissociation. We have suggested an approach to extrapolate such obtained dissociation times to the zero-force limit that was never attempted before, thus allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 seconds with statistically significant values distributed in the interval 0.2-72.0 s, that quantitatively matches the experimental value of 50 ± 8 seconds despite the extrapolation over nine orders of magnitude in time.

Enhanced mechanosensing of cells in synthetic 3D matrix with controlled biophysical dynamics

Abstract3D culture of cells in designer biomaterial matrices provides a biomimetic cellular microenvironment and can yield critical insights into cellular behaviours not available from conventional 2D cultures. Hydrogels with dynamic properties, achieved by incorporating either degradable structural components or reversible dynamic crosslinks, enable efficient cell adaptation of the matrix and support associated cellular functions. Herein we demonstrate that given similar equilibrium binding constants, hydrogels containing dynamic crosslinks with a large dissociation rate constant enable cell force-induced network reorganization, which results in rapid stellate spreading, assembly, mechanosensing, and differentiation of encapsulated stem cells when compared to similar hydrogels containing dynamic crosslinks with a low dissociation rate constant. Furthermore, the static and precise conjugation of cell adhesive ligands to the hydrogel subnetwork connected by such fast-dissociating crosslinks is also required for ultra-rapid stellate spreading (within 18 h post-encapsulation) and enhanced mechanosensing of stem cells in 3D. This work reveals the correlation between microscopic cell behaviours and the molecular level binding kinetics in hydrogel networks. Our findings provide valuable guidance to the design and evaluation of supramolecular biomaterials with cell-adaptable properties for studying cells in 3D cultures.

Reversibility in radionuclide/bentonite bulk and colloidal ternary systems

Ternary systems of 152Eu(III), bulk bentonite and ethylenediaminetetraacetic acid (EDTA) ([Eu] = 7.9 × 10–10 M; pH = 6.0–7.0) have been studied. Without EDTA, there was slow uptake in a two-stage process, with initial rapid sorption of Eu(III) (96%), followed by slower uptake of a much smaller fraction (3.0% over a period of one month). The reversibility of Eu(III) binding was tested by allowing Eu(III) to sorb to bentonite for 1–322 days. EDTA was added to the pre-equilibrated Eu bentonite systems at 0.01 M, a concentration that was sufficient to suppress sorption in a system where EDTA was present prior to the contact of Eu(III) with bentonite. A fraction of the Eu was released instantaneously (30–50%), but a significant amount remained bound. With time, the amount of Eu(III) retained by the bentonite reduced, with a slow fraction dissociation rate constant of approximately 4.3 × 10–8 s–1 (values in the range 2.2 × 10–8 – 1.0 × 10–7 s–1) for pre-equilibration times ≥7 days. Eventually, the amount of Eu(III) remaining bound to the bentonite was within error of that when EDTA was present prior to contact (4.5% ± 0.6), although in systems with pre-equilibration times >100 days, full release took up to 500 days. Europium interactions with colloidal bentonite were also studied, and the dissociation rate constant measured by a resin competition method. For the colloids, more Eu was found in the slowly dissociating fraction (60–70%), but the first-order dissociation rate constant was faster, with an average rate constant of 8.8 × 10–7 s–1 and a range of 7.7 × 10–7 –9.5 × 10–7 s–1. For both bulk and colloidal bentonite, although slow dissociation was observed for Eu(III), there was no convincing evidence for 'irreversible' binding.