Shear strain-induced structure relaxation of Ni Σ17 [110](223) grain boundary: A molecular dynamics simulation

The stabilization of grain boundaries (GBs) is beneficial for improving the stability and mechanical properties of nanocrystalline (NC) metals. Molecular dynamics (MD) calculations were performed to investigate the shear response of Ni [Formula: see text]17 [110](223) symmetrical tilt GB. It was found that under the action of shear, the nucleation and evolution of the GB source Shockley partial dislocations ultimately result in the low-energy-state transformation of the GB structure units (SUs). However, the Ag atom contained in the GB increases the shear stress and strain required for the GB relaxation, and the strain range for the GB relaxation is expanded, indicating the inhibitory effect of the Ag atom on the structural relaxation of Ni [Formula: see text]17 [110](223) GB. As the temperature increases from 10 K to 250 K, the structural relaxation of Ni [Formula: see text]17 [110](223) GB becomes easier to proceed. In addition to segregation-induced GB stabilization, strain-induced GB relaxation and the roles of foreign atom and temperature clarified in this work could provide several new entry points for stabilizing high-energy GBs.

Brownian dynamics simulation of protofilament relaxation during rapid freezing

Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament’s flexural rigidity, and the effect of cooling on water’s viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.

The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation

<pre>Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chomophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. </pre> <pre>Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive Molecular Dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway. </pre>

The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation

<pre>Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chomophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. </pre> <pre>Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive Molecular Dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway. </pre>