The Salmonella transmembrane effector SteD hijacks AP1-mediated vesicular trafficking for delivery to antigen-loading MHCII compartments

SteD is a transmembrane effector of the Salmonella SPI-2 type III secretion system that inhibits T cell activation by reducing the amounts of at least three proteins – major histocompatibility complex II (MHCII), CD86 and CD97 – from the surface of antigen-presenting cells. SteD specifically localises at the trans -Golgi network (TGN) and MHCII compartments; however, the targeting, membrane integration and trafficking of SteD are not understood. Using systematic mutagenesis, we identify distinct regions of SteD that are required for these processes. We show that SteD integrates into membranes of the ER/Golgi through a two-step mechanism of membrane recruitment from the cytoplasm followed by integration. SteD then migrates to and accumulates within the TGN. From here it hijacks the host adaptor protein (AP)1-mediated trafficking pathway from the TGN to MHCII compartments. AP1 binding and post-TGN trafficking require a short sequence in the N-terminal cytoplasmic tail of SteD that resembles the AP1-interacting dileucine sorting signal, but in inverted orientation, suggesting convergent evolution.

Multi-Step Crystallization and Chemical Evolution of Sodium Yttrium Fluoride

Two-step crystallization mechanisms based on spinodal decomposition followed by nucleation are commonly observed both in the laboratory and in nature. While this pathway may require chemical reactions, subsequent nucleation and growth are often considered as separate, discrete events from the reaction itself. Recent work has also shown a distinct intermediate step involving the formation of an amorphous aggregate. Here we report a novel four-step mechanism in the aqueous synthesis of sodium yttrium fluoride involving 1) the segregation of aqueous ions into a dense liquid phase, 2) the formation of an amorphous aggregate, 3) nucleation of a cubic YF3 phase, and 4) subsequent solid-state diffusion of sodium and fluoride ions to form a final NaYF4 phase. The final step involves a continuous, gradual change of the solid phase’s chemical stoichiometry from YF3 toward NaYF4. Unlike previously studied nucleation and growth mechanisms, the stoichiometry of the final solid phase evolves throughout the crystallization process rather than being determined at nucleation. This novel four-step mechanism provides a new perspective into the nucleation and growth of many other crystalline materials given the ubiquity of nonstoichiometric compounds in nature.

Active mechanical threading by a molecular motor

Molecular motors transform external energy input into directional motions and offer exquisite precision for nano-scale manipulations. In order to make full use of molecular motor capacities, their directional motions need to be transmitted and used for powering downstream molecular events – a current great challenge for molecular engineers. Here we present a macrocyclic molecular motor structure able to perform repetitive molecular threading of a flexible polyethylene glycol chain through the macrocycle. This mechanical threading event is actively powered by the motor motions and leads to a direct translation of the unidirectional motor rotation into an unidirectional translation motion (chain versus ring). The step by step mechanism of the active mechanical threading is elucidated and also the actual threading step is identified as a combined helix inversion and threading event. The here established molecular machine function resembles the crucial step of macroscopic weaving or sewing processes and therefore offers a first entry point for realizing a “molecular knitting” counterpart.

On the Question of Zwitterionic Intermediates in the [3 + 2] Cycloaddition Reactions between C-arylnitrones and Perfluoro 2-Methylpent-2-ene

The molecular mechanism of the [3 + 2] cycloaddition reaction between C-arylnitrones and perfluoro 2-methylpent-2-ene was explored on the basis of DFT calculations. It was found that despite the polar nature of the intermolecular interactions, as well as the presence of fluorine atoms near the reaction centers, all reactions considered cycloaddition proceed via a one-step mechanism. All attempts for the localization of zwitterionic intermediates on the reaction paths were not successful. Similar results were obtained regardless of the level of theory applied.

