Macromolecular crowding and protein chemistry: views from inside and outside cells

The cytoplasm is crowded, and the concentration of macromolecules can reach ~ 300 g/L, an environment vastly different from the dilute, idealized conditions usually used in biophysical studies. Macromolecular crowding arise from two phenomena, excluded volume and nonspecific chemical interactions, until recently, only excluded volume effect has been considered. Theory predicts that this macromolecular crowding can have large effects. Most proteins, however, are studied outside cells in dilute solution with macromolecule concentrations of 10 g/L or less. In-cell NMR provides a means to assess protein biophysics at atomic resolution in living cells, but it remains in its infancy, and several potential challenges need to be addressed. One challenge is the inability to observe 15N-1H NMR spectra from many small globular proteins. 19F NMR was used to expand the application of in-cell NMR. This work suggests that high viscosity and weak interactions in the cytoplasm can make routine 15N enrichment a poor choice for in-cell NMR studies of globular proteins in Escherichia coli. To gain insight into this problem, I turned to in vitro experiments where conditions can be controlled with precision. Using both synthetic polymers and globular proteins, I studied the effects of crowding on the diffusion of the test protein, chymotrypsin inhibitor 2. The results not only pinpoint the source of the problem - nonspecific chemical interactions - but also suggest that proteins are more suitable mimics of the intracellular environment. I also measured the stability of ubiquitin in solutions crowded with synthetic polymers or globular proteins to further elucidate the role of nonspecific chemical interactions under crowded conditions. The increased stability observed in synthetic crowders was consistent with a dominant entropic role for excluded volume, but the effect of protein crowders depended on charge. Protein-induced crowding increased stability when the sign of the net charge of the crowder was the same as that of ubiquitin, but decreased stability when the proteins were oppositely charged. The results indicate that synthetic polymers do not provide physiologically relevant insights and that the overall effect of macromolecular crowding depends on the winner of the near stalemate between excluded volume and nonspecific interactions

The Hydration, Microstructure, And Mechanical Properties Of Vaterite Calcined Clay Cement (VC³)

Limestone (calcite) calcined clay cement (LC3) is a promising low-CO2 binder, but the low activity of calcite cannot compensate the reduction in clinker factor, resulting in low one-day strength and limiting its broad applications. As recent carbon capture and utilization technologies allow scalable production of vaterite, a more reactive CaCO3 polymorph, we overcome the challenge by introducing vaterite calcined clay cement (VC3), inspired by the vaterite-calcite phase change. In the present study, VC3 exhibits higher compressive strengths and faster hydration than LC3. Compared to hydrated LC3, hydrated VC3 exhibits increased amount of hemi- and mono-carboaluminate formation and decreased amount of strätlingite formation. With gypsum adjustment, the 1-day strength of VC3 is higher than that of pure cement reference. VC3, a low-CO2 binder, presents great potential as a host of the metastable CaCO3 for carbon storage and utilization and as an enabler of carbon capture at gigaton scales

Fine features of optical potential well induced by nonlinearity

Particles trapped by optical tweezers, behaving as mechanical oscillators in an optomechanical system, have found tremendous applications in various disciplines and are still arousing research interest in frontier and fundamental physics. These optically trapped oscillators provide compact particle confinement and strong oscillator stiffness. But these features are limited by the size of the focused light spot of a laser beam, which is typically restricted by the optical diffraction limit. Here, we propose to build an optical potential well with fine features assisted by the nonlinearity of the particle material, which is independent of the optical diffraction limit. We show that the potential well shape can have super-oscillation-like features and a Fano-resonance-like phenomenon, and the width of the optical trap is far below the diffraction limit. A particle with nonlinearity trapped by an ordinary optical beam provides a new platform with a sub-diffraction potential well and can have applications in high-accuracy optical manipulation and high-precision metrology.Comment: 4 pages, 5 figure