Zn2+ triggered two-step mechanism of CLIC1 membrane insertion and activation into chloride channels

The CLIC protein family displays the unique feature of altering its structure from a soluble form to a membrane-bound chloride channel. CLIC1, a member of this family, is found in the cytoplasm or in internal and the plasma membranes, with membrane relocalisation linked to endothelial disfunction, tumour proliferation and metastasis. The molecular switch promoting CLIC1 activation remains unclear. Here, cellular chloride efflux assays and immunofluorescence microscopy studies have identified Zn2+ intracellular release as the trigger for CLIC1 activation and membrane relocalisation. Biophysical assays confirmed specific binding to Zn2+, inducing membrane association and enhancing chloride efflux in a pH dependent manner. Together, our results identify a two-step mechanism with Zn2+ binding as the molecular switch promoting CLIC1 membrane insertion, followed by pH activation of chloride efflux.

Relevance of Particle Size Distribution to Kinetic Analysis: The Case of Thermal Dehydroxylation of Kaolinite

Kinetic models used for the kinetic analysis of solid-state reactions assume ideal conditions that are very rarely fulfilled by real processes. One of the assumptions of these ideal models is that all sample particles have an identical size, while most real samples have an inherent particle size distribution (PSD). In this study, the influence of particle size distribution, including bimodal PSD, in kinetic analysis is investigated. Thus, it is observed that PSD can mislead the identification of the kinetic model followed by the reaction and even induce complex thermoanalytical curves that could be misinterpreted in terms of complex kinetics or intermediate species. For instance, in the case of a bimodal PSD, kinetics is affected up to the point that the process resembles a reaction driven by a multi-step mechanism. A procedure for considering the PSD in the kinetic analysis is presented and evaluated experimentally by studying the thermal dehydroxylation of kaolinite. This process, which does not fit any of the common ideal kinetic models proposed in the literature, was analyzed considering PSD influence. However, when PSD is taken into account, the process can be successfully described by a 3-D diffusion model (Jander’s equation). Therefore, it is concluded that the deviations from ideal models for this dehydroxylation process could be explained in terms of PSD.

Mechanistic Insights into Binding of Ligands with Thiazolidinedione Warhead to Human Histone Deacetylase 4

Recently, we have reported that non-hydroxamate thiazolidinedione (TZD) analogs are capable of inhibiting human deacetylase 4 (HDAC4). This study aims at the dissection of the molecular determinants and kinetics of the molecular recognition of TZD ligands by HDAC4. For this purpose, a structure activity relationship analysis of 225 analogs was combined with a comprehensive study of the enzyme and binding kinetics of a variety of HDAC4 mutant variants. The experimental data were rationalized by docking to the two major conformations of HDAC4. TZD ligands are competitive inhibitors and bind via a two-step mechanism involving principal molecular recognition and induced fit. The residence time of 24 g is (34 ± 3) min and thus much larger than that of the canonical pan-HDAC inhibitor SAHA ((5 ± 2) min). Importantly, the binding kinetics can be tuned by varying the structure of the CAP group.

Two-step deswelling in the Volume Phase Transition of thermoresponsive microgels

Thermoresponsive microgels are one of the most investigated types of soft colloids, thanks to their ability to undergo a Volume Phase Transition (VPT) close to ambient temperature. However, this fundamental phenomenon still lacks a detailed microscopic understanding, particularly regarding the presence and the role of charges in the deswelling process. This is particularly important for the widely used poly(N-isopropylacrylamide)–based microgels, where the constituent monomers are neutral but charged groups arise due to the initiator molecules used in the synthesis. Here, we address this point combining experiments with state-of-the-art simulations to show that the microgel collapse does not happen in a homogeneous fashion, but through a two-step mechanism, entirely attributable to electrostatic effects. The signature of this phenomenon is the emergence of a minimum in the ratio between gyration and hydrodynamic radii at the VPT. Thanks to simulations of microgels with different cross-linker concentrations, charge contents, and charge distributions, we provide evidence that peripheral charges arising from the synthesis are responsible for this behavior and we further build a universal master curve able to predict the two-step deswelling. Our results have direct relevance on fundamental soft condensed matter science and on applications where microgels are involved, ranging from materials to biomedical technologies.